{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T03:55:53Z","timestamp":1793159753014,"version":"4.5.0"},"reference-count":85,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T00:00:00Z","timestamp":1643587200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T00:00:00Z","timestamp":1643587200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Basic Research Program of China","doi-asserted-by":"publisher","award":["2019YFA0802201"],"award-info":[{"award-number":["2019YFA0802201"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Basic Research Program of China","doi-asserted-by":"publisher","award":["2017YFA0505201"],"award-info":[{"award-number":["2017YFA0505201"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["21820102008"],"award-info":[{"award-number":["21820102008"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Genome Biol"],"published-print":{"date-parts":[[2022,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>\n                      <jats:italic>N<\/jats:italic>\n                      <jats:sup>6<\/jats:sup>\n                      -methyladenosine (m\n                      <jats:sup>6<\/jats:sup>\n                      A) mRNA modification is essential for mammalian and plant viability. The U6 m\n                      <jats:sup>6<\/jats:sup>\n                      A methyltransferases in other species regulate S-adenosylmethionine (SAM) homeostasis through installing m\n                      <jats:sup>6<\/jats:sup>\n                      A in pre-mRNAs of SAM synthetases. However, U6 m\n                      <jats:sup>6<\/jats:sup>\n                      A methyltransferase has not been characterized in Arabidopsis and little is known about its role in regulating photomorphogenesis and flowering.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Here we characterize that FIONA1 is an Arabidopsis U6 m\n                      <jats:sup>6<\/jats:sup>\n                      A methyltransferase that installs m\n                      <jats:sup>6<\/jats:sup>\n                      A in U6 snRNA and a small subset of poly(A)\n                      <jats:sup>+<\/jats:sup>\n                      RNA. Disruption of\n                      <jats:italic>FIONA1<\/jats:italic>\n                      leads to phytochrome signaling-dependent hypocotyl elongation and photoperiod-independent early flowering. Distinct from mammalian METTL16 and worm METT-10, FIONA1 neither installs m\n                      <jats:sup>6<\/jats:sup>\n                      A in the mRNAs of Arabidopsis SAM synthetases nor affects their transcript expression levels under normal or high SAM conditions. We confirm that FIONA1 can methylate plant mRNA m\n                      <jats:sup>6<\/jats:sup>\n                      A motifs in vitro and in vivo. We further show that FIONA1 installs m\n                      <jats:sup>6<\/jats:sup>\n                      A in several phenotypic related transcripts, thereby affecting downstream mRNA stability and regulating phytochrome signaling and floral transition.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      FIONA1 is functional as a U6 m\n                      <jats:sup>6<\/jats:sup>\n                      A methyltransferase in Arabidopsis, distinct from mammalian METTL16 and worm METT-10. Our results demonstrate that FIONA1-mediated m\n                      <jats:sup>6<\/jats:sup>\n                      A post-transcriptional regulation is an autonomous regulator for flowering and phytochrome signaling-dependent photomorphogenesis.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s13059-022-02612-2","type":"journal-article","created":{"date-parts":[[2022,1,31]],"date-time":"2022-01-31T04:03:04Z","timestamp":1643601784000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":130,"title":["FIONA1 is an RNA N6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering"],"prefix":"10.1186","volume":"23","author":[{"given":"Chunling","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junbo","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peizhe","family":"Song","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiang","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiong","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4186-6922","authenticated-orcid":false,"given":"Guifang","family":"Jia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,1,31]]},"reference":[{"issue":"7177","key":"2612_CR1","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1038\/nature06520","volume":"451","author":"M de Lucas","year":"2008","unstructured":"de Lucas M, Daviere JM, Rodriguez-Falcon M, Pontin M, Iglesias-Pedraz JM, Lorrain S, et al. A molecular framework for light and gibberellin control of cell elongation. Nature. 2008;451(7177):480\u20134. https:\/\/doi.org\/10.1038\/nature06520.","journal-title":"Nature."},{"issue":"6785","key":"2612_CR2","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1038\/35013076","volume":"405","author":"MT Osterlund","year":"2000","unstructured":"Osterlund MT, Hardtke CS, Wei N, Deng XW. Targeted destabilization of HY5 during light-regulated development of Arabidopsis. Nature. 