{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,27]],"date-time":"2026-08-27T22:01:54Z","timestamp":1787868114322,"version":"build-2784847793"},"publisher-location":"New York, NY","reference-count":249,"publisher":"Springer US","isbn-type":[{"value":"9781071642894","type":"print"},{"value":"9781071642900","type":"electronic"}],"license":[{"start":{"date-parts":[[2024,12,20]],"date-time":"2024-12-20T00:00:00Z","timestamp":1734652800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,12,20]],"date-time":"2024-12-20T00:00:00Z","timestamp":1734652800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025]]},"DOI":"10.1007\/978-1-0716-4290-0_20","type":"book-chapter","created":{"date-parts":[[2024,12,19]],"date-time":"2024-12-19T19:30:23Z","timestamp":1734636623000},"page":"455-495","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["ncRNA Editing: Functional Characterization and Computational Resources"],"prefix":"10.1007","author":[{"given":"Gioacchino P.","family":"Marceca","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giulia","family":"Romano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Acunzo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giovanni","family":"Nigita","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,12,20]]},"reference":[{"key":"20_CR1","doi-asserted-by":"publisher","first-page":"274","DOI":"10.1016\/j.ydbio.2004.11.028","volume":"278","author":"R Dahm","year":"2005","unstructured":"Dahm R (2005) Friedrich Miescher and the discovery of DNA. Dev Biol 278:274\u2013288. https:\/\/doi.org\/10.1016\/j.ydbio.2004.11.028","journal-title":"Dev Biol"},{"key":"20_CR2","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1084\/jem.79.2.137","volume":"79","author":"OT Avery","year":"1944","unstructured":"Avery OT (1944) Studies on the chemical nature of the substance inducing transformation of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. J Exp Med 79:137\u2013158. https:\/\/doi.org\/10.1084\/jem.79.2.137","journal-title":"J Exp Med"},{"key":"20_CR3","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1085\/jgp.36.1.39","volume":"36","author":"AD Hershey","year":"1952","unstructured":"Hershey AD, Chase M (1952) Independent functions of viral protein and nucleic acid in growth of bacteriophage. J Gen Physiol 36:39\u201356","journal-title":"J Gen Physiol"},{"key":"20_CR4","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/171737a0","volume":"171","author":"JD Watson","year":"1953","unstructured":"Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171:737\u2013738","journal-title":"Nature"},{"key":"20_CR5","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1038\/172156a0","volume":"172","author":"RE Franklin","year":"1953","unstructured":"Franklin RE, Gosling RG (1953) Evidence for 2-chain helix in crystalline structure of sodium deoxyribonucleate. Nature 172:156\u2013157","journal-title":"Nature"},{"key":"20_CR6","first-page":"207","volume":"53","author":"J Brachet","year":"1942","unstructured":"Brachet J (1942) La localization des acides pentosenucleiques dans les tissues animaux et les oufs d\u2019Amphibiens en voie de developpement. Archs Biol 53:207\u2013257","journal-title":"Archs Biol"},{"key":"20_CR7","unstructured":"Caspersson T (1947) The relations between nucleic acid and protein synthesis. Symp Soc Exp Biol (1):127\u2013151"},{"key":"20_CR8","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1146\/annurev.bi.51.070182.003153","volume":"51","author":"H Busch","year":"1982","unstructured":"Busch H, Reddy R, Rothblum L, Choi YC (1982) SnRNAs, SnRNPs, and RNA processing. Annu Rev Biochem 51:617\u2013654. https:\/\/doi.org\/10.1146\/annurev.bi.51.070182.003153","journal-title":"Annu Rev Biochem"},{"key":"20_CR9","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1016\/0092-8674(85)90269-7","volume":"42","author":"AR Krainer","year":"1985","unstructured":"Krainer AR, Maniatis T (1985) Multiple factors including the small nuclear ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. Cell 42:725\u2013736","journal-title":"Cell"},{"key":"20_CR10","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1016\/0092-8674(86)90066-8","volume":"46","author":"MM Konarska","year":"1986","unstructured":"Konarska MM, Sharp PA (1986) Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs. Cell 46:845\u2013855","journal-title":"Cell"},{"key":"20_CR11","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/0005-2787(69)90150-6","volume":"190","author":"R Weinberg","year":"1969","unstructured":"Weinberg R, Penman S (1969) Metabolism of small molecular weight monodisperse nuclear RNA. Biochim Biophys Acta 190:10\u201329","journal-title":"Biochim Biophys Acta"},{"key":"20_CR12","doi-asserted-by":"publisher","first-page":"1368","DOI":"10.1016\/S0021-9258(18)93555-6","volume":"243","author":"T Nakamura","year":"1968","unstructured":"Nakamura T, Prestayko AW, Busch H (1968) Studies on nucleolar 4 to 6 S ribonucleic acid of Novikoff hepatoma cells. J Biol Chem 243:1368\u20131375","journal-title":"J Biol Chem"},{"key":"20_CR13","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1007\/s000180050003","volume":"56","author":"GL Eliceiri","year":"1999","unstructured":"Eliceiri GL (1999) Small nucleolar RNAs. Cell Mol Life Sci 56:22\u201331","journal-title":"Cell Mol Life Sci"},{"key":"20_CR14","doi-asserted-by":"publisher","first-page":"D229","DOI":"10.1093\/nar\/gkad833","volume":"52","author":"V Pliatsika","year":"2023","unstructured":"Pliatsika V, Cherlin T, Loher P et al (2023) MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs). Nucleic Acids Res 52:D229\u2013D238. https:\/\/doi.org\/10.1093\/nar\/gkad833","journal-title":"Nucleic Acids Res"},{"key":"20_CR15","first-page":"28","volume":"10","author":"CI Brannan","year":"1990","unstructured":"Brannan CI, Dees EC, Ingram RS, Tilghman SM (1990) The product of the H19 gene may function as an RNA. Mol Cell Biol 10:28\u201336","journal-title":"Mol Cell Biol"},{"key":"20_CR16","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1038\/351153a0","volume":"351","author":"MS Bartolomei","year":"1991","unstructured":"Bartolomei MS, Zemel S, Tilghman SM (1991) Parental imprinting of the mouse H19 gene. Nature 351:153\u2013155. https:\/\/doi.org\/10.1038\/351153a0","journal-title":"Nature"},{"key":"20_CR17","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1038\/351325a0","volume":"351","author":"G Borsani","year":"1991","unstructured":"Borsani G, Tonlorenzi R, Simmler MC et al (1991) Characterization of a murine gene expressed from the inactive X chromosome. Nature 351:325\u2013329. https:\/\/doi.org\/10.1038\/351325a0","journal-title":"Nature"},{"key":"20_CR18","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/S0092-8674(00)00099-4","volume":"103","author":"RL Kelley","year":"2000","unstructured":"Kelley RL, Kuroda MI (2000) Noncoding RNA genes in dosage compensation and imprinting. Cell 103:9\u201312","journal-title":"Cell"},{"key":"20_CR19","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1016\/0092-8674(93)90529-Y","volume":"75","author":"RC Lee","year":"1993","unstructured":"Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843\u2013854","journal-title":"Cell"},{"key":"20_CR20","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1038\/35002607","volume":"403","author":"BJ Reinhart","year":"2000","unstructured":"Reinhart BJ, Slack FJ, Basson M et al (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901\u2013906. https:\/\/doi.org\/10.1038\/35002607","journal-title":"Nature"},{"key":"20_CR21","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1126\/science.1064921","volume":"294","author":"M Lagos-Quintana","year":"2001","unstructured":"Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science (New York, NY) 294:853\u2013858. https:\/\/doi.org\/10.1126\/science.1064921","journal-title":"Science (New York, NY)"},{"key":"20_CR22","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1126\/science.1065062","volume":"294","author":"NC Lau","year":"2001","unstructured":"Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science (New York, NY) 294:858\u2013862. https:\/\/doi.org\/10.1126\/science.1065062","journal-title":"Science (New York, NY)"},{"key":"20_CR23","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1126\/science.1065329","volume":"294","author":"RC Lee","year":"2001","unstructured":"Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science (New York, NY) 294:862\u2013864. https:\/\/doi.org\/10.1126\/science.1065329","journal-title":"Science (New York, NY)"},{"key":"20_CR24","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/j.tcb.2014.11.004","volume":"25","author":"JA Vidigal","year":"2015","unstructured":"Vidigal JA, Ventura A (2015) The biological functions of miRNAs: lessons from in vivo studies. Trends Cell Biol 25:137\u2013147. https:\/\/doi.org\/10.1016\/j.tcb.2014.11.004","journal-title":"Trends Cell Biol"},{"key":"20_CR25","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1038\/nature07754","volume":"457","author":"H Siomi","year":"2009","unstructured":"Siomi H, Siomi MC (2009) On the road to reading the RNA-interference code. Nature 457:396\u2013404. https:\/\/doi.org\/10.1038\/nature07754","journal-title":"Nature"},{"key":"20_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1146\/annurev-biochem-060614-034258","volume":"84","author":"YW Iwasaki","year":"2015","unstructured":"Iwasaki YW, Siomi MC, Siomi H (2015) PIWI-interacting RNA: its biogenesis and functions. Annu Rev Biochem 84:1\u201329. https:\/\/doi.org\/10.1146\/annurev-biochem-060614-034258","journal-title":"Annu Rev Biochem"},{"key":"20_CR27","doi-asserted-by":"publisher","first-page":"603","DOI":"10.3390\/genes3040603","volume":"3","author":"MR Garcia-Silva","year":"2012","unstructured":"Garcia-Silva MR, Cabrera-Cabrera F, G\u00fcida MC, Cayota A (2012) Hints of tRNA-derived small RNAs role in RNA silencing mechanisms. Genes 3:603\u2013614. https:\/\/doi.org\/10.3390\/genes3040603","journal-title":"Genes"},{"key":"20_CR28","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1016\/j.canlet.2012.11.058","volume":"340","author":"ES Martens-Uzunova","year":"2013","unstructured":"Martens-Uzunova ES, Olvedy M, Jenster G (2013) Beyond microRNA \u2013 novel RNAs derived from small non-coding RNA and their implication in cancer. Cancer Lett 340:201\u2013211. https:\/\/doi.org\/10.1016\/j.canlet.2012.11.058","journal-title":"Cancer Lett"},{"key":"20_CR29","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/preaccept-5867533061403216","volume":"12","author":"P Kumar","year":"2014","unstructured":"Kumar P, Anaya J, Mudunuri SB, Dutta A (2014) Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol 12:78. https:\/\/doi.org\/10.1186\/preaccept-5867533061403216","journal-title":"BMC Biol"},{"key":"20_CR30","doi-asserted-by":"publisher","first-page":"5071","DOI":"10.1073\/pnas.1604266113","volume":"113","author":"Y Pekarsky","year":"2016","unstructured":"Pekarsky Y, Balatti V, Palamarchuk A et al (2016) Dysregulation of a family of short noncoding RNAs, tsRNAs, in human cancer. Proc Natl Acad Sci 113:5071\u20135076. https:\/\/doi.org\/10.1073\/pnas.1604266113","journal-title":"Proc Natl Acad Sci"},{"key":"20_CR31","doi-asserted-by":"publisher","first-page":"8071","DOI":"10.1073\/pnas.1706908114","volume":"114","author":"V Balatti","year":"2017","unstructured":"Balatti V, Nigita G, Veneziano D et al (2017) tsRNA signatures in cancer. Proc Natl Acad Sci 114:8071\u20138076. https:\/\/doi.org\/10.1073\/pnas.1706908114","journal-title":"Proc Natl Acad Sci"},{"key":"20_CR32","doi-asserted-by":"publisher","first-page":"9433","DOI":"10.1093\/nar\/gkaa657","volume":"48","author":"R Magee","year":"2020","unstructured":"Magee R, Rigoutsos I (2020) On the expanding roles of tRNA fragments in modulating cell behavior. Nucleic Acids Res 