{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,21]],"date-time":"2026-10-21T14:18:34Z","timestamp":1792592314737,"version":"4.5.0"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"7679","license":[{"start":{"date-parts":[[2017,10,25]],"date-time":"2017-10-25T00:00:00Z","timestamp":1508889600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2017,10,25]],"date-time":"2017-10-25T00:00:00Z","timestamp":1508889600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nature"],"published-print":{"date-parts":[[2017,11,9]]},"DOI":"10.1038\/nature24456","type":"journal-article","created":{"date-parts":[[2017,10,24]],"date-time":"2017-10-24T10:44:16Z","timestamp":1508841856000},"page":"251-255","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":648,"title":["The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution"],"prefix":"10.1038","volume":"551","author":[{"given":"Modi","family":"Safra","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aldema","family":"Sas-Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ronit","family":"Nir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roni","family":"Winkler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aharon","family":"Nachshon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Bar-Yaacov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthias","family":"Erlacher","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter","family":"Rossmanith","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noam","family":"Stern-Ginossar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Schraga","family":"Schwartz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,10,25]]},"reference":[{"key":"BFnature24456_CR1","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1038\/nchembio.2040","volume":"12","author":"X Li","year":"2016","unstructured":"Li, X. et al. Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome. Nat. Chem. Biol. 12, 311\u2013316 (2016)","journal-title":"Nat. Chem. Biol."},{"key":"BFnature24456_CR2","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1038\/nature16998","volume":"530","author":"D Dominissini","year":"2016","unstructured":"Dominissini, D. et al. The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA. Nature 530, 441\u2013446 (2016)","journal-title":"Nature"},{"key":"BFnature24456_CR3","first-page":"9950","volume":"43","author":"R Hauenschild","year":"2015","unstructured":"Hauenschild, R. et al. The reverse transcription signature of N-1-methyladenosine in RNA-seq is sequence dependent. Nucleic Acids Res. 43, 9950\u20139964 (2015)","journal-title":"Nucleic Acids Res."},{"key":"BFnature24456_CR4","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1021\/ja00885a019","volume":"85","author":"JW Jones","year":"1963","unstructured":"Jones, J. W. & Robins, R. K. Purine nucleosides. III. Methylation studies of certain naturally occurring purine nucleosides. J. Am. Chem. Soc. 85, 193\u2013201 (1963)","journal-title":"J. Am. Chem. Soc."},{"key":"BFnature24456_CR5","first-page":"958","volume":"19","author":"S Mohr","year":"2013","unstructured":"Mohr, S. et al. Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing. RNA 19, 958\u2013970 (2013)","journal-title":"RNA sequencing. RNA"},{"key":"BFnature24456_CR6","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/nmeth.4057","volume":"14","author":"M Zubradt","year":"2017","unstructured":"Zubradt, M. et al. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat. Methods 14, 75\u201382 (2017)","journal-title":"Nat. Methods"},{"key":"BFnature24456_CR7","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1016\/j.cell.2008.10.012","volume":"135","author":"JE Wilusz","year":"2008","unstructured":"Wilusz, J. E., Freier, S. M. & Spector, D. L. 3\u2032 end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135, 919\u2013932 (2008)","journal-title":"Cell"},{"key":"BFnature24456_CR8","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1126\/science.1251110","volume":"344","author":"A Hodgkinson","year":"2014","unstructured":"Hodgkinson, A. et al. High-resolution genomic analysis of human mitochondrial RNA sequence variation. Science 344, 413\u2013415 (2014)","journal-title":"Science"},{"key":"BFnature24456_CR9","doi-asserted-by":"publisher","first-page":"1789","DOI":"10.1101\/gr.161265.113","volume":"23","author":"D Bar-Yaacov","year":"2013","unstructured":"Bar-Yaacov, D. et al. RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA. Genome Res. 23, 1789\u20131796 (2013)","journal-title":"Genome Res."},{"key":"BFnature24456_CR10","unstructured":"GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348, 648\u2013660 (2015)"},{"key":"BFnature24456_CR11","doi-asserted-by":"publisher","first-page":"1281","DOI":"10.1261\/rna.5040605","volume":"11","author":"S Ozanick","year":"2005","unstructured":"Ozanick, S., Krecic, A., Andersland, J. & Anderson, J. T. The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans. RNA 11, 1281\u20131290 (2005)","journal-title":"RNA"},{"key":"BFnature24456_CR12","doi-asserted-by":"publisher","first-page":"D159","DOI":"10.1093\/nar\/gkn772","volume":"37","author":"F J\u00fchling","year":"2009","unstructured":"J\u00fchling, F. et al. tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res. 37, D159\u2013D162 (2009)","journal-title":"Nucleic Acids Res."