2000;405(6785):462\u20136. https:\/\/doi.org\/10.1038\/35013076.","journal-title":"Nature."},{"issue":"1","key":"2612_CR3","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1105\/tpc.113.120857","volume":"26","author":"P Leivar","year":"2014","unstructured":"Leivar P, Monte E. PIFs: systems integrators in plant development. Plant Cell. 2014;26(1):56\u201378. https:\/\/doi.org\/10.1105\/tpc.113.120857.","journal-title":"Plant Cell."},{"key":"2612_CR4","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1016\/j.conb.2015.01.013","volume":"34","author":"VC Galvao","year":"2015","unstructured":"Galvao VC, Fankhauser C. Sensing the light environment in plants: photoreceptors and early signaling steps. Curr Opin Neurobiol. 2015;34:46\u201353. https:\/\/doi.org\/10.1016\/j.conb.2015.01.013.","journal-title":"Curr Opin Neurobiol."},{"issue":"8","key":"2612_CR5","doi-asserted-by":"publisher","first-page":"4429","DOI":"10.1073\/pnas.2001373117","volume":"117","author":"Y Heng","year":"2020","unstructured":"Heng Y, Jiang Y, Zhao X, Zhou H, Wang X, Deng X, et al. Correction for Heng et al., BBX4, a phyB-interacting and modulated regulator, directly interacts with PIF3 to fine tune red light-mediated photomorphogenesis. Proc Natl Acad Sci U S A. 2020;117(8):4429\u201330. https:\/\/doi.org\/10.1073\/pnas.2001373117.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"12","key":"2612_CR6","doi-asserted-by":"publisher","first-page":"885","DOI":"10.1038\/nchembio.687","volume":"7","author":"G Jia","year":"2011","unstructured":"Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, et al. N6-methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nat Chem Biol. 2011;7(12):885\u20137. https:\/\/doi.org\/10.1038\/nchembio.687.","journal-title":"Nat Chem Biol."},{"issue":"4","key":"2612_CR7","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1016\/j.cell.2013.10.026","volume":"155","author":"JM Fustin","year":"2013","unstructured":"Fustin JM, Doi M, Yamaguchi Y, Hida H, Nishimura S, Yoshida M, et al. RNA-methylation-dependent RNA processing controls the speed of the circadian clock. Cell. 2013;155(4):793\u2013806. https:\/\/doi.org\/10.1016\/j.cell.2013.10.026.","journal-title":"Cell."},{"issue":"7632","key":"2612_CR8","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1038\/nature20577","volume":"540","author":"IU Haussmann","year":"2016","unstructured":"Haussmann IU, Bodi Z, Sanchez-Moran E, Mongan NP, Archer N, Fray RG, et al. m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination. Nature. 2016;540(7632):301\u20134. https:\/\/doi.org\/10.1038\/nature20577.","journal-title":"Nature."},{"issue":"9","key":"2612_CR9","doi-asserted-by":"publisher","first-page":"1074","DOI":"10.1038\/s41556-018-0174-4","volume":"20","author":"J Liu","year":"2018","unstructured":"Liu J, Eckert MA, Harada BT, Liu SM, Lu Z, Yu K, et al. m6A mRNA methylation regulates AKT activity to promote the proliferation and tumorigenicity of endometrial cancer. Nat Cell Biol. 2018;20(9):1074\u201383. https:\/\/doi.org\/10.1038\/s41556-018-0174-4.","journal-title":"Nat Cell Biol."},{"issue":"7481","key":"2612_CR10","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1038\/nature12730","volume":"505","author":"X Wang","year":"2014","unstructured":"Wang X, Lu Z, Gomez A, Hon GC, Yue Y, Han D, et al. N6-methyladenosine-dependent regulation of messenger RNA stability. Nature. 2014;505(7481):117\u201320. https:\/\/doi.org\/10.1038\/nature12730.","journal-title":"Nature."},{"issue":"6","key":"2612_CR11","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1016\/j.cell.2015.05.014","volume":"161","author":"X Wang","year":"2015","unstructured":"Wang X, Zhao BS, Roundtree IA, Lu Z, Han D, Ma H, et al. N6-methyladenosine modulates messenger RNA translation efficiency. Cell. 2015;161(6):1388\u201399. https:\/\/doi.org\/10.1016\/j.cell.2015.05.014.","journal-title":"Cell."},{"issue":"4","key":"2612_CR12","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1016\/j.molcel.2016.01.012","volume":"61","author":"W Xiao","year":"2016","unstructured":"Xiao W, Adhikari S, Dahal U, Chen YS, Hao YJ, Sun BF, et al. Nuclear m6A reader YTHDC1 regulates mRNA splicing. Mol Cell. 2016;61(4):507\u201319. https:\/\/doi.org\/10.1016\/j.molcel.2016.01.012.","journal-title":"Mol Cell."},{"issue":"12","key":"2612_CR13","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1038\/cr.2014.151","volume":"24","author":"X Zhao","year":"2014","unstructured":"Zhao X, Yang Y, Sun BF, Shi Y, Yang X, Xiao W, et al. FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res. 2014;24(12):1403\u201319. https:\/\/doi.org\/10.1038\/cr.2014.151.","journal-title":"Cell Res."},{"issue":"1","key":"2612_CR14","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.molcel.2012.10.015","volume":"49","author":"G Zheng","year":"2013","unstructured":"Zheng G, Dahl JA, Niu Y, Fedorcsak P, Huang CM, Li CJ, et al. ALKBH5 is a mammalian RNA demethylase that impacts RNA metabolism and mouse fertility. Mol Cell. 2013;49(1):18\u201329. https:\/\/doi.org\/10.1016\/j.molcel.2012.10.015.","journal-title":"Mol Cell."