48:9433\u20139448. https:\/\/doi.org\/10.1093\/nar\/gkaa657","journal-title":"Nucleic Acids Res"},{"key":"20_CR33","doi-asserted-by":"publisher","first-page":"D141","DOI":"10.1093\/nar\/gku1138","volume":"43","author":"P Kumar","year":"2015","unstructured":"Kumar P, Mudunuri SB, Anaya J, Dutta A (2015) tRFdb: a database for transfer RNA fragments. Nucleic Acids Res 43:D141\u2013D145. https:\/\/doi.org\/10.1093\/nar\/gku1138","journal-title":"Nucleic Acids Res"},{"key":"20_CR34","doi-asserted-by":"publisher","first-page":"D152","DOI":"10.1093\/nar\/gkx1075","volume":"46","author":"V Pliatsika","year":"2017","unstructured":"Pliatsika V, Loher P, Magee R et al (2017) MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res 46:D152\u2013D159. https:\/\/doi.org\/10.1093\/nar\/gkx1075","journal-title":"Nucleic Acids Res"},{"key":"20_CR35","doi-asserted-by":"publisher","first-page":"baz115","DOI":"10.1093\/database\/baz115","volume":"2019","author":"AL Ferlita","year":"2019","unstructured":"Ferlita AL, Alaimo S, Veneziano D et al (2019) Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. Database 2019:baz115. https:\/\/doi.org\/10.1093\/database\/baz115","journal-title":"Database"},{"key":"20_CR36","doi-asserted-by":"publisher","first-page":"1081","DOI":"10.1080\/15476286.2020.1776506","volume":"17","author":"D Yao","year":"2020","unstructured":"Yao D, Sun X, Zhou L et al (2020) OncotRF: an online resource for exploration of tRNA-derived fragments in human cancers. RNA Biol 17:1081\u20131091. https:\/\/doi.org\/10.1080\/15476286.2020.1776506","journal-title":"RNA Biol"},{"key":"20_CR37","doi-asserted-by":"publisher","first-page":"108810","DOI":"10.1016\/j.isci.2024.108810","volume":"27","author":"AL Ferlita","year":"2024","unstructured":"Ferlita AL, Alaimo S, Nigita G et al (2024) tRFUniverse: a comprehensive resource for the interactive analyses of tRNA-derived ncRNAs in human cancer. iScience 27:108810. https:\/\/doi.org\/10.1016\/j.isci.2024.108810","journal-title":"iScience"},{"key":"20_CR38","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1007\/978-1-4939-8982-9_6","volume":"1912","author":"G Nigita","year":"2019","unstructured":"Nigita G, Marceca GP, Tomasello L et al (2019) ncRNA editing: functional characterization and computational resources. Methods Mol Biol 1912:133\u2013174. https:\/\/doi.org\/10.1007\/978-1-4939-8982-9_6","journal-title":"Methods Mol Biol"},{"key":"20_CR39","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1186\/gb-2012-13-10-175","volume":"13","author":"Y Saletore","year":"2012","unstructured":"Saletore Y, Meyer K, Korlach J et al (2012) The birth of the Epitranscriptome: deciphering the function of RNA modifications. Genome Biol 13:175\u2013175. https:\/\/doi.org\/10.1186\/gb-2012-13-10-175","journal-title":"Genome Biol"},{"key":"20_CR40","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1107\/s0365110x63002437","volume":"16","author":"K Hoogsteen","year":"1963","unstructured":"Hoogsteen K (1963) The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine. Acta Crystallogr 16:907\u2013916. https:\/\/doi.org\/10.1107\/s0365110x63002437","journal-title":"Acta Crystallogr"},{"key":"20_CR41","doi-asserted-by":"publisher","first-page":"548","DOI":"10.1016\/S0022-2836(66)80022-0","volume":"19","author":"FH Crick","year":"1966","unstructured":"Crick FH (1966) Codon--anticodon pairing: the wobble hypothesis. J Mol Biol 19:548\u2013555","journal-title":"J Mol Biol"},{"key":"20_CR42","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1093\/embo-reports\/kvd001","volume":"1","author":"G Varani","year":"2000","unstructured":"Varani G, McClain WH (2000) The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep 1:18\u201323. https:\/\/doi.org\/10.1093\/embo-reports\/kvd001","journal-title":"EMBO Rep"},{"key":"20_CR43","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1017\/S1355838201002515","volume":"7","author":"NB Leontis","year":"2001","unstructured":"Leontis NB, Westhof E (2001) Geometric nomenclature and classification of RNA base pairs. RNA 7:499\u2013512","journal-title":"RNA"},{"key":"20_CR44","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1146\/annurev.bi.56.070187.001403","volume":"56","author":"GR Bjork","year":"1987","unstructured":"Bjork GR, Ericson JU, Gustafsson CED et al (1987) Transfer RNA modification. Annu Rev Biochem 56:263\u2013285. https:\/\/doi.org\/10.1146\/annurev.bi.56.070187.001403","journal-title":"Annu Rev Biochem"},{"key":"20_CR45","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1016\/S0079-6603(08)60629-7","volume":"39","author":"BE Maden","year":"1990","unstructured":"Maden BE (1990) The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol 39:241\u2013303","journal-title":"Prog Nucleic Acid Res Mol Biol"},{"key":"20_CR46","doi-asserted-by":"publisher","first-page":"1832","DOI":"10.1101\/gad.1956510","volume":"24","author":"EM Phizicky","year":"2010","unstructured":"Phizicky EM, Hopper AK (2010) tRNA biology charges to the front. Genes Dev 24:1832\u20131860. https:\/\/doi.org\/10.1101\/gad.1956510","journal-title":"Genes Dev"},{"key":"20_CR47","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1016\/j.tibs.2015.07.008","volume":"40","author":"S Sharma","year":"2015","unstructured":"Sharma S, Lafontaine DLJ (2015) \u201cView from a bridge\u201d: a new perspective on eukaryotic rRNA base modification. Trends Biochem Sci 40:560\u2013575. https:\/\/doi.org\/10.1016\/j.tibs.2015.07.008","journal-title":"Trends Biochem Sci"},{"key":"20_CR48","doi-asserted-by":"publisher","first-page":"D239","DOI":"10.1093\/nar\/gkad1083","volume":"52","author":"A Cappannini","year":"2023","unstructured":"Cappannini A, Ray A, Purta E et al (2023) MODOMICS: a database of RNA modifications and related information. 2023 update. Nucleic Acids Res 52:D239\u2013D244. https:\/\/doi.org\/10.1093\/nar\/gkad1083","journal-title":"Nucleic Acids Res"},{"key":"20_CR49","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1021\/acschembio.6b00960","volume":"12","author":"J Song","year":"2017","unstructured":"Song J, Yi C (2017) Chemical modifications to RNA: a new layer of gene expression regulation. ACS Chem Biol 12:316\u2013325. https:\/\/doi.org\/10.1021\/acschembio.6b00960","journal-title":"ACS Chem Biol"},{"key":"20_CR50","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1016\/j.cell.2022.02.007","volume":"185","author":"S Moshitch-Moshkovitz","year":"2021","unstructured":"Moshitch-Moshkovitz S, Dominissini D, Rechavi G (2021) The epitranscriptome toolbox. Cell 185:764\u2013776. https:\/\/doi.org\/10.1016\/j.cell.2022.02.007","journal-title":"Cell"},{"key":"20_CR51","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1038\/nrm.2015.4","volume":"17","author":"K Nishikura","year":"2016","unstructured":"Nishikura K (2016) A-to-I editing of coding and non-coding RNAs by ADARs. Nat Rev Mol Cell Biol 17:83\u201396. https:\/\/doi.org\/10.1038\/nrm.2015.4","journal-title":"Nat Rev Mol Cell Biol"},{"key":"20_CR52","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/nrg3724","volume":"15","author":"Y Fu","year":"2014","unstructured":"Fu Y, Dominissini D, Rechavi G, He C (2014) Gene expression regulation mediated through reversible m6A RNA methylation. Nat Rev Genet 15:293\u2013306. https:\/\/doi.org\/10.1038\/nrg3724","journal-title":"Nat Rev Genet"},{"key":"20_CR53","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1016\/j.tig.2012.11.003","volume":"29","author":"G Jia","year":"2013","unstructured":"Jia G, Fu Y, He C (2013) Reversible RNA adenosine methylation in biological regulation. Trends Genet 29:108\u2013115. https:\/\/doi.org\/10.1016\/j.tig.2012.11.003","journal-title":"Trends Genet"},{"key":"20_CR54","first-page":"59","volume-title":"Modification and editing of RNA","author":"MJ Gait","year":"1998","unstructured":"Gait MJ, Moore MJ, Zimmermann RA (1998) Incorporation of modified nucleotides into RNA for studies on RNA structure, function and intermolecular interactions. In: Modification and editing of RNA. American Society of Microbiology, pp 59\u201384"},{"key":"20_CR55","doi-asserted-by":"publisher","first-page":"6024","DOI":"10.1021\/bi0473399","volume":"44","author":"A Vermeulen","year":"2005","unstructured":"Vermeulen A, McCallum SA, Pardi A (2005) Comparison of the global structure and dynamics of native and unmodified tRNA val\u2020. Biochemistry 44:6024\u20136033. https:\/\/doi.org\/10.1021\/bi0473399","journal-title":"Biochemistry"},{"key":"20_CR56","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1093\/nar\/gkj471","volume":"34","author":"M Helm","year":"2006","unstructured":"Helm M (2006) Post-transcriptional nucleotide modification and alternative folding of RNA. Nucleic Acids Res 34:721\u2013733. https:\/\/doi.org\/10.1093\/nar\/gkj471","journal-title":"Nucleic Acids Res"},{"key":"20_CR57","doi-asserted-by":"publisher","first-page":"1640","DOI":"10.1021\/acs.biochem.7b01100","volume":"57","author":"Y Wang","year":"2018","unstructured":"Wang Y, Park S, Beal PA (2018) Selective recognition of RNA substrates by ADAR deaminase domains. Biochemistry 57:1640\u20131651. https:\/\/doi.org\/10.1021\/acs.biochem.7b01100","journal-title":"Biochemistry"},{"key":"20_CR58","doi-asserted-by":"publisher","first-page":"4621","DOI":"10.1073\/pnas.96.8.4621","volume":"96","author":"CX George","year":"1999","unstructured":"George CX, Samuel CE (1999) Human RNA-specific adenosine deaminase ADAR1 transcripts possess alternative exon 1 structures that initiate from different promoters, one constitutively active and the other interferon inducible. Proc Natl Acad Sci USA 96:4621\u20134626. https:\/\/doi.org\/10.1073\/pnas.96.8.4621","journal-title":"Proc Natl Acad Sci USA"},{"key":"20_CR59","doi-asserted-by":"publisher","first-page":"1911","DOI":"10.1091\/mbc.12.7.1911","volume":"12","author":"CR Eckmann","year":"2001","unstructured":"Eckmann CR, Neunteufl A, Pfaffstetter L, Jantsch MF (2001) The human but not the Xenopus RNA-editing enzyme ADAR1 has an atypical nuclear localization signal and displays the characteristics of a shuttling protein. Mol Biol Cell 12:1911\u20131924. https:\/\/doi.org\/10.1091\/mbc.12.7.1911","journal-title":"Mol Biol Cell"},{"key":"20_CR60","doi-asserted-by":"publisher","first-page":"7862","DOI":"10.1128\/mcb.21.22.7862-7871.2001","volume":"21","author":"H Poulsen","year":"2001","unstructured":"Poulsen H, Nilsson J, Damgaard CK et al (2001) CRM1 mediates the export of ADAR1 through a nuclear export signal within the Z-DNA binding domain. Mol Cell Biol 21:7862\u20137871. https:\/\/doi.org\/10.1128\/mcb.21.22.7862-7871.2001","journal-title":"Mol Cell Biol"},{"key":"20_CR61","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1016\/j.neuron.2006.01.025","volume":"49","author":"PL Peng","year":"2006","unstructured":"Peng PL, Zhong X, Tu W et al (2006) ADAR2-dependent RNA editing of AMPA receptor subunit GluR2 determines vulnerability of neurons in forebrain ischemia. Neuron 49:719\u2013733. https:\/\/doi.org\/10.1016\/j.neuron.2006.01.025","journal-title":"Neuron"},{"key":"20_CR62","doi-asserted-by":"publisher","first-page":"460","DOI":"10.1038\/379460a0","volume":"379","author":"T Melcher","year":"1996","unstructured":"Melcher T, Maas S, Herb A et al (1996) A mammalian RNA editing enzyme. Nature 379:460\u2013464. https:\/\/doi.org\/10.1038\/379460a0","journal-title":"Nature"},{"key":"20_CR63","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0048611","volume":"7","author":"L Yang","year":"2012","unstructured":"Yang L, Huang P, Li F et al (2012) c-Jun amino-terminal kinase-1 mediates glucose-responsive upregulation of the RNA editing enzyme ADAR2 in pancreatic beta-cells. PLoS One 7:e48611. https:\/\/doi.org\/10.1371\/journal.pone.0048611","journal-title":"PLoS One"},{"key":"20_CR64","doi-asserted-by":"publisher","first-page":"14018","DOI":"10.1073\/pnas.2336131100","volume":"100","author":"CL