},{"key":"BFnature24456_CR13","doi-asserted-by":"publisher","unstructured":"Safra, M., Nir, R., Farouq, D. & Schwartz, S. TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code. Genome Res. http:\/\/dx.doi.org\/10.1101\/gr.207613.116 (2017)","DOI":"10.1101\/gr.207613.116"},{"key":"BFnature24456_CR14","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1016\/j.cell.2016.03.023","volume":"165","author":"S Petropoulos","year":"2016","unstructured":"Petropoulos, S. et al. Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell 165, 1012\u20131026 (2016)","journal-title":"Cell"},{"key":"BFnature24456_CR15","doi-asserted-by":"publisher","first-page":"e1002557","DOI":"10.1371\/journal.pbio.1002557","volume":"14","author":"D Bar-Yaacov","year":"2016","unstructured":"Bar-Yaacov, D. et al. Mitochondrial 16S rRNA is methylated by tRNA methyltransferase TRMT61B in all vertebrates. PLoS Biol. 14, e1002557 (2016)","journal-title":"PLoS Biol."},{"key":"BFnature24456_CR16","doi-asserted-by":"publisher","first-page":"1131","DOI":"10.1038\/nsmb.2660","volume":"20","author":"L Yan","year":"2013","unstructured":"Yan, L. et al. Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1131\u20131139 (2013)","journal-title":"Nat. Struct. Mol. Biol."},{"key":"BFnature24456_CR17","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1016\/0012-1606(87)90395-2","volume":"123","author":"L Pik\u00f3","year":"1987","unstructured":"Pik\u00f3, L. & Taylor, K. D. Amounts of mitochondrial DNA and abundance of some mitochondrial gene transcripts in early mouse embryos. Dev. Biol. 123, 364\u2013374 (1987)","journal-title":"Dev. Biol."},{"key":"BFnature24456_CR18","doi-asserted-by":"publisher","first-page":"11583","DOI":"10.1093\/nar\/gks910","volume":"40","author":"E Vilardo","year":"2012","unstructured":"Vilardo, E. et al. A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase\u2014extensive moonlighting in mitochondrial tRNA biogenesis. Nucleic Acids Res. 40, 11583\u201311593 (2012)","journal-title":"Nucleic Acids Res."},{"key":"BFnature24456_CR19","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1086\/519394","volume":"81","author":"G Hudson","year":"2007","unstructured":"Hudson, G. et al. Clinical expression of Leber hereditary optic neuropathy is affected by the mitochondrial DNA-haplogroup background. Am. J. Hum. Genet. 81, 228\u2013233 (2007)","journal-title":"Am. J. Hum. Genet."},{"key":"BFnature24456_CR20","first-page":"1107","volume":"60","author":"A Torroni","year":"1997","unstructured":"Torroni, A. et al. Haplotype and phylogenetic analyses suggest that one European-specific mtDNA background plays a role in the expression of Leber hereditary optic neuropathy by increasing the penetrance of the primary mutations 11778 and 14484. Am. J. Hum. Genet. 60, 1107\u20131121 (1997)","journal-title":"Am. J. Hum. Genet."},{"key":"BFnature24456_CR21","doi-asserted-by":"publisher","first-page":"564","DOI":"10.1086\/501236","volume":"78","author":"V Carelli","year":"2006","unstructured":"Carelli, V. et al. Haplogroup effects and recombination of mitochondrial DNA: novel clues from the analysis of Leber hereditary optic neuropathy pedigrees. Am. J. Hum. Genet. 78, 564\u2013574 (2006)","journal-title":"Am. J. Hum. Genet."},{"key":"BFnature24456_CR22","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1086\/515488","volume":"60","author":"MD Brown","year":"1997","unstructured":"Brown, M. D., Sun, F. & Wallace, D. C. Clustering of Caucasian Leber hereditary optic neuropathy patients containing the 11778 or 14484 mutations on an mtDNA lineage. Am. J. Hum. Genet. 60, 381\u2013387 (1997)","journal-title":"Am. J. Hum. Genet."},{"key":"BFnature24456_CR23","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1016\/j.cell.2014.08.028","volume":"159","author":"S Schwartz","year":"2014","unstructured":"Schwartz, S. et al. Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA. Cell 159, 148\u2013162 (2014)","journal-title":"Cell"},{"key":"BFnature24456_CR24","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1038\/nature13802","volume":"515","author":"TM Carlile","year":"2014","unstructured":"Carlile, T. M. et al. Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells. Nature 515, 143\u2013146 (2014)","journal-title":"Nature"},{"key":"BFnature24456_CR25","doi-asserted-by":"publisher","first-page":"e110799","DOI":"10.1371\/journal.pone.0110799","volume":"9","author":"AF Lovejoy","year":"2014","unstructured":"Lovejoy, A. F., Riordan, D. P. & Brown, P. O. Transcriptome-wide mapping of pseudouridines: pseudouridine synthases modify specific mRNAs in S. cerevisiae. PLoS ONE 9, e110799 (2014)","journal-title":"PLoS ONE"},{"key":"BFnature24456_CR26","doi-asserted-by":"publisher","first-page":"e1003602","DOI":"10.1371\/journal.pgen.1003602","volume":"9","author":"S Edelheit","year":"2013","unstructured":"Edelheit, S., Schwartz, S., Mumbach, M. R., Wurtzel, O. & Sorek, R. Transcriptome-wide mapping of 5-methylcytidine RNA modifications in bacteria, archaea, and yeast reveals m5C within archaeal mRNAs. PLoS Genet. 9, e1003602 (2013)","journal-title":"PLoS Genet."},{"key":"BFnature24456_CR27","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/0014-4827(67)90236-4","volume":"47","author":"RM Mills","year":"1967","unstructured":"Mills, R. M. & Brinster, R. L. Oxygen consumption of preimplantation mouse embryos. Exp. Cell Res. 47, 337\u2013344 (1967)","journal-title":"Exp. Cell Res."