},{"issue":"5","key":"2612_CR15","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. Gene expression regulation mediated through reversible m6A RNA methylation. Nat Rev Genet. 2014;15(5):293\u2013306. https:\/\/doi.org\/10.1038\/nrg3724.","journal-title":"Nat Rev Genet."},{"issue":"13","key":"2612_CR16","doi-asserted-by":"publisher","first-page":"1343","DOI":"10.1101\/gad.262766.115","volume":"29","author":"YN Yue","year":"2020","unstructured":"Yue YN, Liu JZ, He C. RNA N6-methyladenosine methylation in post-transcriptional gene expression regulation. Genes Dev. 2020;29(13):1343\u201355. https:\/\/doi.org\/10.1101\/gad.262766.115.","journal-title":"Genes Dev."},{"issue":"2","key":"2612_CR17","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1038\/ncb2902","volume":"16","author":"Y Wang","year":"2014","unstructured":"Wang Y, Li Y, Toth JI, Petroski MD, Zhang Z, Zhao JC. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat Cell Biol. 2014;16(2):191\u20138. https:\/\/doi.org\/10.1038\/ncb2902.","journal-title":"Nat Cell Biol."},{"issue":"6","key":"2612_CR18","doi-asserted-by":"publisher","first-page":"616","DOI":"10.1038\/s41422-018-0040-8","volume":"28","author":"Y Yang","year":"2018","unstructured":"Yang Y, Hsu PJ, Chen YS, Yang YG. Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism. Cell Res. 2018;28(6):616\u201324. https:\/\/doi.org\/10.1038\/s41422-018-0040-8.","journal-title":"Cell Res."},{"key":"2612_CR19","doi-asserted-by":"publisher","first-page":"291","DOI":"10.3389\/fcell.2020.00291","volume":"8","author":"H Zheng","year":"2020","unstructured":"Zheng H, Li S, Zhang X, Sui N. Functional implications of active N6-methyladenosine in plants. Front Cell Dev Biol. 2020;8:291. https:\/\/doi.org\/10.3389\/fcell.2020.00291.","journal-title":"Front Cell Dev Biol."},{"issue":"1","key":"2612_CR20","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1016\/j.molp.2019.12.007","volume":"13","author":"Z Liang","year":"2020","unstructured":"Liang Z, Riaz A, Chachar S, Ding Y, Du H, Gu X. Epigenetic modifications of mRNA and DNA in plants. Mol Plant. 2020;13(1):14\u201330. https:\/\/doi.org\/10.1016\/j.molp.2019.12.007.","journal-title":"Mol Plant."},{"issue":"1","key":"2612_CR21","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1104\/pp.19.01156","volume":"182","author":"L Arribas-Hernandez","year":"2020","unstructured":"Arribas-Hernandez L, Brodersen P. Occurrence and functions of m6A and other covalent modifications in plant mRNA. Plant Physiol. 2020;182(1):79\u201396. https:\/\/doi.org\/10.1104\/pp.19.01156.","journal-title":"Plant Physiol."},{"issue":"5","key":"2612_CR22","doi-asserted-by":"publisher","first-page":"952","DOI":"10.1105\/tpc.17.00833","volume":"30","author":"L Arribas-Hernandez","year":"2018","unstructured":"Arribas-Hernandez L, Bressendorff S, Hansen MH, Poulsen C, Erdmann S, Brodersen P. An m6A-YTH module controls developmental timing and morphogenesis in Arabidopsis. Plant Cell. 2018;30(5):952\u201367. https:\/\/doi.org\/10.1105\/tpc.17.00833.","journal-title":"Plant Cell."},{"issue":"5","key":"2612_CR23","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1105\/tpc.17.00854","volume":"30","author":"J Scutenaire","year":"2018","unstructured":"Scutenaire J, Deragon J-M, Jean V, Benhamed M, Raynaud C, Favory J-J, et al. The YTH domain protein ECT2 is an m6A reader required for normal trichome branching in Arabidopsis. Plant Cell. 2018;30(5):986\u20131005. https:\/\/doi.org\/10.1105\/tpc.17.00854.","journal-title":"Plant Cell."},{"issue":"5","key":"2612_CR24","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1105\/tpc.17.00934","volume":"30","author":"LH Wei","year":"2018","unstructured":"Wei LH, Song P, Wang Y, Lu Z, Tang Q, Yu Q, et al. The m6A reader ECT2 controls trichome morphology by affecting mRNA stability in Arabidopsis. Plant Cell. 2018;30(5):968\u201385. https:\/\/doi.org\/10.1105\/tpc.17.00934.","journal-title":"Plant Cell."},{"issue":"4","key":"2612_CR25","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1016\/j.molp.2021.01.014","volume":"14","author":"P Song","year":"2021","unstructured":"Song P, Yang J, Wang C, Lu Q, Shi L, Tayier S, et al. Arabidopsis N6-methyladenosine reader CPSF30-L recognizes FUE signal to control polyadenylation site choice in liquid-like nuclear body. Mol Plant. 2021;14(4):571\u201387. https:\/\/doi.org\/10.1016\/j.molp.2021.01.014.","journal-title":"Mol Plant."},{"issue":"4","key":"2612_CR26","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1016\/j.molp.2021.01.013","volume":"14","author":"Y Hou","year":"2021","unstructured":"Hou Y, Sun J, Wu B, Gao Y, Nie H, Nie Z, et al. CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis. Mol Plant. 2021;14(4):688\u201399. https:\/\/doi.org\/10.1016\/j.molp.2021.01.013.","journal-title":"Mol Plant."