Sansam","year":"2003","unstructured":"Sansam CL, Wells KS, Emeson RB (2003) Modulation of RNA editing by functional nucleolar sequestration of ADAR2. Proc Natl Acad Sci USA 100:14018\u201314023. https:\/\/doi.org\/10.1073\/pnas.2336131100","journal-title":"Proc Natl Acad Sci USA"},{"key":"20_CR65","doi-asserted-by":"publisher","first-page":"79","DOI":"10.3390\/genes9020079","volume":"9","author":"A Filippini","year":"2018","unstructured":"Filippini A, Bonini D, Giacopuzzi E et al (2018) Differential enzymatic activity of rat ADAR2 splicing variants is due to altered capability to interact with RNA in the deaminase domain. Genes 9:79. https:\/\/doi.org\/10.3390\/genes9020079","journal-title":"Genes"},{"key":"20_CR66","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1017\/S1355838200000170","volume":"6","author":"C-X Chen","year":"2000","unstructured":"Chen C-X, Cho D-SC, Wang Q et al (2000) A third member of the RNA-specific adenosine deaminase gene family, ADAR3, contains both single- and double-stranded RNA binding domains. RNA 6:755\u2013767","journal-title":"RNA"},{"key":"20_CR67","doi-asserted-by":"publisher","DOI":"10.3389\/fnins.2018.00243","volume":"12","author":"D Mladenova","year":"2018","unstructured":"Mladenova D, Barry G, Konen LM et al (2018) Adar3 is involved in learning and memory in mice. Front Neurosci 12:e118. https:\/\/doi.org\/10.3389\/fnins.2018.00243","journal-title":"Front Neurosci"},{"key":"20_CR68","doi-asserted-by":"publisher","first-page":"4326","DOI":"10.1074\/jbc.m117.779868","volume":"292","author":"E Oakes","year":"2017","unstructured":"Oakes E, Anderson A, Cohen-Gadol A, Hundley HA (2017) Adenosine deaminase that acts on RNA 3 (ADAR3) binding to glutamate receptor subunit B pre-mRNA inhibits RNA editing in glioblastoma. J Biol Chem 292:4326\u20134335. https:\/\/doi.org\/10.1074\/jbc.m117.779868","journal-title":"J Biol Chem"},{"key":"20_CR69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.0020391.st001","volume":"2","author":"A Athanasiadis","year":"2004","unstructured":"Athanasiadis A, Rich A, Maas S (2004) Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome. PLoS Biol 2:e391. https:\/\/doi.org\/10.1371\/journal.pbio.0020391.st001","journal-title":"PLoS Biol"},{"key":"20_CR70","doi-asserted-by":"publisher","first-page":"1719","DOI":"10.1101\/gr.2855504","volume":"14","author":"DDY Kim","year":"2004","unstructured":"Kim DDY, Kim TTY, Walsh T et al (2004) Widespread RNA editing of embedded Alu elements in the human transcriptome. Genome Res 14:1719\u20131725. https:\/\/doi.org\/10.1101\/gr.2855504","journal-title":"Genome Res"},{"key":"20_CR71","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/nbt996","volume":"22","author":"EY Levanon","year":"2004","unstructured":"Levanon EY, Eisenberg E, Yelin R et al (2004) Systematic identification of abundant A-to-I editing sites in the human transcriptome. Nat Biotechnol 22:1001\u20131005. https:\/\/doi.org\/10.1038\/nbt996","journal-title":"Nat Biotechnol"},{"key":"20_CR72","doi-asserted-by":"publisher","first-page":"6876","DOI":"10.1093\/nar\/gku414","volume":"42","author":"L Bazak","year":"2014","unstructured":"Bazak L, Levanon EY, Eisenberg E (2014) Genome-wide analysis of Alu editability. Nucleic Acids Res 42:6876\u20136884. https:\/\/doi.org\/10.1093\/nar\/gku414","journal-title":"Nucleic Acids Res"},{"key":"20_CR73","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1101\/gr.164749.113","volume":"24","author":"L Bazak","year":"2014","unstructured":"Bazak L, Haviv A, Barak M et al (2014) A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res 24:365\u2013376. https:\/\/doi.org\/10.1101\/gr.164749.113","journal-title":"Genome Res"},{"key":"20_CR74","doi-asserted-by":"publisher","first-page":"14941","DOI":"10.1038\/srep14941","volume":"5","author":"E Picardi","year":"2015","unstructured":"Picardi E, Manzari C, Mastropasqua F et al (2015) Profiling RNA editing in human tissues: towards the inosinome Atlas. Sci Rep 5:14941. https:\/\/doi.org\/10.1038\/srep14941","journal-title":"Sci Rep"},{"key":"20_CR75","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/nmeth.3314","volume":"12","author":"Q Zhang","year":"2015","unstructured":"Zhang Q, Xiao X (2015) Genome sequence-independent identification of RNA editing sites. Nat Methods 12:347\u2013350. https:\/\/doi.org\/10.1038\/nmeth.3314","journal-title":"Nat Methods"},{"key":"20_CR76","doi-asserted-by":"publisher","first-page":"35726","DOI":"10.18632\/oncotarget.6132","volume":"6","author":"R Soundararajan","year":"2015","unstructured":"Soundararajan R, Stearns TM, Griswold AJ et al (2015) Detection of canonical A-to-G editing events at 3\u2019 UTRs and microRNA target sites in human lungs using next-generation sequencing. Oncotarget 6:35726\u201335736. https:\/\/doi.org\/10.18632\/oncotarget.6132","journal-title":"Oncotarget"},{"key":"20_CR77","doi-asserted-by":"publisher","first-page":"1255","DOI":"10.1038\/s41467-017-01459-7","volume":"8","author":"A Br\u00fcmmer","year":"2017","unstructured":"Br\u00fcmmer A, Yang Y, Chan TW, Xiao X (2017) Structure-mediated modulation of mRNA abundance by A-to-I editing. Nat Commun 8:1255. https:\/\/doi.org\/10.1038\/s41467-017-01459-7","journal-title":"Nat Commun"},{"key":"20_CR78","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1038\/nmeth.1982","volume":"9","author":"G Ramaswami","year":"2012","unstructured":"Ramaswami G, Lin W, Piskol R et al (2012) Accurate identification of human Alu and non-Alu RNA editing sites. Nat Methods 9:579\u2013581. https:\/\/doi.org\/10.1038\/nmeth.1982","journal-title":"Nat Methods"},{"key":"20_CR79","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1038\/nmeth.2330","volume":"10","author":"G Ramaswami","year":"2013","unstructured":"Ramaswami G, Zhang R, Piskol R et al (2013) Identifying RNA editing sites using RNA sequencing data alone. Nat Methods 10:128\u2013132. https:\/\/doi.org\/10.1038\/nmeth.2330","journal-title":"Nat Methods"},{"key":"20_CR80","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1038\/nature24041","volume":"550","author":"MH Tan","year":"2017","unstructured":"Tan MH, Li Q, Shanmugam R et al (2017) Dynamic landscape and regulation of RNA editing in mammals. Nature 550:249\u2013254. https:\/\/doi.org\/10.1038\/nature24041","journal-title":"Nature"},{"key":"20_CR81","doi-asserted-by":"publisher","first-page":"1110","DOI":"10.1261\/rna.923308","volume":"14","author":"EM Riedmann","year":"2008","unstructured":"Riedmann EM, Schopoff S, Hartner JC, Jantsch MF (2008) Specificity of ADAR-mediated RNA editing in newly identified targets. RNA 14:1110\u20131118. https:\/\/doi.org\/10.1261\/rna.923308","journal-title":"RNA"},{"key":"20_CR82","doi-asserted-by":"publisher","first-page":"5701","DOI":"10.1002\/j.1460-2075.1994.tb06908.x","volume":"13","author":"AG Polson","year":"1994","unstructured":"Polson AG, Bass BL (1994) Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J 13:5701\u20135711","journal-title":"EMBO J"},{"key":"20_CR83","doi-asserted-by":"publisher","first-page":"12875","DOI":"10.1021\/bi001383g","volume":"39","author":"KA Lehmann","year":"2000","unstructured":"Lehmann KA, Bass BL (2000) Double-stranded RNA adenosine deaminases ADAR1 and ADAR2 have overlapping specificities \u2020. Biochemistry 39:12875\u201312884. https:\/\/doi.org\/10.1021\/bi001383g","journal-title":"Biochemistry"},{"key":"20_CR84","doi-asserted-by":"publisher","first-page":"1440","DOI":"10.1038\/s41467-017-01458-8","volume":"8","author":"O Solomon","year":"2017","unstructured":"Solomon O, Segni AD, Cesarkas K et al (2017) RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure. Nat Commun 8:1440. https:\/\/doi.org\/10.1038\/s41467-017-01458-8","journal-title":"Nat Commun"},{"key":"20_CR85","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1001074","volume":"6","author":"M Halvorsen","year":"2010","unstructured":"Halvorsen M, Martin JS, Broadaway S, Laederach A (2010) Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet 6:e1001074. https:\/\/doi.org\/10.1371\/journal.pgen.1001074","journal-title":"PLoS Genet"},{"key":"20_CR86","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1093\/nar\/gks1009","volume":"41","author":"R Salari","year":"2013","unstructured":"Salari R, Kimchi-Sarfaty C, Gottesman MM, Przytycka TM (2013) Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies. Nucleic Acids Res 41:44\u201353. https:\/\/doi.org\/10.1093\/nar\/gks1009","journal-title":"Nucleic Acids Res"},{"key":"20_CR87","doi-asserted-by":"publisher","first-page":"5115","DOI":"10.1091\/mbc.e05-06-0536","volume":"16","author":"JMP Desterro","year":"2005","unstructured":"Desterro JMP, Keegan LP, Jaffray E et al (2005) SUMO-1 modification alters ADAR1 editing activity. Mol Biol Cell 16:5115\u20135126. https:\/\/doi.org\/10.1091\/mbc.e05-06-0536","journal-title":"Mol Biol Cell"},{"key":"20_CR88","doi-asserted-by":"publisher","first-page":"192","DOI":"10.4161\/rna.23208","volume":"10","author":"W Garncarz","year":"2013","unstructured":"Garncarz W, Tariq A, Handl C et al (2013) A high-throughput screen to identify enhancers of ADAR-mediated RNA-editing. RNA Biol 10:192\u2013204. https:\/\/doi.org\/10.4161\/rna.23208","journal-title":"RNA Biol"},{"key":"20_CR89","doi-asserted-by":"publisher","first-page":"2652","DOI":"10.1016\/j.jmb.2016.02.019","volume":"428","author":"TM Eidem","year":"2016","unstructured":"Eidem TM, Kugel JF, Goodrich JA (2016) Noncoding RNAs: regulators of the mammalian transcription machinery. J Mol Biol 428:2652\u20132659. https:\/\/doi.org\/10.1016\/j.jmb.2016.02.019","journal-title":"J Mol Biol"},{"key":"20_CR90","doi-asserted-by":"publisher","first-page":"e2333","DOI":"10.1038\/cddis.2016.210","volume":"7","author":"Y Su","year":"2016","unstructured":"Su Y, Wu H, Pavlosky A et al (2016) Regulatory non-coding RNA: new instruments in the orchestration of cell death. Cell Death Dis 7:e2333. https:\/\/doi.org\/10.1038\/cddis.2016.210","journal-title":"Cell Death Dis"},{"key":"20_CR91","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature08909","volume":"463","author":"TW Nilsen","year":"2010","unstructured":"Nilsen TW, Graveley BR (2010) Expansion of the eukaryotic proteome by alternative splicing. Nature 463:457\u2013463. https:\/\/doi.org\/10.1038\/nature08909","journal-title":"Nature"},{"key":"20_CR92","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/nrg.2015.17","volume":"17","author":"E Khurana","year":"2016","unstructured":"Khurana E, Fu Y, Chakravarty D et al (2016) Role of non-coding sequence variants in cancer. Nat Rev Genet 17:93\u2013108. https:\/\/doi.org\/10.1038\/nrg.2015.17","journal-title":"Nat Rev Genet"},{"key":"20_CR93","doi-asserted-by":"publisher","first-page":"1616","DOI":"10.1101\/gr.134445.111","volume":"22","author":"H Tilgner","year":"2012","unstructured":"Tilgner H, Knowles DG, Johnson R et al (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res 22:1616\u20131625. https:\/\/doi.org\/10.1101\/gr.134445.111","journal-title":"Genome Res"},{"key":"20_CR94","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/nrg1807","volume":"7","author":"SW Roy","year":"2006","unstructured":"Roy SW, Gilbert W (2006) The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet 7:211\u2013221. https:\/\/doi.org\/10.1038\/nrg1807","journal-title":"Nat Rev Genet"},{"key":"20_CR95","doi-asserted-by":"publisher","first-page":"11093","DOI":"10.1073\/pnas.1101135108","volume":"108","author":"KH Lim","year":"2011","unstructured":"Lim KH, Ferraris L, Filloux ME et al (2011) Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc Natl Acad Sci USA 108:11093\u201311098. https:\/\/doi.org\/10.1073\/pnas.1101135108","journal-title":"Proc Natl Acad Sci USA"},{"key":"20_CR96","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1146\/annurev-biochem-060614-034316","volume":"84","author":"Y