},{"key":"BFnature24456_CR28","first-page":"267","volume":"30","author":"L Ginsberg","year":"1973","unstructured":"Ginsberg, L. & Hillman, N. ATP metabolism in cleavage-staged mouse embryos. J. Embryol. Exp. Morphol. 30, 267\u2013282 (1973)","journal-title":"J. Embryol. Exp. Morphol."},{"key":"BFnature24456_CR29","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1146\/annurev.ph.38.030176.000523","volume":"38","author":"JD Biggers","year":"1976","unstructured":"Biggers, J. D. & Borland, R. M. Physiological aspects of growth and development of the preimplantation mammalian embryo. Annu. Rev. Physiol. 38, 95\u2013119 (1976)","journal-title":"Annu. Rev. Physiol."},{"key":"BFnature24456_CR30","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1002\/jmor.1051560206","volume":"156","author":"PM Wassarman","year":"1978","unstructured":"Wassarman, P. M. & Josefowicz, W. J. Oocyte development in the mouse: an ultrastructural comparison of oocytes isolated at various stages of growth and meiotic competence. J. Morphol. 156, 209\u2013235 (1978)","journal-title":"J. Morphol."},{"key":"BFnature24456_CR31","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. et al. High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis. Cell 155, 1409\u20131421 (2013)","journal-title":"Cell"},{"key":"BFnature24456_CR32","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1038\/nmeth.3313","volume":"12","author":"AA Shishkin","year":"2015","unstructured":"Shishkin, A. A. et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat. Methods 12, 323\u2013325 (2015)","journal-title":"Nat. Methods"},{"key":"BFnature24456_CR33","doi-asserted-by":"publisher","first-page":"1237973","DOI":"10.1126\/science.1237973","volume":"341","author":"JM Engreitz","year":"2013","unstructured":"Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341, 1237973 (2013)","journal-title":"Science"},{"key":"BFnature24456_CR34","doi-asserted-by":"publisher","first-page":"D262","DOI":"10.1093\/nar\/gks1007","volume":"41","author":"MA Machnicka","year":"2013","unstructured":"Machnicka, M. A. et al. MODOMICS: a database of RNA modification pathways--2013 update. Nucleic Acids Res. 41, D262\u2013D267 (2013)","journal-title":"Nucleic Acids Res."},{"key":"BFnature24456_CR35","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A . et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013)","journal-title":"Bioinformatics"},{"key":"BFnature24456_CR36","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1016\/j.celrep.2014.05.048","volume":"8","author":"S Schwartz","year":"2014","unstructured":"Schwartz, S. et al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5\u2032 sites. Cell Reports 8, 284\u2013296 (2014)","journal-title":"Cell Reports"},{"key":"BFnature24456_CR37","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1186\/1471-2105-12-323","volume":"12","author":"B Li","year":"2011","unstructured":"Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011)","journal-title":"BMC Bioinformatics"},{"key":"BFnature24456_CR38","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","volume":"11","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 11, R25 (2010)","journal-title":"Genome Biol."},{"key":"BFnature24456_CR39","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson, M. D., McCarthy, D. J. & Smyth, G. K . edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139\u2013140 (2010)","journal-title":"Bioinformatics"},{"key":"BFnature24456_CR40","doi-asserted-by":"publisher","unstructured":"Gandin, V. et al. Polysome fractionation and analysis of mammalian translatomes on a genome-wide scale. J. Vis. Exp. 87, http:\/\/dx.doi.org\/10.3791\/51455 (2014)","DOI":"10.3791\/51455"},{"key":"BFnature24456_CR41","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1038\/nature11112","volume":"485","author":"D Dominissini","year":"2012","unstructured":"Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201\u2013206 (2012)","journal-title":"Nature"}],"container-title":["Nature"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nature24456.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nature24456","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/doifinder\/10.1038\/nature24456","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"http:\/\/www.nature.com\/articles\/nature24456.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T14:07:18Z","timestamp":1684418838000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nature24456"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,25]]},"references-count":41,"journal-issue":{"issue":"7679","published-print":{"date-parts":[[2017,11,9]]}},"alternative-id":["BFnature24456"],"URL":"https:\/\/doi.org\/10.1038\/nature24456","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.732030467.793554844","asserted-by":"object"}]},"ISSN":["0028-0836","1476-4687"],"issn-type":[{"value":"0028-0836","type":"print"},{"value":"1476-4687","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10,25]]},"assertion":[{"value":"18 April 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 September 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 October 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}