},{"key":"2612_CR27","doi-asserted-by":"publisher","first-page":"dev189134","DOI":"10.1242\/dev.189134","volume":"147","author":"L Arribas-Hern\u00e1ndez","year":"2020","unstructured":"Arribas-Hern\u00e1ndez L, Simonini S, Hansen MH, Botterweg Paredes E, Bressendorff S, Dong Y, et al. Recurrent requirement for the m6A-ECT2\/ECT3\/ECT4 axis in the control of cell proliferation during plant organogenesis. Development. 2020;147:dev189134. https:\/\/doi.org\/10.1242\/dev.189134.","journal-title":"Development."},{"issue":"40","key":"2612_CR28","doi-asserted-by":"publisher","first-page":"10755","DOI":"10.1073\/pnas.1703139114","volume":"114","author":"M Mart\u00ednez-P\u00e9rez","year":"2017","unstructured":"Mart\u00ednez-P\u00e9rez M, Aparicio F, L\u00f3pez-Gresa MP, Bell\u00e9s JM, S\u00e1nchez-Navarro JA, Pall\u00e1s V. Arabidopsis m6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs. Proc Natl Acad Sci U S A. 2017;114(40):10755\u201360. https:\/\/doi.org\/10.1073\/pnas.1703139114.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"12","key":"2612_CR29","doi-asserted-by":"publisher","first-page":"2995","DOI":"10.1105\/tpc.16.00912","volume":"29","author":"HC Duan","year":"2017","unstructured":"Duan HC, Wei LH, Zhang C, Wang Y, Chen L, Lu Z, et al. ALKBH10B is an RNA N6-methyladenosine demethylase affecting Arabidopsis floral transition. Plant Cell. 2017;29(12):2995\u20133011. https:\/\/doi.org\/10.1105\/tpc.16.00912.","journal-title":"Plant Cell."},{"issue":"1","key":"2612_CR30","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1186\/s13059-019-1771-7","volume":"20","author":"L Zhou","year":"2019","unstructured":"Zhou L, Tian S, Qin G. RNA methylomes reveal the m6A-mediated regulation of DNA demethylase gene SlDML2 in tomato fruit ripening. Genome Biol. 2019;20(1):156. https:\/\/doi.org\/10.1186\/s13059-019-1771-7.","journal-title":"Genome Biol."},{"issue":"2","key":"2612_CR31","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/nchembio.1432","volume":"10","author":"J Liu","year":"2014","unstructured":"Liu J, Yue Y, Han D, Wang X, Fu Y, Zhang L, et al. A METTL3-METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation. Nat Chem Biol. 2014;10(2):93\u20135. https:\/\/doi.org\/10.1038\/nchembio.1432.","journal-title":"Nat Chem Biol."},{"issue":"5","key":"2612_CR32","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1016\/j.cell.2017.05.003","volume":"169","author":"KE Pendleton","year":"2017","unstructured":"Pendleton KE, Chen B, Liu K, Hunter OV, Xie Y, Tu BP, et al. The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell. 2017;169(5):824\u201335. https:\/\/doi.org\/10.1016\/j.cell.2017.05.003.","journal-title":"Cell."},{"issue":"2","key":"2612_CR33","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1016\/j.molcel.2016.05.041","volume":"63","author":"P Wang","year":"2016","unstructured":"Wang P, Doxtader KA, Nam Y. Structural basis for cooperative function of Mettl3 and Mettl14 methyltransferases. Mol Cell. 2016;63(2):306\u201317. https:\/\/doi.org\/10.1016\/j.molcel.2016.05.041.","journal-title":"Mol Cell."},{"issue":"7608","key":"2612_CR34","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1038\/nature18298","volume":"534","author":"X Wang","year":"2016","unstructured":"Wang X, Feng J, Xue Y, Guan Z, Zhang D, Liu Z, et al. Structural basis of N6-adenosine methylation by the METTL3-METTL14 complex. Nature. 2016;534(7608):575\u20138. https:\/\/doi.org\/10.1038\/nature18298.","journal-title":"Nature."},{"issue":"2","key":"2612_CR35","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/cr.2014.3","volume":"24","author":"XL Ping","year":"2014","unstructured":"Ping XL, Sun BF, Wang L, Xiao W, Yang X, Wang WJ, et al. Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. Cell Res. 2014;24(2):177\u201389. https:\/\/doi.org\/10.1038\/cr.2014.3.","journal-title":"Cell Res."},{"issue":"5","key":"2612_CR36","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1105\/tpc.108.058883","volume":"20","author":"S Zhong","year":"2008","unstructured":"Zhong S, Li H, Bodi Z, Button J, Vespa L, Herzog M, et al. MTA is an Arabidopsis messenger RNA adenosine methylase and interacts with a homolog of a sex-specific splicing factor. Plant Cell. 2008;20(5):1278\u201388. https:\/\/doi.org\/10.1105\/tpc.108.058883.","journal-title":"Plant Cell."},{"key":"2612_CR37","doi-asserted-by":"publisher","first-page":"48","DOI":"10.3389\/fpls.2012.00048","volume":"3","author":"Z Bodi","year":"2012","unstructured":"Bodi Z, Zhong S, Mehra S, Song J, Graham N, Li H, et al. Adenosine methylation in Arabidopsis mRNA is associated with the 3' end and reduced levels cause developmental defects. Front Plant Sci. 2012;3:48. https:\/\/doi.org\/10.3389\/fpls.2012.00048.","journal-title":"Front Plant Sci."},{"issue":"2","key":"2612_CR38","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1016\/j.devcel.2016.06.008","volume":"38","author":"L Shen","year":"2016","unstructured":"Shen L, Liang Z, Gu X, Chen Y, Teo ZW, Hou X, et al. N6-methyladenosine RNA modification regulates shoot stem cell fate in Arabidopsis. Dev Cell. 2016;38(2):186\u2013200. https:\/\/doi.org\/10.1016\/j.devcel.2016.06.008.","journal-title":"Dev Cell."