Lee","year":"2015","unstructured":"Lee Y, Rio DC (2015) Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem 84:291\u2013323. https:\/\/doi.org\/10.1146\/annurev-biochem-060614-034316","journal-title":"Annu Rev Biochem"},{"key":"20_CR97","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1002\/bies.201500117","volume":"38","author":"JJL Wong","year":"2015","unstructured":"Wong JJL, Au AYM, Ritchie W, Rasko JEJ (2015) Intron retention in mRNA: no longer nonsense. Bioessays 38:41\u201349. https:\/\/doi.org\/10.1002\/bies.201500117","journal-title":"Bioessays"},{"key":"20_CR98","doi-asserted-by":"publisher","first-page":"1025","DOI":"10.1002\/bies.201200073","volume":"34","author":"AA Bicknell","year":"2012","unstructured":"Bicknell AA, Cenik C, Chua HN et al (2012) Introns in UTRs: why we should stop ignoring them. Bioessays 34:1025\u20131034. https:\/\/doi.org\/10.1002\/bies.201200073","journal-title":"Bioessays"},{"key":"20_CR99","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1038\/nrm4063","volume":"16","author":"S Lykke-Andersen","year":"2015","unstructured":"Lykke-Andersen S, Jensen TH (2015) Nonsense-mediated mRNA decay: an intricate machinery that shapes transcriptomes. Nat Rev Mol Cell Biol 16:665\u2013677. https:\/\/doi.org\/10.1038\/nrm4063","journal-title":"Nat Rev Mol Cell Biol"},{"key":"20_CR100","doi-asserted-by":"publisher","first-page":"812","DOI":"10.1101\/gr.231209.117","volume":"28","author":"Y-HE Hsiao","year":"2018","unstructured":"Hsiao Y-HE, Bahn JH, Yang Y et al (2018) RNA editing in nascent RNA affects pre-mRNA splicing. Genome Res 28:812\u2013823. https:\/\/doi.org\/10.1101\/gr.231209.117","journal-title":"Genome Res"},{"key":"20_CR101","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/19992","volume":"399","author":"SM Rueter","year":"1999","unstructured":"Rueter SM, Dawson TR, Emeson RB (1999) Regulation of alternative splicing by RNA editing. Nature 399:75\u201380. https:\/\/doi.org\/10.1038\/19992","journal-title":"Nature"},{"key":"20_CR102","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1128\/mcb.26.2.480-488.2006","volume":"26","author":"Y Feng","year":"2006","unstructured":"Feng Y, Sansam CL, Singh M, Emeson RB (2006) Altered RNA editing in mice lacking ADAR2 autoregulation. Mol Cell Biol 26:480\u2013488. https:\/\/doi.org\/10.1128\/mcb.26.2.480-488.2006","journal-title":"Mol Cell Biol"},{"key":"20_CR103","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4161\/rna.3.1.2495","volume":"3","author":"S Maas","year":"2006","unstructured":"Maas S, Kawahara Y, Tamburro KM, Nishikura K (2006) A-to-I RNA editing and human disease. RNA Biol 3:1\u20139","journal-title":"RNA Biol"},{"key":"20_CR104","doi-asserted-by":"publisher","first-page":"10158","DOI":"10.1074\/jbc.ra117.001197","volume":"293","author":"Y-T Chen","year":"2018","unstructured":"Chen Y-T, Chang IY-F, Liu H et al (2018) Tumor-associated intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation. J Biol Chem 293:10158\u201310171. https:\/\/doi.org\/10.1074\/jbc.ra117.001197","journal-title":"J Biol Chem"},{"key":"20_CR105","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1101\/gr.3715005","volume":"15","author":"A Siepel","year":"2005","unstructured":"Siepel A, Bejerano G, Pedersen JS et al (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 15:1034\u20131050. https:\/\/doi.org\/10.1101\/gr.3715005","journal-title":"Genome Res"},{"key":"20_CR106","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1079\/AHR200460","volume":"5","author":"TJ Gingerich","year":"2004","unstructured":"Gingerich TJ, Feige J-J, LaMarre J (2004) AU-rich elements and the control of gene expression through regulated mRNA stability. Anim Health Res Rev 5:49\u201363","journal-title":"Anim Health Res Rev"},{"key":"20_CR107","doi-asserted-by":"publisher","first-page":"681","DOI":"10.4161\/rna.8.4.16283","volume":"8","author":"AS Halees","year":"2011","unstructured":"Halees AS, Hitti E, Al-Saif M et al (2011) Global assessment of GU-rich regulatory content and function in the human transcriptome. RNA Biol 8:681\u2013691. https:\/\/doi.org\/10.4161\/rna.8.4.16283","journal-title":"RNA Biol"},{"key":"20_CR108","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1126\/science.1215691","volume":"336","author":"S Djuranovic","year":"2012","unstructured":"Djuranovic S, Nahvi A, Green R (2012) miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science (New York, NY) 336:237\u2013240. https:\/\/doi.org\/10.1126\/science.1215691","journal-title":"Science (New York, NY)"},{"key":"20_CR109","doi-asserted-by":"publisher","first-page":"1931","DOI":"10.1126\/science.1149460","volume":"318","author":"S Vasudevan","year":"2007","unstructured":"Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science (New York, NY) 318:1931\u20131934. https:\/\/doi.org\/10.1126\/science.1149460","journal-title":"Science (New York, NY)"},{"key":"20_CR110","doi-asserted-by":"publisher","first-page":"6318","DOI":"10.1093\/nar\/gkn624","volume":"36","author":"T Ghosh","year":"2008","unstructured":"Ghosh T, Soni K, Scaria V et al (2008) MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic \u03b2-actin gene. Nucleic Acids Res 36:6318\u20136332. https:\/\/doi.org\/10.1093\/nar\/gkn624","journal-title":"Nucleic Acids Res"},{"key":"20_CR111","doi-asserted-by":"publisher","first-page":"1175","DOI":"10.1101\/gr.089367.108","volume":"19","author":"I Lee","year":"2009","unstructured":"Lee I, Ajay SS, Yook JI et al (2009) New class of microRNA targets containing simultaneous 5\u2019-UTR and 3\u2019-UTR interaction sites. Genome Res 19:1175\u20131183. https:\/\/doi.org\/10.1101\/gr.089367.108","journal-title":"Genome Res"},{"key":"20_CR112","doi-asserted-by":"publisher","first-page":"1694","DOI":"10.1038\/emboj.2008.94","volume":"27","author":"L-L Chen","year":"2008","unstructured":"Chen L-L, DeCerbo JN, Carmichael GG (2008) Alu element-mediated gene silencing. EMBO J 27:1694\u20131705. https:\/\/doi.org\/10.1038\/emboj.2008.94","journal-title":"EMBO J"},{"key":"20_CR113","doi-asserted-by":"publisher","first-page":"465","DOI":"10.1016\/s0092-8674(01)00466-4","volume":"106","author":"Z Zhang","year":"2001","unstructured":"Zhang Z, Carmichael GG (2001) The fate of dsRNA in the nucleus: a p54nrb-containing complex mediates the nuclear retention of promiscuously A-to-I edited RNAs. Cell 106:465\u2013476. https:\/\/doi.org\/10.1016\/s0092-8674(01)00466-4","journal-title":"Cell"},{"key":"20_CR114","doi-asserted-by":"publisher","first-page":"1525","DOI":"10.1261\/rna.041533.113","volume":"19","author":"Q Wang","year":"2013","unstructured":"Wang Q, Hui H, Guo Z et al (2013) ADAR1 regulates ARHGAP26 gene expression through RNA editing by disrupting miR-30b-3p and miR-573 binding. RNA 19:1525\u20131536. https:\/\/doi.org\/10.1261\/rna.041533.113","journal-title":"RNA"},{"key":"20_CR115","doi-asserted-by":"publisher","first-page":"23226","DOI":"10.1038\/srep23226","volume":"6","author":"L Zhang","year":"2016","unstructured":"Zhang L, Yang C-S, Varelas X, Monti S (2016) Altered RNA editing in 3\u2032 UTR perturbs microRNA-mediated regulation of oncogenes and tumor-suppressors. Sci Rep 6:23226. https:\/\/doi.org\/10.1038\/srep23226","journal-title":"Sci Rep"},{"key":"20_CR116","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1038\/ng2135","volume":"39","author":"M Kertesz","year":"2007","unstructured":"Kertesz M, Iovino N, Unnerstall U et al (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39:1278\u20131284. https:\/\/doi.org\/10.1038\/ng2135","journal-title":"Nat Genet"},{"key":"20_CR117","doi-asserted-by":"publisher","first-page":"D155","DOI":"10.1093\/nar\/gky1141","volume":"47","author":"A Kozomara","year":"2019","unstructured":"Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) miRBase: from microRNA sequences to function. Nucleic Acids Res 47:D155\u2013D162. https:\/\/doi.org\/10.1093\/nar\/gky1141","journal-title":"Nucleic Acids Res"},{"key":"20_CR118","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1038\/sj.emboj.7601512","volume":"26","author":"Y-K Kim","year":"2007","unstructured":"Kim Y-K, Kim VN (2007) Processing of intronic microRNAs. EMBO J 26:775\u2013783. https:\/\/doi.org\/10.1038\/sj.emboj.7601512","journal-title":"EMBO J"},{"key":"20_CR119","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1038\/nrm3838","volume":"15","author":"M Ha","year":"2014","unstructured":"Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509\u2013524. https:\/\/doi.org\/10.1038\/nrm3838","journal-title":"Nat Rev Mol Cell Biol"},{"key":"20_CR120","doi-asserted-by":"publisher","first-page":"1897","DOI":"10.1016\/j.biochi.2011.06.017","volume":"93","author":"JO Westholm","year":"2011","unstructured":"Westholm JO, Lai EC (2011) Mirtrons: microRNA biogenesis via splicing. Biochimie 93:1897\u20131904. https:\/\/doi.org\/10.1016\/j.biochi.2011.06.017","journal-title":"Biochimie"},{"key":"20_CR121","doi-asserted-by":"publisher","first-page":"743","DOI":"10.1038\/s41580-018-0045-7","volume":"21","author":"LFR Gebert","year":"2018","unstructured":"Gebert LFR, Macrae IJ (2018) Regulation of microRNA function in animals. Nat Rev Mol Cell Biol 21:743. https:\/\/doi.org\/10.1038\/s41580-018-0045-7","journal-title":"Nat Rev Mol Cell Biol"},{"key":"20_CR122","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2021.668648","volume":"9","author":"L Tomasello","year":"2021","unstructured":"Tomasello L, Distefano R, Nigita G, Croce CM (2021) The microRNA family gets wider: the isomiRs classification and role. Front Cell Dev Biol 9:668648. https:\/\/doi.org\/10.3389\/fcell.2021.668648","journal-title":"Front Cell Dev Biol"},{"key":"20_CR123","doi-asserted-by":"publisher","first-page":"1204","DOI":"10.1016\/j.molcel.2019.01.010","volume":"73","author":"S Shukla","year":"2019","unstructured":"Shukla S, Bjerke GA, Muhlrad D et al (2019) The RNase PARN controls the levels of specific miRNAs that contribute to p53 regulation. Mol Cell 73:1204\u20131216.e4. https:\/\/doi.org\/10.1016\/j.molcel.2019.01.010","journal-title":"Mol Cell"},{"key":"20_CR124","doi-asserted-by":"publisher","first-page":"388","DOI":"10.1261\/rna.069633.118","volume":"25","author":"D Lee","year":"2019","unstructured":"Lee D, Park D, Park JH et al (2019) Poly(A)-specific ribonuclease sculpts the 3\u2032 ends of microRNAs. RNA 25:388\u2013405. https:\/\/doi.org\/10.1261\/rna.069633.118","journal-title":"RNA"},{"key":"20_CR125","doi-asserted-by":"publisher","first-page":"11467","DOI":"10.1073\/pnas.1317751111","volume":"111","author":"J Boele","year":"2014","unstructured":"Boele J, Persson H, Shin JW et al (2014) PAPD5-mediated 3\u2032 adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease. Proc Natl Acad Sci 111:11467\u201311472. https:\/\/doi.org\/10.1073\/pnas.1317751111","journal-title":"Proc Natl Acad Sci"},{"key":"20_CR126","doi-asserted-by":"publisher","first-page":"9850","DOI":"10.1093\/nar\/gks705","volume":"40","author":"A Dueck","year":"2012","unstructured":"Dueck A, Ziegler C, Eichner A et al (2012) microRNAs associated with the different human Argonaute proteins. Nucleic Acids Res 40:9850\u20139862. https:\/\/doi.org\/10.1093\/nar\/gks705","journal-title":"Nucleic Acids Res"},{"key":"20_CR127","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","volume":"136","author":"DP Bartel","year":"2009","unstructured":"Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215\u2013233. https:\/\/doi.org\/10.1016\/j.cell.2009.01.002","journal-title":"Cell"},{"key":"20_CR128","doi-asserted-by":"publisher","first-page":"2493","DOI":"10.1261\/rna.2384610","volume":"16","author":"F Moretti","year":"2010","unstructured":"Moretti F, Thermann R, Hentze MW (2010) Mechanism of translational regulation by miR-2 from sites in the 5\u2032 untranslated region or the open reading frame. RNA 