},{"issue":"1","key":"2612_CR39","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1111\/nph.14586","volume":"215","author":"K Ruzicka","year":"2017","unstructured":"Ruzicka K, Zhang M, Campilho A, Bodi Z, Kashif M, Saleh M, et al. Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI. New Phytol. 2017;215(1):157\u201372. https:\/\/doi.org\/10.1111\/nph.14586.","journal-title":"New Phytol."},{"issue":"6225","key":"2612_CR40","doi-asserted-by":"publisher","first-page":"1002","DOI":"10.1126\/science.1261417","volume":"347","author":"S Geula","year":"2015","unstructured":"Geula S, Moshitch-Moshkovitz S, Dominissini D, Mansour AA, Kol N, Salmon-Divon M, et al. m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation. Science. 2015;347(6225):1002\u20136. https:\/\/doi.org\/10.1126\/science.1261417.","journal-title":"Science."},{"issue":"5","key":"2612_CR41","doi-asserted-by":"publisher","first-page":"e1008120","DOI":"10.1371\/journal.pgen.1008120","volume":"15","author":"F Zhang","year":"2019","unstructured":"Zhang F, Zhang YC, Liao JY, Yu Y, Zhou YF, Feng YZ, et al. The subunit of RNA N6-methyladenosine methyltransferase OsFIP regulates early degeneration of microspores in rice. PLoS Genet. 2019;15(5):e1008120. https:\/\/doi.org\/10.1371\/journal.pgen.1008120.","journal-title":"PLoS Genet."},{"issue":"12","key":"2612_CR42","doi-asserted-by":"publisher","first-page":"3125","DOI":"10.1016\/j.cell.2021.03.062","volume":"184","author":"M Mendel","year":"2021","unstructured":"Mendel M, Delaney K, Pandey RR, Chen KM, Wenda JM, Vagbo CB, et al. Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing. Cell. 2021;184(12):3125\u201342. https:\/\/doi.org\/10.1016\/j.cell.2021.03.062.","journal-title":"Cell."},{"issue":"23","key":"2612_CR43","doi-asserted-by":"publisher","first-page":"11269","DOI":"10.1073\/pnas.89.23.11269","volume":"89","author":"H Sawa","year":"1992","unstructured":"Sawa H, Abelson J. Evidence for a base-pairing interaction between U6 small nuclear-RNA and the 5' splice site during the splicing reaction in yeast. Proc Natl Acad Sci U S A. 1992;89(23):11269\u201373. https:\/\/doi.org\/10.1073\/pnas.89.23.11269.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"12","key":"2612_CR44","doi-asserted-by":"publisher","first-page":"3354","DOI":"10.1016\/j.celrep.2017.11.092","volume":"21","author":"H Shima","year":"2017","unstructured":"Shima H, Matsumoto M, Ishigami Y, Ebina M, Muto A, Sato Y, et al. S-Adenosylmethionine synthesis is regulated by selective N6-adenosine methylation and mRNA degradation involving METTL16 and YTHDC1. Cell Rep. 2017;21(12):3354\u201363. https:\/\/doi.org\/10.1016\/j.celrep.2017.11.092.","journal-title":"Cell Rep."},{"issue":"6","key":"2612_CR45","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1016\/j.molcel.2018.08.004","volume":"71","author":"M Mendel","year":"2018","unstructured":"Mendel M, Chen KM, Homolka D, Gos P, Pandey RR, McCarthy AA, et al. Methylation of structured RNA by the m6A writer METTL16 is essential for mouse embryonic development. Mol Cell. 2018;71(6):986\u20131000. https:\/\/doi.org\/10.1016\/j.molcel.2018.08.004.","journal-title":"Mol Cell."},{"issue":"1","key":"2612_CR46","doi-asserted-by":"publisher","first-page":"5636","DOI":"10.1038\/s41467-019-13561-z","volume":"10","author":"CWQ Koh","year":"2019","unstructured":"Koh CWQ, Goh YT, Goh WSS. Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes. Nat Commun. 2019;10(1):5636. https:\/\/doi.org\/10.1038\/s41467-019-13561-z.","journal-title":"Nat Commun."},{"issue":"2","key":"2612_CR47","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1105\/tpc.107.055715","volume":"20","author":"J Kim","year":"2008","unstructured":"Kim J, Kim Y, Yeom M, Kim JH, Nam HG. FIONA1 is essential for regulating period length in the Arabidopsis circadian clock. Plant Cell. 2008;20(2):307\u201319. https:\/\/doi.org\/10.1105\/tpc.107.055715.","journal-title":"Plant Cell."},{"issue":"1","key":"2612_CR48","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1186\/s13059-015-0715-0","volume":"16","author":"ZP Wang","year":"2015","unstructured":"Wang ZP, Xing HL, Dong L, Zhang HY, Han CY, Wang XC, et al. Egg cell-specific promoter-controlled CRISPR\/Cas9 efficiently generates homozygous mutants for multiple target genes in Arabidopsis in a single generation. Genome Biol. 2015;16(1):144. https:\/\/doi.org\/10.1186\/s13059-015-0715-0.","journal-title":"Genome Biol."},{"issue":"6","key":"2612_CR49","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1016\/j.molcel.2018.07.025","volume":"71","author":"KA Doxtader","year":"2018","unstructured":"Doxtader KA, Wang P, Scarborough AM, Seo D, Conrad NK, Nam Y. Structural basis for regulation of METTL16, an S-adenosylmethionine homeostasis factor. Mol Cell. 2018;71(6):1001\u201311. https:\/\/doi.org\/10.1016\/j.molcel.2018.07.025.","journal-title":"Mol Cell."