16:2493\u20132502. https:\/\/doi.org\/10.1261\/rna.2384610","journal-title":"RNA"},{"key":"20_CR129","doi-asserted-by":"publisher","first-page":"14879","DOI":"10.1073\/pnas.0803230105","volume":"105","author":"JJ Forman","year":"2008","unstructured":"Forman JJ, Legesse-Miller A, Coller HA (2008) A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence. Proc Natl Acad Sci USA 105:14879\u201314884. https:\/\/doi.org\/10.1073\/pnas.0803230105","journal-title":"Proc Natl Acad Sci USA"},{"key":"20_CR130","doi-asserted-by":"publisher","first-page":"789","DOI":"10.1016\/j.molcel.2010.06.005","volume":"38","author":"C Shin","year":"2010","unstructured":"Shin C, Nam J-W, Farh KK-H et al (2010) Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell 38:789\u2013802. https:\/\/doi.org\/10.1016\/j.molcel.2010.06.005","journal-title":"Mol Cell"},{"key":"20_CR131","first-page":"109","volume-title":"Computational prediction of microRNA target genes, target prediction databases, and web resources","author":"JT Roberts","year":"2017","unstructured":"Roberts JT, Borchert GM (2017) Computational prediction of microRNA target genes, target prediction databases, and web resources. Humana Press, New York, pp 109\u2013122"},{"key":"20_CR132","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1038\/s41597-021-00979-8","volume":"8","author":"GP Marceca","year":"2021","unstructured":"Marceca GP, Distefano R, Tomasello L et al (2021) MiREDiBase, a manually curated database of validated and putative editing events in microRNAs. Sci Data 8:199. https:\/\/doi.org\/10.1038\/s41597-021-00979-8","journal-title":"Sci Data"},{"key":"20_CR133","doi-asserted-by":"publisher","first-page":"5270","DOI":"10.1093\/nar\/gkn479","volume":"36","author":"Y Kawahara","year":"2008","unstructured":"Kawahara Y, Megraw M, Kreider E et al (2008) Frequency and fate of microRNA editing in human brain. Nucleic Acids Res 36:5270\u20135280. https:\/\/doi.org\/10.1093\/nar\/gkn479","journal-title":"Nucleic Acids Res"},{"key":"20_CR134","doi-asserted-by":"publisher","first-page":"R27","DOI":"10.1186\/gb-2006-7-4-r27","volume":"7","author":"MJ Blow","year":"2006","unstructured":"Blow MJ, Grocock RJ, Dongen SV et al (2006) RNA editing of human microRNAs. Genome Biol 7:R27. https:\/\/doi.org\/10.1186\/gb-2006-7-4-r27","journal-title":"Genome Biol"},{"key":"20_CR135","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.1101\/gr.131573.111","volume":"22","author":"S Alon","year":"2012","unstructured":"Alon S, Mor E, Vigneault F et al (2012) Systematic identification of edited microRNAs in the human brain. Genome Res 22:1533\u20131540. https:\/\/doi.org\/10.1101\/gr.131573.111","journal-title":"Genome Res"},{"key":"20_CR136","doi-asserted-by":"publisher","first-page":"1112","DOI":"10.1101\/gr.219741.116","volume":"27","author":"Y Wang","year":"2017","unstructured":"Wang Y, Xu X, Yu S et al (2017) Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers. Genome Res 27:1112\u20131125. https:\/\/doi.org\/10.1101\/gr.219741.116","journal-title":"Genome Res"},{"key":"20_CR137","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1101\/gr.224386.117","volume":"28","author":"L Li","year":"2018","unstructured":"Li L, Song Y, Shi X et al (2018) The landscape of miRNA editing in animals and its impact on miRNA biogenesis and targeting. Genome Res 28:132\u2013143. https:\/\/doi.org\/10.1101\/gr.224386.117","journal-title":"Genome Res"},{"key":"20_CR138","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1093\/nar\/gkx1176","volume":"46","author":"Y Pinto","year":"2018","unstructured":"Pinto Y, Buchumenski I, Levanon EY, Eisenberg E (2018) Human cancer tissues exhibit reduced A-to-I editing of miRNAs coupled with elevated editing of their targets. Nucleic Acids Res 46:71\u201382. https:\/\/doi.org\/10.1093\/nar\/gkx1176","journal-title":"Nucleic Acids Res"},{"key":"20_CR139","doi-asserted-by":"publisher","first-page":"3687","DOI":"10.1158\/0008-5472.can-22-0240","volume":"82","author":"R Distefano","year":"2022","unstructured":"Distefano R, Tomasello L, Vinciguerra GLR et al (2022) Pan-cancer analysis of canonical and modified miRNAs enhances the resolution of the functional miRNAome in cancer. Cancer Res 82:3687\u20133700. https:\/\/doi.org\/10.1158\/0008-5472.can-22-0240","journal-title":"Cancer Res"},{"key":"20_CR140","doi-asserted-by":"publisher","first-page":"773","DOI":"10.3390\/cancers14030773","volume":"14","author":"R Distefano","year":"2022","unstructured":"Distefano R, Nigita G, Le P et al (2022) Disparities in lung cancer: miRNA isoform characterization in lung adenocarcinoma. Cancers 14:773. https:\/\/doi.org\/10.3390\/cancers14030773","journal-title":"Cancers"},{"key":"20_CR141","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1038\/nsmb1041","volume":"13","author":"W Yang","year":"2006","unstructured":"Yang W, Chendrimada TP, Wang Q et al (2006) Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol 13:13\u201321. https:\/\/doi.org\/10.1038\/nsmb1041","journal-title":"Nat Struct Mol Biol"},{"key":"20_CR142","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1038\/sj.embor.7401011","volume":"8","author":"Y Kawahara","year":"2007","unstructured":"Kawahara Y, Zinshteyn B, Chendrimada TP et al (2007) RNA editing of the microRNA-151 precursor blocks cleavage by the Dicer-TRBP complex. EMBO Rep 8:763\u2013769. https:\/\/doi.org\/10.1038\/sj.embor.7401011","journal-title":"EMBO Rep"},{"key":"20_CR143","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1007\/s13238-014-0124-2","volume":"6","author":"Z Liu","year":"2014","unstructured":"Liu Z, Wang J, Li G, Wang H-W (2014) Structure of precursor microRNA\u2019s terminal loop regulates human Dicer\u2019s dicing activity by switching DExH\/D domain. Protein Cell 6:185\u2013193. https:\/\/doi.org\/10.1007\/s13238-014-0124-2","journal-title":"Protein Cell"},{"key":"20_CR144","doi-asserted-by":"publisher","first-page":"1137","DOI":"10.1126\/science.1138050","volume":"315","author":"Y Kawahara","year":"2007","unstructured":"Kawahara Y, Zinshteyn B, Sethupathy P et al (2007) Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315:1137\u20131140. https:\/\/doi.org\/10.1126\/science.1138050","journal-title":"Science"},{"key":"20_CR145","doi-asserted-by":"publisher","first-page":"6298","DOI":"10.1093\/nar\/gkw532","volume":"44","author":"G Nigita","year":"2016","unstructured":"Nigita G, Acunzo M, Romano G et al (2016) microRNA editing in seed region aligns with cellular changes in hypoxic conditions. Nucleic Acids Res 44:6298\u20136308. https:\/\/doi.org\/10.1093\/nar\/gkw532","journal-title":"Nucleic Acids Res"},{"key":"20_CR146","doi-asserted-by":"publisher","first-page":"10222","DOI":"10.1038\/s41598-018-28528-1","volume":"8","author":"G Nigita","year":"2018","unstructured":"Nigita G, Distefano R, Veneziano D et al (2018) Tissue and exosomal miRNA editing in Non-Small Cell Lung Cancer. Sci Rep 8:10222. https:\/\/doi.org\/10.1038\/s41598-018-28528-1","journal-title":"Sci Rep"},{"key":"20_CR147","doi-asserted-by":"publisher","first-page":"4059","DOI":"10.1172\/jci62925","volume":"122","author":"Y Choudhury","year":"2012","unstructured":"Choudhury Y, Tay FC, Lam DH et al (2012) Attenuated adenosine-to-inosine editing of microRNA-376a* promotes invasiveness of glioblastoma cells. J Clin Invest 122:4059\u20134076. https:\/\/doi.org\/10.1172\/jci62925","journal-title":"J Clin Invest"},{"key":"20_CR148","doi-asserted-by":"publisher","first-page":"15117","DOI":"10.1038\/s41598-023-42302-y","volume":"13","author":"Y Liu","year":"2023","unstructured":"Liu Y, Guo S, Xie W et al (2023) Identification of microRNA editing sites in clear cell renal cell carcinoma. Sci Rep 13:15117. https:\/\/doi.org\/10.1038\/s41598-023-42302-y","journal-title":"Sci Rep"},{"key":"20_CR149","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbc.2022.101682","volume":"298","author":"A Widmark","year":"2022","unstructured":"Widmark A, Sagredo EA, Karlstr\u00f6m V et al (2022) ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism. J Biol Chem 298:101682. https:\/\/doi.org\/10.1016\/j.jbc.2022.101682","journal-title":"J Biol Chem"},{"key":"20_CR150","doi-asserted-by":"publisher","first-page":"1105278","DOI":"10.3389\/fnmol.2022.1105278","volume":"15","author":"X Wu","year":"2023","unstructured":"Wu X, Yang H, Lin H et al (2023) Characterizing microRNA editing and mutation sites in Autism Spectrum Disorder. Front Mol Neurosci 15:1105278. https:\/\/doi.org\/10.3389\/fnmol.2022.1105278","journal-title":"Front Mol Neurosci"},{"key":"20_CR151","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1002\/1878-0261.13121","volume":"16","author":"M Soler","year":"2022","unstructured":"Soler M, Davalos V, S\u00e1nchez-Castillo A et al (2022) The transcribed ultraconserved region uc.160+ enhances processing and A-to-I editing of the miR-376 cluster: hypermethylation improves glioma prognosis. Mol Oncol 16:648\u2013664. https:\/\/doi.org\/10.1002\/1878-0261.13121","journal-title":"Mol Oncol"},{"key":"20_CR152","doi-asserted-by":"publisher","first-page":"932","DOI":"10.1016\/j.omtn.2020.07.020","volume":"21","author":"RVCT van der Kwast","year":"2020","unstructured":"van der Kwast RVCT, Parma L, van der Bent ML et al (2020) Adenosine-to-inosine editing of vasoactive microRNAs alters their targetome and function in ischemia. Mol Ther Nucleic Acids 21:932\u2013953. https:\/\/doi.org\/10.1016\/j.omtn.2020.07.020","journal-title":"Mol Ther Nucleic Acids"},{"key":"20_CR153","doi-asserted-by":"publisher","first-page":"3738","DOI":"10.1038\/s41388-020-1248-x","volume":"39","author":"J Ram\u00edrez-Moya","year":"2020","unstructured":"Ram\u00edrez-Moya J, Baker AR, Slack FJ, Santisteban P (2020) ADAR1-mediated RNA editing is a novel oncogenic process in thyroid cancer and regulates miR-200 activity. Oncogene 39:3738\u20133753. https:\/\/doi.org\/10.1038\/s41388-020-1248-x","journal-title":"Oncogene"},{"key":"20_CR154","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/s12276-022-00916-8","volume":"55","author":"HS Kim","year":"2023","unstructured":"Kim HS, Na MJ, Son KH et al (2023) ADAR1-dependent miR-3144-3p editing simultaneously induces MSI2 expression and suppresses SLC38A4 expression in liver cancer. Exp Mol Med 55:95\u2013107. https:\/\/doi.org\/10.1038\/s12276-022-00916-8","journal-title":"Exp Mol Med"},{"key":"20_CR155","doi-asserted-by":"publisher","first-page":"1597","DOI":"10.1038\/s41388-023-02673-y","volume":"42","author":"G Romano","year":"2023","unstructured":"Romano G, Le P, Nigita G et al (2023) A-to-I edited miR-411-5p targets MET and promotes TKI response in NSCLC-resistant cells. Oncogene 42:1597\u20131606. https:\/\/doi.org\/10.1038\/s41388-023-02673-y","journal-title":"Oncogene"},{"key":"20_CR156","doi-asserted-by":"publisher","first-page":"2045","DOI":"10.1093\/nar\/gkx1257","volume":"46","author":"V Cesarini","year":"2018","unstructured":"Cesarini V, Silvestris DA, Tassinari V et al (2018) ADAR2\/miR-589-3p axis controls glioblastoma cell migration\/invasion. Nucleic Acids Res 46:2045\u20132059. https:\/\/doi.org\/10.1093\/nar\/gkx1257","journal-title":"Nucleic Acids Res"},{"key":"20_CR157","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1261\/rna.030775.111","volume":"18","author":"S Mahlab","year":"2012","unstructured":"Mahlab S, Tuller T, Linial M (2012) Conservation of the relative tRNA composition in healthy and cancerous tissues. RNA 18:640\u2013652. https:\/\/doi.org\/10.1261\/rna.030775.111","journal-title":"RNA"},{"key":"20_CR158","doi-asserted-by":"publisher","first-page":"6729","DOI":"10.1093\/nar\/gkt321","volume":"41","author":"Y Itoh","year":"2013","unstructured":"Itoh Y, Sekine S, Suetsugu S, Yokoyama S (2013) Tertiary structure of bacterial selenocysteine tRNA. Nucleic Acids Res 41:6729\u20136738. https:\/\/doi.org\/10.1093\/nar\/gkt321","journal-title":"Nucleic Acids