},{"issue":"18","key":"2612_CR50","doi-asserted-by":"publisher","first-page":"8901","DOI":"10.1016\/S0021-9258(18)43587-9","volume":"255","author":"P Epstein","year":"1980","unstructured":"Epstein P, Reddy R, Henning DaB H. The nucleotide sequence of nuclear U6 (4.7\u2009S) RNA. J Biol Chem. 1980;255(18):8901\u20136. https:\/\/doi.org\/10.1016\/S0021-9258(18)43587-9.","journal-title":"J Biol Chem."},{"issue":"49","key":"2612_CR51","doi-asserted-by":"publisher","first-page":"15995","DOI":"10.1002\/anie.201807942","volume":"57","author":"Y Xiao","year":"2018","unstructured":"Xiao Y, Wang Y, Tang Q, Wei L, Zhang X, Jia G. An elongation- and ligation-based qPCR amplification method for the radiolabeling-free detection of locus-specific N6-methyladenosine modification. Angew Chem Int Ed Engl. 2018;57(49):15995\u20136000. https:\/\/doi.org\/10.1002\/anie.201807942.","journal-title":"Angew Chem Int Ed Engl."},{"issue":"1","key":"2612_CR52","doi-asserted-by":"publisher","first-page":"5630","DOI":"10.1038\/ncomms6630","volume":"5","author":"GZ Luo","year":"2014","unstructured":"Luo GZ, MacQueen A, Zheng G, Duan H, Dore LC, Lu Z, et al. Unique features of the m6A methylome in Arabidopsis thaliana. Nat Commun. 2014;5(1):5630. https:\/\/doi.org\/10.1038\/ncomms6630.","journal-title":"Nat Commun."},{"issue":"4","key":"2612_CR53","doi-asserted-by":"publisher","first-page":"1139","DOI":"10.1104\/pp.104.4.1139","volume":"104","author":"JW Reed","year":"1994","unstructured":"Reed JW, Nagatani A, Elich TD, Fagan M, Chory J. Phytochrome-A and phytochrome-B have overlapping but distinct functions in Arabidopsis development. Plant Physiol. 1994;104(4):1139\u201349. https:\/\/doi.org\/10.1104\/pp.104.4.1139.","journal-title":"Plant Physiol."},{"issue":"1","key":"2612_CR54","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1038\/nprot.2012.148","volume":"8","author":"D Dominissini","year":"2013","unstructured":"Dominissini D, Moshitch-Moshkovitz S, Salmon-Divon M, Amariglio N, Rechavi G. Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing. Nat Protoc. 2013;8(1):176\u201389. https:\/\/doi.org\/10.1038\/nprot.2012.148.","journal-title":"Nat Protoc."},{"issue":"7397","key":"2612_CR55","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1038\/nature11112","volume":"485","author":"D Dominissini","year":"2012","unstructured":"Dominissini D, Moshitch-Moshkovitz S, Schwartz S, Salmon-Divon M, Ungar L, Osenberg S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012;485(7397):201\u20136. https:\/\/doi.org\/10.1038\/nature11112.","journal-title":"Nature."},{"issue":"7","key":"2612_CR56","doi-asserted-by":"publisher","first-page":"1635","DOI":"10.1016\/j.cell.2012.05.003","volume":"149","author":"KD Meyer","year":"2012","unstructured":"Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR. Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell. 2012;149(7):1635\u201346. https:\/\/doi.org\/10.1016\/j.cell.2012.05.003.","journal-title":"Cell."},{"key":"2612_CR57","doi-asserted-by":"publisher","first-page":"e56980","DOI":"10.7554\/eLife.56980","volume":"9","author":"L Xi","year":"2020","unstructured":"Xi L, Carroll T, Matos I, Luo JD, Polak L, Pasolli HA, et al. m6A RNA methylation impacts fate choices during skin morphogenesis. Elife. 2020;9:e56980. https:\/\/doi.org\/10.7554\/eLife.56980.","journal-title":"Elife."},{"issue":"2","key":"2612_CR58","doi-asserted-by":"publisher","first-page":"E325","DOI":"10.1073\/pnas.1717794115","volume":"115","author":"C Tang","year":"2018","unstructured":"Tang C, Klukovich R, Peng H, Wang Z, Yu T, Zhang Y, et al. ALKBH5-dependent m6A demethylation controls splicing and stability of long 3'-UTR mRNAs in male germ cells. Proc Natl Acad Sci U S A. 2018;115(2):E325\u201333. https:\/\/doi.org\/10.1073\/pnas.1717794115.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"1","key":"2612_CR59","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. Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem. 2015;84(1):291\u2013323. https:\/\/doi.org\/10.1146\/annurev-biochem-060614-034316.","journal-title":"Annu Rev Biochem."},{"issue":"1","key":"2612_CR60","doi-asserted-by":"publisher","first-page":"a032409","DOI":"10.1101\/cshperspect.a032409","volume":"11","author":"C Yan","year":"2019","unstructured":"Yan C, Wan R, Shi Y. Molecular mechanisms of pre-mRNA splicing through structural biology of the spliceosome. Cold Spring Harb Perspect Biol. 2019;11(1):a032409. https:\/\/doi.org\/10.1101\/cshperspect.a032409.","journal-title":"Cold Spring Harb Perspect Biol."},{"issue":"51","key":"2612_CR61","doi-asserted-by":"publisher","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","volume":"111","author":"S Shen","year":"2014","unstructured":"Shen S, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, et al. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proc Natl Acad Sci U S A. 2014;111(51):E5593\u2013601. https:\/\/doi.org\/10.1073\/pnas.1419161111.