Res"},{"key":"20_CR159","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1038\/s41422-018-0013-y","volume":"28","author":"T Pan","year":"2018","unstructured":"Pan T (2018) Modifications and functional genomics of human transfer RNA. Cell Res 28:395\u2013404. https:\/\/doi.org\/10.1038\/s41422-018-0013-y","journal-title":"Cell Res"},{"key":"20_CR160","doi-asserted-by":"publisher","first-page":"4279","DOI":"10.1016\/j.febslet.2014.09.025","volume":"588","author":"AG Torres","year":"2014","unstructured":"Torres AG, Pi\u00f1eyro D, Filonava L et al (2014) A-to-I editing on tRNAs: biochemical, biological and evolutionary implications. FEBS Lett 588:4279\u20134286. https:\/\/doi.org\/10.1016\/j.febslet.2014.09.025","journal-title":"FEBS Lett"},{"key":"20_CR161","doi-asserted-by":"publisher","first-page":"8895","DOI":"10.1073\/pnas.96.16.8895","volume":"96","author":"S Maas","year":"1999","unstructured":"Maas S, Gerber AP, Rich A (1999) Identification and characterization of a human tRNA-specific adenosine deaminase related to the ADAR family of pre-mRNA editing enzymes. Proc Natl Acad Sci USA 96:8895\u20138900","journal-title":"Proc Natl Acad Sci USA"},{"key":"20_CR162","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1093\/emboj\/20.1.231","volume":"20","author":"GR Bjork","year":"2001","unstructured":"Bjork GR, Jacobsson K, Nilsson K et al (2001) A primordial tRNA modification required for the evolution of life? EMBO J 20:231\u2013239. https:\/\/doi.org\/10.1093\/emboj\/20.1.231","journal-title":"EMBO J"},{"key":"20_CR163","doi-asserted-by":"publisher","first-page":"5145","DOI":"10.1093\/nar\/gkv277","volume":"43","author":"AG Torres","year":"2015","unstructured":"Torres AG, Pi\u00f1eyro D, Rodr\u00edguez-Escrib\u00e0 M et al (2015) Inosine modifications in human tRNAs are incorporated at the precursor tRNA level. Nucleic Acids Res 43:5145\u20135157. https:\/\/doi.org\/10.1093\/nar\/gkv277","journal-title":"Nucleic Acids Res"},{"key":"20_CR164","doi-asserted-by":"publisher","first-page":"6391","DOI":"10.1093\/nar\/gks296","volume":"40","author":"VA Moran","year":"2012","unstructured":"Moran VA, Perera RJ, Khalil AM (2012) Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res 40:6391\u20136400. https:\/\/doi.org\/10.1093\/nar\/gks296","journal-title":"Nucleic Acids Res"},{"key":"20_CR165","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1038\/s41580-020-00315-9","volume":"22","author":"L Statello","year":"2021","unstructured":"Statello L, Guo C-J, Chen L-L, Huarte M (2021) Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Biol 22:96\u2013118. https:\/\/doi.org\/10.1038\/s41580-020-00315-9","journal-title":"Nat Rev Mol Cell Biol"},{"key":"20_CR166","doi-asserted-by":"publisher","first-page":"D916","DOI":"10.1093\/nar\/gkaa1087","volume":"49","author":"A Frankish","year":"2020","unstructured":"Frankish A, Diekhans M, Jungreis I et al (2020) GENCODE 2021. Nucleic Acids Res 49:D916\u2013D923. https:\/\/doi.org\/10.1093\/nar\/gkaa1087","journal-title":"Nucleic Acids Res"},{"key":"20_CR167","doi-asserted-by":"publisher","first-page":"D168","DOI":"10.1093\/nar\/gku988","volume":"43","author":"XC Quek","year":"2015","unstructured":"Quek XC, Thomson DW, Maag JLV et al (2015) lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res 43:D168\u2013D173. https:\/\/doi.org\/10.1093\/nar\/gku988","journal-title":"Nucleic Acids Res"},{"key":"20_CR168","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1038\/s41580-022-00566-8","volume":"24","author":"JS Mattick","year":"2023","unstructured":"Mattick JS, Amaral PP, Carninci P et al (2023) Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 24:430\u2013447. https:\/\/doi.org\/10.1038\/s41580-022-00566-8","journal-title":"Nat Rev Mol Cell Biol"},{"key":"20_CR169","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1111\/1440-1681.12795","volume":"44","author":"W Xing","year":"2017","unstructured":"Xing W, Gao W, Mao G et al (2017) Long non-coding RNAs in aging organs and tissues. Clin Exp Pharmacol Physiol 44:30\u201337. https:\/\/doi.org\/10.1111\/1440-1681.12795","journal-title":"Clin Exp Pharmacol Physiol"},{"key":"20_CR170","doi-asserted-by":"publisher","first-page":"R75","DOI":"10.1186\/gb-2012-13-8-r75","volume":"13","author":"AL Brunner","year":"2012","unstructured":"Brunner AL, Beck AH, Edris B et al (2012) Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers. Genome Biol 13:R75\u2013R75. https:\/\/doi.org\/10.1186\/gb-2012-13-8-r75","journal-title":"Genome Biol"},{"key":"20_CR171","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1016\/j.tig.2015.03.007","volume":"31","author":"GS Laurent","year":"2015","unstructured":"Laurent GS, Wahlestedt C, Kapranov P (2015) The Landscape of long noncoding RNA classification. Trends Genet 31:239\u2013251. https:\/\/doi.org\/10.1016\/j.tig.2015.03.007","journal-title":"Trends Genet"},{"key":"20_CR172","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1016\/j.bbagrm.2015.07.017","volume":"1859","author":"G Housman","year":"2016","unstructured":"Housman G, Ulitsky I (2016) Methods for distinguishing between protein-coding and long noncoding RNAs and the elusive biological purpose of translation of long noncoding RNAs. Biochim Biophys Acta 1859:31\u201340. https:\/\/doi.org\/10.1016\/j.bbagrm.2015.07.017","journal-title":"Biochim Biophys Acta"},{"key":"20_CR173","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1126\/science.aad4076","volume":"351","author":"BR Nelson","year":"2016","unstructured":"Nelson BR, Makarewich CA, Anderson DM et al (2016) A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle. Science (New York, NY) 351:271\u2013275. https:\/\/doi.org\/10.1126\/science.aad4076","journal-title":"Science (New York, NY)"},{"key":"20_CR174","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1002\/1878-0261.13424","volume":"17","author":"B Zhou","year":"2023","unstructured":"Zhou B, Wu Y, Cheng P, Wu C (2023) Long noncoding RNAs with peptide-encoding potential identified in esophageal squamous cell carcinoma: KDM4A-AS1-encoded peptide weakens cancer cell viability and migratory capacity. Mol Oncol 17:1419\u20131436. https:\/\/doi.org\/10.1002\/1878-0261.13424","journal-title":"Mol Oncol"},{"key":"20_CR175","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1038\/nrg.2016.20","volume":"17","author":"DW Thomson","year":"2016","unstructured":"Thomson DW, Dinger ME (2016) Endogenous microRNA sponges: evidence and controversy. Nat Rev Genet 17:272\u2013283. https:\/\/doi.org\/10.1038\/nrg.2016.20","journal-title":"Nat Rev Genet"},{"key":"20_CR176","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1038\/nature06992","volume":"454","author":"X Wang","year":"2008","unstructured":"Wang X, Arai S, Song X et al (2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454:126\u2013130. https:\/\/doi.org\/10.1038\/nature06992","journal-title":"Nature"},{"key":"20_CR177","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1016\/j.molcel.2014.08.023","volume":"56","author":"K Schaukowitch","year":"2014","unstructured":"Schaukowitch K, Joo J-Y, Liu X et al (2014) Enhancer RNA facilitates NELF release from immediate early genes. Mol Cell 56:29\u201342. https:\/\/doi.org\/10.1016\/j.molcel.2014.08.023","journal-title":"Mol Cell"},{"key":"20_CR178","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1126\/science.aad3346","volume":"350","author":"AA Sigova","year":"2015","unstructured":"Sigova AA, Abraham BJ, Ji X et al (2015) Transcription factor trapping by RNA in gene regulatory elements. Science (New York, NY) 350:978\u2013981. https:\/\/doi.org\/10.1126\/science.aad3346","journal-title":"Science (New York, NY)"},{"key":"20_CR179","doi-asserted-by":"publisher","first-page":"7743","DOI":"10.1038\/ncomms8743","volume":"6","author":"T Mondal","year":"2015","unstructured":"Mondal T, Subhash S, Vaid R et al (2015) MEG3 long noncoding RNA regulates the TGF-\u03b2 pathway genes through formation of RNA-DNA triplex structures. Nat Commun 6:7743. https:\/\/doi.org\/10.1038\/ncomms8743","journal-title":"Nat Commun"},{"key":"20_CR180","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1016\/j.molcel.2015.10.001","volume":"60","author":"A Postepska-Igielska","year":"2015","unstructured":"Postepska-Igielska A, Giwojna A, Gasri-Plotnitsky L et al (2015) LncRNA Khps1 regulates expression of the proto-oncogene SPHK1 via triplex-mediated changes in chromatin structure. Mol Cell 60:626\u2013636. https:\/\/doi.org\/10.1016\/j.molcel.2015.10.001","journal-title":"Mol Cell"},{"key":"20_CR181","doi-asserted-by":"publisher","first-page":"675","DOI":"10.1038\/s41576-019-0158-7","volume":"20","author":"LS Kristensen","year":"2019","unstructured":"Kristensen LS, Andersen MS, Stagsted LVW et al (2019) The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet 20:675\u2013691. https:\/\/doi.org\/10.1038\/s41576-019-0158-7","journal-title":"Nat Rev Genet"},{"key":"20_CR182","doi-asserted-by":"publisher","first-page":"2016","DOI":"10.1016\/j.cell.2022.04.021","volume":"185","author":"C-X Liu","year":"2022","unstructured":"Liu C-X, Chen L-L (2022) Circular RNAs: characterization, cellular roles, and applications. Cell 185:2016\u20132034. https:\/\/doi.org\/10.1016\/j.cell.2022.04.021","journal-title":"Cell"},{"key":"20_CR183","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1080\/15476286.2016.1227905","volume":"14","author":"JE Wilusz","year":"2017","unstructured":"Wilusz JE (2017) Circular RNAs: unexpected outputs of many protein-coding genes. RNA Biol 14:1007\u20131017. https:\/\/doi.org\/10.1080\/15476286.2016.1227905","journal-title":"RNA Biol"},{"key":"20_CR184","doi-asserted-by":"publisher","first-page":"D79","DOI":"10.1093\/nar\/gkw835","volume":"45","author":"J Gong","year":"2017","unstructured":"Gong J, Liu C, Liu W et al (2017) LNCediting: a database for functional effects of RNA editing in lncRNAs. Nucleic Acids Res 45:D79\u2013D84. https:\/\/doi.org\/10.1093\/nar\/gkw835","journal-title":"Nucleic Acids Res"},{"key":"20_CR185","doi-asserted-by":"publisher","first-page":"64","DOI":"10.3389\/fbioe.2014.00064","volume":"2","author":"E Picardi","year":"2014","unstructured":"Picardi E, D\u2019Erchia AM, Gallo A et al (2014) Uncovering RNA editing sites in long non-coding RNAs. Front Bioeng Biotechnol 2:64. https:\/\/doi.org\/10.3389\/fbioe.2014.00064","journal-title":"Front Bioeng Biotechnol"},{"key":"20_CR186","doi-asserted-by":"publisher","first-page":"230","DOI":"10.3389\/fgene.2017.00230","volume":"8","author":"H Luo","year":"2017","unstructured":"Luo H, Fang S, Sun L et al (2017) Comprehensive characterization of the RNA editomes in cancer development and progression. Front Genet 8:230. https:\/\/doi.org\/10.3389\/fgene.2017.00230","journal-title":"Front Genet"},{"key":"20_CR187","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2020.632187","volume":"10","author":"H Wang","year":"2020","unstructured":"Wang H, Chen S, Wei J et al (2020) A-to-I RNA editing in cancer: from evaluating the editing level to exploring the editing effects. Front Oncol 10:632187. https:\/\/doi.org\/10.3389\/fonc.2020.632187","journal-title":"Front Oncol"},{"key":"20_CR188","doi-asserted-by":"publisher","first-page":"167036","DOI":"10.1016\/j.bbadis.2024.167036","volume":"1870","author":"G Margvelani","year":"2024","unstructured":"Margvelani G, Welden JR, Maquera AA et al (2024) Influence of FTDP-17 mutants on circular tau RNAs. Biochim Biophys Acta (BBA) \u2013 Mol Basis Dis 1870:167036. https:\/\/doi.org\/10.1016\/j.bbadis.2024.167036","journal-title":"Biochim Biophys Acta (BBA) \u2013 Mol Basis Dis"},{"key":"20_CR189","doi-asserted-by":"publisher","first-page":"355","DOI":"10.3389\/fphys.2016.00355","volume":"7","author":"N Abu","year":"2016","unstructured":"Abu N, Jamal R (2016) Circular RNAs as promising biomarkers: a mini-review. Front Physiol 7:355. https:\/\/doi.org\/10.3389\/fphys.2016.00355","journal-title":"Front