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"5660","key":"2612_CR62","doi-asserted-by":"publisher","first-page":"1003","DOI":"10.1126\/science.1091761","volume":"303","author":"F Valverde","year":"2004","unstructured":"Valverde F, Mouradov A, Soppe W, Ravenscroft D, Samach A, Coupland G. Photoreceptor regulation of CONSTANS protein in photoperiodic flowering. Science. 2004;303(5660):1003\u20136. https:\/\/doi.org\/10.1126\/science.1091761.","journal-title":"Science."},{"issue":"10","key":"2612_CR63","doi-asserted-by":"publisher","first-page":"2441","DOI":"10.1093\/emboj\/21.10.2441","volume":"21","author":"E Huq","year":"2002","unstructured":"Huq E, Quail P. PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. EMBO J. 2002;21(10):2441\u201350. https:\/\/doi.org\/10.1093\/emboj\/21.10.2441.","journal-title":"EMBO J."},{"issue":"3","key":"2612_CR64","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1111\/j.1365-313X.2009.03971.x","volume":"60","author":"S Lorrain","year":"2009","unstructured":"Lorrain S, Trevisan M, Pradervand S, Fankhauser C. Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light. Plant J. 2009;60(3):449\u201361. https:\/\/doi.org\/10.1111\/j.1365-313X.2009.03971.x.","journal-title":"Plant J."},{"issue":"3","key":"2612_CR65","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1038\/s41556-018-0045-z","volume":"20","author":"H Huang","year":"2018","unstructured":"Huang H, Weng H, Sun W, Qin X, Shi H, Wu H, et al. Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation. Nat Cell Biol. 2018;20(3):285\u201395. https:\/\/doi.org\/10.1038\/s41556-018-0045-z.","journal-title":"Nat Cell Biol."},{"issue":"6","key":"2612_CR66","doi-asserted-by":"publisher","first-page":"1409","DOI":"10.1016\/j.cell.2013.10.047","volume":"155","author":"S Schwartz","year":"2013","unstructured":"Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell. 2013;155(6):1409\u201321. https:\/\/doi.org\/10.1016\/j.cell.2013.10.047.","journal-title":"Cell."},{"issue":"9","key":"2612_CR67","doi-asserted-by":"publisher","first-page":"1180","DOI":"10.4161\/rna.36281","volume":"11","author":"YL Li","year":"2014","unstructured":"Li YL, Wang XL, Li CP, Hu SN, Yu J, Song SH. Transcriptome-wide N6-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification. RNA Biol. 2014;11(9):1180\u20138. https:\/\/doi.org\/10.4161\/rna.36281.","journal-title":"RNA Biol."},{"issue":"4","key":"2612_CR68","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1016\/0092-8674(75)90158-0","volume":"4","author":"CM Wei","year":"1975","unstructured":"Wei CM, Gershowitz A, Moss B. Methylated nucleotides block 5' terminus of hela-cell messenger-RNA. Cell. 1975;4(4):379\u201386. https:\/\/doi.org\/10.1016\/0092-8674(75)90158-0.","journal-title":"Cell."},{"issue":"1","key":"2612_CR69","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1186\/s13059-021-02385-0","volume":"22","author":"L Zhou","year":"2021","unstructured":"Zhou L, Tang R, Li X, Tian S, Li B, Qin G. N6-methyladenosine RNA modification regulates strawberry fruit ripening in an ABA-dependent manner. Genome Biol. 2021;22(1):168. https:\/\/doi.org\/10.1186\/s13059-021-02385-0.","journal-title":"Genome Biol."},{"issue":"6","key":"2612_CR70","doi-asserted-by":"publisher","first-page":"1759","DOI":"10.1111\/tpj.15270","volume":"106","author":"J Hu","year":"2021","unstructured":"Hu J, Cai J, Park SJ, Lee K, Li Y, Chen Y, et al. N6-Methyladenosine mRNA methylation is important for salt stress tolerance in Arabidopsis. Plant J. 2021;106(6):1759\u201375. https:\/\/doi.org\/10.1111\/tpj.15270.","journal-title":"Plant J."},{"issue":"10","key":"2612_CR71","doi-asserted-by":"publisher","first-page":"e45762","DOI":"10.15252\/embr.201845762","volume":"19","author":"Y Liu","year":"2018","unstructured":"Liu Y, Li X, Ma D, Chen Z, Wang JW, Liu H. CIB1 and CO interact to mediate CRY2-dependent regulation of flowering. EMBO Rep. 2018;19(10):e45762. https:\/\/doi.org\/10.15252\/embr.201845762.","journal-title":"EMBO Rep."},{"issue":"5","key":"2612_CR72","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1105\/tpc.11.5.949","volume":"11","author":"SD Michaels","year":"1999","unstructured":"Michaels SD, Amasino RM. FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell. 1999;11(5):949\u201356. https:\/\/doi.org\/10.1105\/tpc.11.5.949.","journal-title":"Plant Cell."},{"issue":"11","key":"2612_CR73","doi-asserted-by":"publisher","first-page":"2971","DOI":"10.1105\/tpc.106.043299","volume":"18","author":"S Wenkel","year":"2006","unstructured":"Wenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, Samach A, et al. CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Plant Cell. 2006;18(11):2971\u201384. https:\/\/doi.org\/10.1105\/tpc.106.043299.","journal-title":"Plant Cell."},{"issue":"6890","key":"2612_CR74","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1038\/nature00815","volume":"417","author":"D Shalitin","year":"2002","unstructured":"Shalitin D, Yang HY, Mockler TC, Maymon M, Guo HW, Whitelam GC, et al. Regulation of Arabidopsis cryptochrome 2 by blue-light-dependent phosphorylation. Nature. 2002;417(6890):763\u20137. https:\/\/doi.org\/10.1038\/nature00815.","journal-title":"Nature."