Physiol"},{"key":"20_CR190","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.1007\/s11427-014-4770-7","volume":"57","author":"L Yang","year":"2014","unstructured":"Yang L, Chen L-L (2014) Competition of RNA splicing: line in or circle up. Sci China Life Sci 57:1232\u20131233. https:\/\/doi.org\/10.1007\/s11427-014-4770-7","journal-title":"Sci China Life Sci"},{"key":"20_CR191","doi-asserted-by":"publisher","first-page":"6048","DOI":"10.1073\/pnas.96.11.6048","volume":"96","author":"DP Morse","year":"1999","unstructured":"Morse DP, Bass BL (1999) Long RNA hairpins that contain inosine are present in Caenorhabditis elegans poly(A)+ RNA. Proc Natl Acad Sci USA 96:6048\u20136053","journal-title":"Proc Natl Acad Sci USA"},{"key":"20_CR192","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1126\/science.1086763","volume":"301","author":"B Hoopengardner","year":"2003","unstructured":"Hoopengardner B, Bhalla T, Staber C, Reenan R (2003) Nervous system targets of RNA editing identified by comparative genomics. Science (New York, NY) 301:832\u2013836. https:\/\/doi.org\/10.1126\/science.1086763","journal-title":"Science (New York, NY)"},{"issue":"4","key":"20_CR193","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1038\/ng0893-332","volume":"4","author":"MS Boguski","year":"1993","unstructured":"Boguski MS, Lowe T, Tolstoshev CM (1993) dbEST\u2014database for \u201cexpressed sequence tags\u201d. Nat Genet 4(4):332\u2013333","journal-title":"Nat Genet"},{"key":"20_CR194","doi-asserted-by":"publisher","first-page":"1813","DOI":"10.1093\/bioinformatics\/btt287","volume":"29","author":"E Picardi","year":"2013","unstructured":"Picardi E, Pesole G (2013) REDItools: high-throughput RNA editing detection made easy. Bioinformatics 29:1813\u20131814. https:\/\/doi.org\/10.1093\/bioinformatics\/btt287","journal-title":"Bioinformatics"},{"key":"20_CR195","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1186\/s12859-020-03562-x","volume":"21","author":"T Flati","year":"2020","unstructured":"Flati T, Gioiosa S, Spallanzani N et al (2020) HPC-REDItools: a novel HPC-aware tool for improved large scale RNA-editing analysis. BMC Bioinformatics 21:353. https:\/\/doi.org\/10.1186\/s12859-020-03562-x","journal-title":"BMC Bioinformatics"},{"key":"20_CR196","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1007\/978-1-0716-1307-8_14","volume":"2284","author":"CL Giudice","year":"2021","unstructured":"Giudice CL, Mansi L, Flati T et al (2021) RNA editing detection in HPC infrastructures. Methods Mol Biol 2284:253\u2013270. https:\/\/doi.org\/10.1007\/978-1-0716-1307-8_14","journal-title":"Methods Mol Biol"},{"key":"20_CR197","doi-asserted-by":"publisher","first-page":"3906","DOI":"10.1093\/bioinformatics\/btv505","volume":"31","author":"J Ahn","year":"2015","unstructured":"Ahn J, Xiao X (2015) RASER: reads aligner for SNPs and editing sites of RNA. Bioinformatics 31:3906\u20133913. https:\/\/doi.org\/10.1093\/bioinformatics\/btv505","journal-title":"Bioinformatics"},{"key":"20_CR198","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1186\/s13742-016-0143-4","volume":"5","author":"Z Wang","year":"2016","unstructured":"Wang Z, Lian J, Li Q et al (2016) RES-Scanner: a software package for genome-wide identification of RNA-editing sites. Gigascience 5:37. https:\/\/doi.org\/10.1186\/s13742-016-0143-4","journal-title":"Gigascience"},{"issue":"Suppl 1","key":"20_CR199","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1186\/s12864-015-2301-y","volume":"17","author":"M-S Kim","year":"2016","unstructured":"Kim M-S, Hur B, Kim S (2016) RDDpred: a condition-specific RNA-editing prediction model from RNA-seq data. BMC Genomics 17(Suppl 1):5. https:\/\/doi.org\/10.1186\/s12864-015-2301-y","journal-title":"BMC Genomics"},{"key":"20_CR200","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/gigascience\/gix012","volume":"6","author":"H Xiong","year":"2017","unstructured":"Xiong H, Liu D, Li Q et al (2017) RED-ML: a novel, effective RNA editing detection method based on machine learning. Gigascience 6:1\u20138. https:\/\/doi.org\/10.1093\/gigascience\/gix012","journal-title":"Gigascience"},{"key":"20_CR201","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1093\/bib\/bbw087","volume":"18","author":"D John","year":"2016","unstructured":"John D, Weirick T, Dimmeler S, Uchida S (2016) RNAEditor: easy detection of RNA editing events and the introduction of editing islands. Brief Bioinform 18:993\u20131001. https:\/\/doi.org\/10.1093\/bib\/bbw087","journal-title":"Brief Bioinform"},{"key":"20_CR202","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1186\/s12859-016-1432-8","volume":"18","author":"M Piechotta","year":"2017","unstructured":"Piechotta M, Wyler E, Ohler U et al (2017) JACUSA: site-specific identification of RNA editing events from replicate sequencing data. BMC Bioinformatics 18:7. https:\/\/doi.org\/10.1186\/s12859-016-1432-8","journal-title":"BMC Bioinformatics"},{"key":"20_CR203","doi-asserted-by":"publisher","first-page":"3538","DOI":"10.1093\/bioinformatics\/btx473","volume":"33","author":"F Zhang","year":"2017","unstructured":"Zhang F, Lu Y, Yan S et al (2017) SPRINT: an SNP-free toolkit for identifying RNA editing sites. Bioinformatics 33:3538\u20133548. https:\/\/doi.org\/10.1093\/bioinformatics\/btx473","journal-title":"Bioinformatics"},{"key":"20_CR204","doi-asserted-by":"publisher","first-page":"6005","DOI":"10.1038\/s41598-018-24298-y","volume":"8","author":"Z Ouyang","year":"2018","unstructured":"Ouyang Z, Liu F, Zhao C et al (2018) Accurate identification of RNA editing sites from primitive sequence with deep neural networks. Sci Rep 8:6005. https:\/\/doi.org\/10.1038\/s41598-018-24298-y","journal-title":"Sci Rep"},{"key":"20_CR205","doi-asserted-by":"publisher","first-page":"5064","DOI":"10.1038\/s41598-019-41294-y","volume":"9","author":"W Hwang","year":"2019","unstructured":"Hwang W, Calza S, Silvestri M et al (2019) CREDO: highly confident disease-relevant A-to-I RNA-editing discovery in breast cancer. Sci Rep 9:5064. https:\/\/doi.org\/10.1038\/s41598-019-41294-y","journal-title":"Sci Rep"},{"key":"20_CR206","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2021.686851","volume":"12","author":"D Light","year":"2021","unstructured":"Light D, Haas R, Yazbak M et al (2021) RESIC: a tool for comprehensive adenosine to inosine RNA editing site identification and classification. Front Genet 12:686851. https:\/\/doi.org\/10.3389\/fgene.2021.686851","journal-title":"Front Genet"},{"key":"20_CR207","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1186\/s12859-023-05452-4","volume":"24","author":"E Kofman","year":"2023","unstructured":"Kofman E, Yee B, Medina-Munoz HC, Yeo GW (2023) FLARE: a fast and flexible workflow for identifying RNA editing foci. BMC Bioinformatics 24:370. https:\/\/doi.org\/10.1186\/s12859-023-05452-4","journal-title":"BMC Bioinformatics"},{"key":"20_CR208","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1186\/s13059-022-02676-0","volume":"23","author":"M Piechotta","year":"2022","unstructured":"Piechotta M, Vries ISN, Wang Q et al (2022) RNA modification mapping with JACUSA2. Genome Biol 23:115. https:\/\/doi.org\/10.1186\/s13059-022-02676-0","journal-title":"Genome Biol"},{"key":"20_CR209","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1186\/s13059-023-02921-0","volume":"24","author":"L Chen","year":"2023","unstructured":"Chen L, Ou L, Jing X et al (2023) DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing. Genome Biol 24:75. https:\/\/doi.org\/10.1186\/s13059-023-02921-0","journal-title":"Genome Biol"},{"key":"20_CR210","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1186\/s13059-023-03012-w","volume":"24","author":"Z Liu","year":"2023","unstructured":"Liu Z, Quinones-Valdez G, Fu T et al (2023) L-GIREMI uncovers RNA editing sites in long-read RNA-seq. Genome Biol 24:171. https:\/\/doi.org\/10.1186\/s13059-023-03012-w","journal-title":"Genome Biol"},{"key":"20_CR211","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1002\/humu.23066","volume":"37","author":"D Veneziano","year":"2016","unstructured":"Veneziano D, Bella SD, Nigita G et al (2016) Noncoding RNA: current deep sequencing data analysis approaches and challenges. Hum Mutat 37:1283\u20131298. https:\/\/doi.org\/10.1002\/humu.23066","journal-title":"Hum Mutat"},{"key":"20_CR212","doi-asserted-by":"publisher","first-page":"1210","DOI":"10.1126\/science.1170995","volume":"324","author":"JB Li","year":"2009","unstructured":"Li JB, Levanon EY, Yoon J-K et al (2009) Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science 324:1210\u20131213. https:\/\/doi.org\/10.1126\/science.1170995","journal-title":"Science"},{"key":"20_CR213","doi-asserted-by":"publisher","first-page":"37","DOI":"10.3389\/fbioe.2015.00037","volume":"3","author":"G Nigita","year":"2015","unstructured":"Nigita G, Veneziano D, Ferro A (2015) A-to-I RNA editing: current knowledge sources and computational approaches with special emphasis on non-coding RNA molecules. Front Bioeng Biotechnol 3:37. https:\/\/doi.org\/10.3389\/fbioe.2015.00037","journal-title":"Front Bioeng Biotechnol"},{"key":"20_CR214","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pgen.1002317","volume":"7","author":"S Carmi","year":"2011","unstructured":"Carmi S, Borukhov I, Levanon EY (2011) Identification of widespread ultra-edited human RNAs. PLoS Genet 7:1\u201311. https:\/\/doi.org\/10.1371\/journal.pgen.1002317","journal-title":"PLoS Genet"},{"key":"20_CR215","doi-asserted-by":"publisher","DOI":"10.7554\/elife.28625","volume":"6","author":"SN Deffit","year":"2017","unstructured":"Deffit SN, Yee BA, Manning AC et al (2017) The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis. elife 6:e28625. https:\/\/doi.org\/10.7554\/elife.28625","journal-title":"elife"},{"key":"20_CR216","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1101\/gr.095273.109","volume":"20","author":"MJL de Hoon","year":"2010","unstructured":"de Hoon MJL, Taft RJ, Hashimoto T et al (2010) Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res 20:257\u2013264. https:\/\/doi.org\/10.1101\/gr.095273.109","journal-title":"Genome Res"},{"key":"20_CR217","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1007\/978-1-62703-514-9_9","volume":"1038","author":"S Alon","year":"2013","unstructured":"Alon S, Eisenberg E (2013) Identifying RNA editing sites in miRNAs by deep sequencing. Methods Mol Biol 1038:159\u2013170. https:\/\/doi.org\/10.1007\/978-1-62703-514-9_9","journal-title":"Methods Mol Biol"},{"key":"20_CR218","doi-asserted-by":"publisher","first-page":"lqab068","DOI":"10.1093\/nargab\/lqab068","volume":"3","author":"AH Patil","year":"2021","unstructured":"Patil AH, Halushka MK (2021) miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline. NAR Genom Bioinform 3:lqab068. https:\/\/doi.org\/10.1093\/nargab\/lqab068","journal-title":"NAR Genom Bioinform"},{"key":"20_CR219","doi-asserted-by":"publisher","first-page":"1769","DOI":"10.1101\/gr.222067.117","volume":"27","author":"MN McCall","year":"2017","unstructured":"McCall MN, Kim M-S, Adil M et al (2017) Toward the human cellular microRNAome. Genome Res 27:1769\u20131781. https:\/\/doi.org\/10.1101\/gr.222067.117","journal-title":"Genome Res"},{"key":"20_CR220","doi-asserted-by":"publisher","first-page":"2973","DOI":"10.1093\/nar\/gkx082","volume":"45","author":"AG Telonis","year":"2017","unstructured":"Telonis AG, Magee R, Loher P et al (2017) Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types. Nucleic Acids Res 45:2973\u20132985. https:\/\/doi.org\/10.1093\/nar\/gkx082","journal-title":"Nucleic Acids Res"},{"key":"20_CR221","doi-asserted-by":"publisher","first-page":"100","DOI":"10.12688\/f1000research.10571.2","volume":"6","author":"JL Weirather","year":"2017","unstructured":"Weirather JL, de Cesare M, Wang Y et al (2017) Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Res 6:100. https:\/\/doi.org\/10.12688\/f1000research.10571.2","journal-title":"F1000Res"},{"key":"20_CR222","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/s41592-022-01724-8","volume":"20","author":"MC Lucas","year":"2023","unstructured":"Lucas MC, Novoa EM (2023) Long-read sequencing in the era of epigenomics and epitranscriptomics. Nat Methods 20:25\u201329. https:\/\/doi.org\/10.1038\/s41592-022-01724-8","journal-title":"Nat Methods"},{"key":"20_CR223","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1038\/s12276-020-00499-2","volume":"52","author":"Y Kashima","year":"2020","unstructured":"Kashima Y, Sakamoto Y, Kaneko K et al (2020) Single-cell sequencing techniques from individual to multiomics analyses. Exp Mol Med 52:1419\u20131427. https:\/\/doi.org\/10.1038\/s12276-020-00499-2","journal-title":"Exp Mol Med"},{"key":"20_CR224","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1007\/978-1-0716-2756-3_18","volume":"2584","author":"A Fonzino","year":"2022","unstructured":"Fonzino A, Pesole G, Picardi E (2022) Profiling RNA editing in single cells. Methods Mol Biol 2584:347\u2013370. https:\/\/doi.org\/10.1007\/978-1-0716-2756-3_18","journal-title":"Methods Mol Biol"},{"key":"20_CR225","doi-asserted-by":"publisher","first-page":"D750","DOI":"10.1093\/nar\/gkw767","volume":"45","author":"E Picardi","year":"2017","unstructured":"Picardi E, D\u2019Erchia AM, Giudice CL, Pesole G (2017) REDIportal: a comprehensive database of A-to-I RNA editing events in humans. Nucleic Acids Res 45:D750\u2013D757. https:\/\/doi.org\/10.1093\/nar\/gkw767","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"20_CR226","doi-asserted-by":"publisher","first-page":"374","DOI":"10.1158\/0008-5472.can-22-1062","volume":"83","author":"TW Chan","year":"2022","unstructured":"Chan TW, Dodson JP, Arbet J et al (2022) Single-cell analysis in lung adenocarcinoma implicates RNA editing in cancer innate immunity and patient prognosis. Cancer Res 83(3):374\u2013385. https:\/\/doi.org\/10.1158\/0008-5472.can-22-1062","journal-title":"Cancer Res"},{"key":"20_CR227","doi-asserted-by":"publisher","first-page":"10335","DOI":"10.1038\/s41598-023-37325-4","volume":"13","author":"Y Wu","year":"2023","unstructured":"Wu Y, Hao S, Xu X et al (2023) A novel computational method enables RNA editome profiling during human hematopoiesis from scRNA-seq data. Sci Rep 13:10335. https:\/\/doi.org\/10.1038\/s41598-023-37325-4","journal-title":"Sci Rep"},{"key":"20_CR228","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1038\/nchembio.434","volume":"6","author":"M Sakurai","year":"2010","unstructured":"Sakurai M, Yano T, Kawabata H et al (2010) Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome. Nat Chem Biol 6:733\u2013740. https:\/\/doi.org\/10.1038\/nchembio.434","journal-title":"Nat Chem Biol"},{"key":"20_CR229","doi-asserted-by":"publisher","first-page":"522","DOI":"10.1101\/gr.162537.113","volume":"24","author":"M Sakurai","year":"2014","unstructured":"Sakurai M, Ueda H, Yano T et al (2014) A biochemical landscape of A-to-I RNA editing in the human brain transcriptome. Genome Res 24:522\u2013534. https:\/\/doi.org\/10.1101\/gr.162537.113","journal-title":"Genome Res"},{"key":"20_CR230","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/978-1-0716-0787-9_8","volume":"2181","author":"M Sakurai","year":"2020","unstructured":"Sakurai M, Okada S, Ueda H, Yang Y (2020) Discovering A-to-I RNA editing through chemical methodology \u201cICE-seq\u201d. Methods Mol Biol 2181:113\u2013148. https:\/\/doi.org\/10.1007\/978-1-0716-0787-9_8","journal-title":"Methods Mol Biol"},{"key":"20_CR231","doi-asserted-by":"publisher","first-page":"5241","DOI":"10.1021\/jacs.9b13406","volume":"142","author":"SD Knutson","year":"2020","unstructured":"Knutson SD, Arthur RA, Johnston HR, Heemstra JM (2020) Selective enrichment of A-to-I edited transcripts from cellular RNA using endonuclease V. J Am Chem Soc 142:5241\u20135251. https:\/\/doi.org\/10.1021\/jacs.9b13406","journal-title":"J Am Chem Soc"},{"key":"20_CR232","doi-asserted-by":"publisher","DOI":"10.1002\/cpch.82","volume":"12","author":"SD Knutson","year":"2020","unstructured":"Knutson SD, Heemstra JM (2020) EndoVIPER-seq for improved detection of A-to-I editing sites in cellular RNA. Curr Protoc Chem Biol 12:e82. https:\/\/doi.org\/10.1002\/cpch.82","journal-title":"Curr Protoc Chem Biol"},{"key":"20_CR233","doi-asserted-by":"publisher","first-page":"1772","DOI":"10.1093\/bioinformatics\/btq285","volume":"26","author":"A Kiran","year":"2010","unstructured":"Kiran A, Baranov PV (2010) DARNED: a DAtabase of RNa EDiting in humans. Bioinformatics 26:1772\u20131776. https:\/\/doi.org\/10.1093\/bioinformatics\/btq285","journal-title":"Bioinformatics"},{"key":"20_CR234","doi-asserted-by":"publisher","first-page":"D258","DOI":"10.1093\/nar\/gks961","volume":"41","author":"AM Kiran","year":"2013","unstructured":"Kiran AM, O\u2019Mahony JJ, Sanjeev K, Baranov PV (2013) Darned in 2013: inclusion of model organisms and linking with Wikipedia. Nucleic Acids Res 41:D258\u2013D261. https:\/\/doi.org\/10.1093\/nar\/gks961","journal-title":"Nucleic Acids Res"},{"key":"20_CR235","doi-asserted-by":"publisher","first-page":"3166","DOI":"10.1093\/bioinformatics\/bts589","volume":"28","author":"A Lagan\u00e0","year":"2012","unstructured":"Lagan\u00e0 A, Paone A, Veneziano D et al (2012) miR-EdiTar: a database of predicted A-to-I edited miRNA target sites. Bioinformatics 28:3166\u20133168. https:\/\/doi.org\/10.1093\/bioinformatics\/bts589","journal-title":"Bioinformatics"},{"key":"20_CR236","doi-asserted-by":"publisher","first-page":"D109","DOI":"10.1093\/nar\/gkt996","volume":"42","author":"G Ramaswami","year":"2014","unstructured":"Ramaswami G, Li JB (2014) RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res 42:D109\u2013D113. https:\/\/doi.org\/10.1093\/nar\/gkt996","journal-title":"Nucleic Acids Res"},{"key":"20_CR237","doi-asserted-by":"publisher","first-page":"D78","DOI":"10.1093\/nar\/gky958","volume":"47","author":"G Niu","year":"2019","unstructured":"Niu G, Zou D, Li M et al (2019) Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human. Nucleic Acids Res 47:D78\u2013D83. https:\/\/doi.org\/10.1093\/nar\/gky958","journal-title":"Nucleic Acids Res"},{"key":"20_CR238","doi-asserted-by":"publisher","first-page":"canres.3501.201","DOI":"10.1158\/0008-5472.can-18-3501","volume":"79","author":"C-H Lin","year":"2019","unstructured":"Lin C-H, Chen SC-C (2019) The cancer Editome Atlas: a resource for exploratory analysis of the adenosine-to-inosine RNA Editome in cancer. Cancer Res 79:canres.3501.2018. https:\/\/doi.org\/10.1158\/0008-5472.can-18-3501","journal-title":"Cancer Res"},{"key":"20_CR239","doi-asserted-by":"publisher","first-page":"D1231","DOI":"10.1093\/nar\/gkab810","volume":"50","author":"H Ruan","year":"2021","unstructured":"Ruan H, Li Q, Liu Y et al (2021) GPEdit: the genetic and pharmacogenomic landscape of A-to-I RNA editing in cancers. Nucleic Acids Res 50:D1231\u2013D1237. https:\/\/doi.org\/10.1093\/nar\/gkab810","journal-title":"Nucleic Acids Res"},{"key":"20_CR240","doi-asserted-by":"publisher","first-page":"2472","DOI":"10.7150\/ijbs.69458","volume":"18","author":"H Zhu","year":"2022","unstructured":"Zhu H, Huang L, Liu S et al (2022) REIA: a database for cancer A-to-I RNA editing with interactive analysis. Int J Biol Sci 18:2472\u20132483. https:\/\/doi.org\/10.7150\/ijbs.69458","journal-title":"Int J Biol Sci"},{"key":"20_CR241","doi-asserted-by":"publisher","first-page":"2207357","DOI":"10.1002\/advs.202207357","volume":"10","author":"X Zhou","year":"2023","unstructured":"Zhou X, Mitra R, Hou F et al (2023) Genomic landscape and potential regulation of RNA editing in drug resistance. Adv Sci 10:2207357. https:\/\/doi.org\/10.1002\/advs.202207357","journal-title":"Adv Sci"},{"key":"20_CR242","doi-asserted-by":"publisher","first-page":"819","DOI":"10.3389\/fpls.2018.00482","volume":"9","author":"CL Giudice","year":"2018","unstructured":"Giudice CL, Pesole G, Picardi E (2018) REDIdb 3.0: a comprehensive collection of RNA editing events in plant organellar genomes. Front Plant Sci 9:819\u2013819. https:\/\/doi.org\/10.3389\/fpls.2018.00482","journal-title":"Front Plant Sci"},{"key":"20_CR243","doi-asserted-by":"publisher","first-page":"D170","DOI":"10.1093\/nar\/gky1026","volume":"47","author":"M Li","year":"2019","unstructured":"Li M, Xia L, Zhang Y et al (2019) Plant editosome database: a curated database of RNA editosome in plants. Nucleic Acids Res 47:D170\u2013D174. https:\/\/doi.org\/10.1093\/nar\/gky1026","journal-title":"Nucleic Acids Res"},{"key":"20_CR244","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1186\/s12859-018-2244-9","volume":"19","author":"H Lenz","year":"2018","unstructured":"Lenz H, Hein A, Knoop V (2018) Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0. BMC Bioinformatics 19:255. https:\/\/doi.org\/10.1186\/s12859-018-2244-9","journal-title":"BMC Bioinformatics"},{"key":"20_CR245","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1007\/978-1-4939-9207-2_12","volume":"1970","author":"R Distefano","year":"2019","unstructured":"Distefano R, Nigita G, Veneziano D et al (2019) isoTar: consensus target prediction with enrichment analysis for microRNAs harboring editing sites and other variations. Methods Mol Biol 1970:211\u2013235. https:\/\/doi.org\/10.1007\/978-1-4939-9207-2_12","journal-title":"Methods Mol Biol"},{"key":"20_CR246","doi-asserted-by":"publisher","first-page":"1311","DOI":"10.1093\/bioinformatics\/btr117","volume":"27","author":"E Picardi","year":"2011","unstructured":"Picardi E, D\u2019Antonio M, Carrabino D et al (2011) ExpEdit: a webserver to explore human RNA editing in RNA-seq experiments. Bioinformatics 27:1311\u20131312. https:\/\/doi.org\/10.1093\/bioinformatics\/btr117","journal-title":"Bioinformatics"},{"issue":"Suppl 7","key":"20_CR247","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-14-s7-s5","volume":"14","author":"R Distefano","year":"2013","unstructured":"Distefano R, Nigita G, Macca V et al (2013) VIRGO: visualization of A-to-I RNA editing sites in genomic sequences. BMC Bioinformatics 14(Suppl 7):S5. https:\/\/doi.org\/10.1186\/1471-2105-14-s7-s5","journal-title":"BMC Bioinformatics"},{"key":"20_CR248","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1101\/gr.089409.108","volume":"19","author":"H Wahlstedt","year":"2009","unstructured":"Wahlstedt H, Luciano DJ, Enstero M, \u00d6hman M (2009) Large-scale mRNA sequencing determines global regulation of RNA editing during brain development. Genome Res 19:978\u2013986. https:\/\/doi.org\/10.1101\/gr.089409.108","journal-title":"Genome Res"},{"key":"20_CR249","doi-asserted-by":"publisher","first-page":"3117","DOI":"10.1002\/prot.24672","volume":"82","author":"O Solomon","year":"2014","unstructured":"Solomon O, Bazak L, Levanon EY et al (2014) Characterizing of functional human coding RNA editing from evolutionary, structural, and dynamic perspectives. Proteins 82:3117\u20133131. https:\/\/doi.org\/10.1002\/prot.24672","journal-title":"Proteins"}],"container-title":["Methods in Molecular Biology","Computational Biology of Non-Coding RNA"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-4290-0_20","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,6]],"date-time":"2025-02-06T20:25:11Z","timestamp":1738873511000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-4290-0_20"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,20]]},"ISBN":["9781071642894","9781071642900"],"references-count":249,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-4290-0_20","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,20]]},"assertion":[{"value":"20 December 2024","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}