},{"issue":"2","key":"2612_CR75","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1111\/j.1365-313X.2006.02686.x","volume":"46","author":"CA Helliwell","year":"2006","unstructured":"Helliwell CA, Wood CC, Robertson M, James Peacock W, Dennis ES. The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex. Plant J. 2006;46(2):183\u201392. https:\/\/doi.org\/10.1111\/j.1365-313X.2006.02686.x.","journal-title":"Plant J."},{"issue":"5446","key":"2612_CR76","doi-asserted-by":"publisher","first-page":"1960","DOI":"10.1126\/science.286.5446.1960","volume":"286","author":"Y Kobayashi","year":"1999","unstructured":"Kobayashi Y, Kaya H, Goto K, Iwabuchi M, Araki T. A pair of related genes with antagonistic roles in mediating flowering signals. Science. 1999;286(5446):1960\u20132. https:\/\/doi.org\/10.1126\/science.286.5446.1960.","journal-title":"Science."},{"issue":"8","key":"2612_CR77","doi-asserted-by":"publisher","first-page":"587","DOI":"10.14348\/molcells.2016.0126","volume":"39","author":"H Choi","year":"2016","unstructured":"Choi H, Oh E. PIF4 integrates multiple environmental and hormonal signals for plant growth regulation in Arabidopsis. Mol Cells. 2016;39(8):587\u201393. https:\/\/doi.org\/10.14348\/molcells.2016.0126.","journal-title":"Mol Cells."},{"issue":"10","key":"2612_CR78","doi-asserted-by":"publisher","first-page":"3565","DOI":"10.1105\/tpc.111.091058","volume":"23","author":"W Wang","year":"2011","unstructured":"Wang W, Ye R, Xin Y, Fang X, Li C, Shi H, et al. An importin beta protein negatively regulates MicroRNA activity in Arabidopsis. Plant Cell. 2011;23(10):3565\u201376. https:\/\/doi.org\/10.1105\/tpc.111.091058.","journal-title":"Plant Cell."},{"issue":"1","key":"2612_CR79","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","volume":"17","author":"M Martin","year":"2011","unstructured":"Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 2011;17(1):10\u20132. https:\/\/doi.org\/10.14806\/ej.17.1.200.","journal-title":"EMBnet J."},{"issue":"9","key":"2612_CR80","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1038\/nprot.2016.095","volume":"11","author":"M Pertea","year":"2016","unstructured":"Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc. 2016;11(9):1650\u201367. https:\/\/doi.org\/10.1038\/nprot.2016.095.","journal-title":"Nat Protoc"},{"issue":"9","key":"2612_CR81","doi-asserted-by":"publisher","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","volume":"9","author":"Y Zhang","year":"2008","unstructured":"Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. https:\/\/doi.org\/10.1186\/gb-2008-9-9-r137.","journal-title":"Genome Biol."},{"issue":"12","key":"2612_CR82","doi-asserted-by":"publisher","first-page":"1565","DOI":"10.1093\/bioinformatics\/btt171","volume":"29","author":"J Meng","year":"2013","unstructured":"Meng J, Cui X, Rao MK, Chen Y, Huang Y. Exome-based analysis for RNA epigenome sequencing data. Bioinformatics. 2013;29(12):1565\u20137. https:\/\/doi.org\/10.1093\/bioinformatics\/btt171.","journal-title":"Bioinformatics."},{"issue":"6","key":"2612_CR83","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841\u20132. https:\/\/doi.org\/10.1093\/bioinformatics\/btq033.","journal-title":"Bioinformatics."},{"issue":"4","key":"2612_CR84","doi-asserted-by":"publisher","first-page":"1867","DOI":"10.1104\/pp.111.176685","volume":"156","author":"E Seo","year":"2011","unstructured":"Seo E, Yu J, Ryu KH, Lee MM, Lee I. Werewolf, a regulator of root hair pattern formation, controls flowering time through the regulation of FT mRNA stability. Plant Physiol. 2011;156(4):1867\u201377. https:\/\/doi.org\/10.1104\/pp.111.176685.","journal-title":"Plant Physiol."},{"key":"2612_CR85","doi-asserted-by":"crossref","unstructured":"Wang C, Yang J, Song P, Zhang W, Lu Q, Yu Q, et al. FIONA1 is an RNA N6-methyladenosine methyltransferase affecting Arabidopsis photomorphogenesis and flowering. NGDC. https:\/\/ngdc.cncb.ac.cn\/gsa\/browse\/CRA004052. 2022.","DOI":"10.1186\/s13059-022-02612-2"}],"container-title":["Genome Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13059-022-02612-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13059-022-02612-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13059-022-02612-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T02:36:47Z","timestamp":1674614207000},"score":1,"resource":{"primary":{"URL":"https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-022-02612-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,1,31]]},"references-count":85,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2022,12]]}},"alternative-id":["2612"],"URL":"https:\/\/doi.org\/10.1186\/s13059-022-02612-2","relation":{},"ISSN":["1474-760X"],"issn-type":[{"value":"1474-760X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,31]]},"assertion":[{"value":"31 May 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 January 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 January 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"40"}}