{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T06:50:31Z","timestamp":1784357431962,"version":"3.55.0"},"reference-count":68,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T00:00:00Z","timestamp":1748390400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T00:00:00Z","timestamp":1748390400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["82301866"],"award-info":[{"award-number":["82301866"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["32370917"],"award-info":[{"award-number":["32370917"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100002858","name":"Chinese Postdoctoral Science Foundation","doi-asserted-by":"crossref","award":["2023M743202"],"award-info":[{"award-number":["2023M743202"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Joint Construction Youth Fund Project of Henan Provincial Health Commission and Provincial Ministry","award":["SBGJ202303035"],"award-info":[{"award-number":["SBGJ202303035"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Biol"],"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Omics technologies are widely applied in assisted reproductive technology (ART), such as embryo selection, investigation of infertility causes, and mechanisms underlying reproductive cell development. While RNAomics has shown great potential in investigating the physiology and pathology in female reproductive system, its applications are still not fully developed. More studies on epitranscriptomic regulation mechanisms and novel sequencing methods are needed to advance the field.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here, we developed a method named Cap to Tail sequencing application (C2T-APP) and simultaneously characterized the m<jats:sup>7<\/jats:sup>G cap, poly(A) tail structure, and gene expression level for the intact RNA molecules in single cells. C2T-APP distinguished the N6, 2\u2032-O-dimethyladenosine modification (m<jats:sup>6<\/jats:sup>A<jats:sub>m<\/jats:sub>) from <jats:italic>N<\/jats:italic>\n              <jats:sup>6<\/jats:sup>-methyladenosine (m<jats:sup>6<\/jats:sup>A) modification with our published single-cell m<jats:sup>6<\/jats:sup>A sequencing (scm<jats:sup>6<\/jats:sup>A-seq) data. During oocyte maturation, we found a positive correlation of m<jats:sup>7<\/jats:sup>G and m<jats:sup>6<\/jats:sup>A<jats:sub>m<\/jats:sub> with translation efficiency and finely dissected the step-wised maternal RNA de-capping and de-tailing of different types of genes. Strikingly, we uncovered a subtle structural mechanism regulating poly(A) tails in oocytes: maternal RNA translation is temporarily suppressed by removing the poly(A) tails without complete degradation, while the poly(A)-tail regulators themselves depend strictly on translation initiated after meiotic resumption. Furthermore, we profiled single-cell RNA-multi-omic features of human oocytes with different qualities during in vitro culture maturation (IVM). Defects of epi-transcriptome features, including m<jats:sup>6<\/jats:sup>A, m<jats:sup>6<\/jats:sup>A<jats:sub>m<\/jats:sub>, m<jats:sup>7<\/jats:sup>G, and poly(A) structure of maternal RNA in the oocytes with poor quality, were detected.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our results provided a valuable tool for RNAomics research and data resources provided novel insights into human oocyte maturation, which is helpful for IVM and oocyte selection for ART.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/s12915-025-02250-7","type":"journal-article","created":{"date-parts":[[2025,5,28]],"date-time":"2025-05-28T21:19:16Z","timestamp":1748467156000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation"],"prefix":"10.1186","volume":"23","author":[{"given":"Huan","family":"Yao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Danru","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haixia","family":"Jin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanjie","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengnan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tong","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shenli","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gang","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingpu","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,5,28]]},"reference":[{"key":"2250_CR1","doi-asserted-by":"publisher","first-page":"880","DOI":"10.1071\/RD14441","volume":"27","author":"K Zhang","year":"2015","unstructured":"Zhang K, Smith GW. Maternal control of early embryogenesis in mammals. Reprod Fertil Dev. 2015;27:880.","journal-title":"Reprod Fertil Dev"},{"key":"2250_CR2","doi-asserted-by":"publisher","first-page":"eabj3967","DOI":"10.1126\/sciadv.abj3967","volume":"8","author":"C Zhang","year":"2022","unstructured":"Zhang C, Wang M, Li Y, Zhang Y. Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition. Sci Adv. 2022;8:eabj3967.","journal-title":"Sci Adv"},{"key":"2250_CR3","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1038\/s41556-022-00928-6","volume":"24","author":"Z Xiong","year":"2022","unstructured":"Xiong Z, Xu K, Lin Z, Kong F, Wang Q, Quan Y, et al. Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development. Nat Cell Biol. 2022;24:968\u201380.","journal-title":"Nat Cell Biol"},{"key":"2250_CR4","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-022-32791-2","volume":"13","author":"W Hu","year":"2022","unstructured":"Hu W, Zeng H, Shi Y, Zhou C, Huang J, Jia L, et al. Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation. Nat Commun. 2022;13:5114.","journal-title":"Nat Commun"},{"key":"2250_CR5","doi-asserted-by":"publisher","first-page":"abo7923","DOI":"10.1126\/science.abo7923","volume":"378","author":"Z Zou","year":"2022","unstructured":"Zou Z, Zhang C, Wang Q, Hou Z, Xiong Z, Kong F, et al. Translatome and transcriptome co-profiling reveals a role of TPRXs in human zygotic genome activation. Science. 2022;378:abo7923.","journal-title":"Science"},{"key":"2250_CR6","doi-asserted-by":"publisher","first-page":"eabq4835","DOI":"10.1126\/science.abq4835","volume":"378","author":"S Cheng","year":"2022","unstructured":"Cheng S, Altmeppen G, So C, Welp LM, Penir S, Ruhwedel T, et al. Mammalian oocytes store mRNAs in a mitochondria-associated membraneless compartment. Science. 2022;378:eabq4835.","journal-title":"Science"},{"key":"2250_CR7","doi-asserted-by":"publisher","first-page":"nwac003","DOI":"10.1093\/nsr\/nwac003","volume":"9","author":"H Jin","year":"2022","unstructured":"Jin H, Han Y, Wang H, Li JXH, Shen W, Zhang L, et al. The second polar body contributes to the fate asymmetry in the mouse embryo. Natl Sci Rev. 2022;9:nwac003.","journal-title":"Natl Sci Rev"},{"key":"2250_CR8","doi-asserted-by":"publisher","first-page":"2776","DOI":"10.1016\/j.devcel.2023.10.005","volume":"58","author":"H Hwang","year":"2023","unstructured":"Hwang H, Chen S, Ma M, Fan H-C, Borwick E, B\u00f6ke E, et al. Solubility phase transition of maternal RNAs during vertebrate oocyte-to-embryo transition. Dev Cell. 2023;58:2776-2788.e5.","journal-title":"Dev Cell"},{"key":"2250_CR9","doi-asserted-by":"publisher","first-page":"4917","DOI":"10.1038\/s41467-020-18680-6","volume":"11","author":"QQ Sha","year":"2020","unstructured":"Sha QQ, Zheng W, Wu YW, Li S, Guo L, Zhang S, et al. Dynamics and clinical relevance of maternal mRNA clearance during the oocyte-to-embryo transition in humans. Nat Commun. 2020;11:4917.","journal-title":"Nat Commun"},{"key":"2250_CR10","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1038\/s41419-021-04272-9","volume":"12","author":"H Mu","year":"2021","unstructured":"Mu H, Zhang T, Yang Y, Zhang D, Gao J, Li J, et al. METTL3-mediated mRNA N6-methyladenosine is required for oocyte and follicle development in mice. Cell Death Dis. 2021;12:989.","journal-title":"Cell Death Dis"},{"key":"2250_CR11","doi-asserted-by":"publisher","first-page":"917","DOI":"10.1038\/s41556-022-00915-x","volume":"24","author":"Y Wu","year":"2022","unstructured":"Wu Y, Xu X, Qi M, Chen C, Li M, Yan R, et al. N6-methyladenosine regulates maternal RNA maintenance in oocytes and timely RNA decay during mouse maternal-to-zygotic transition. Nat Cell Biol. 2022;24:917\u201327.","journal-title":"Nat Cell Biol"},{"key":"2250_CR12","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1038\/s41467-023-35958-7","volume":"14","author":"H Yao","year":"2023","unstructured":"Yao H, Gao CC, Zhang D, Xu J, Song G, Fan X, et al. scm6A-seq reveals single-cell landscapes of the dynamic m6A during oocyte maturation and early embryonic development. Nat Commun. 2023;14:315.","journal-title":"Nat Commun"},{"key":"2250_CR13","doi-asserted-by":"publisher","first-page":"6532","DOI":"10.1038\/s41467-023-42302-6","volume":"14","author":"L Bai","year":"2023","unstructured":"Bai L, Xiang Y, Tang M, Liu S, Chen Q, Chen Q, et al. ALKBH5 controls the meiosis-coupled mRNA clearance in oocytes by removing the N6-methyladenosine methylation. Nat Commun. 2023;14:6532.","journal-title":"Nat Commun"},{"key":"2250_CR14","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/s41594-022-00908-2","volume":"30","author":"Y Liu","year":"2023","unstructured":"Liu Y, Zhao H, Shao F, Zhang Y, Nie H, Zhang J, et al. Remodeling of maternal mRNA through poly(A) tail orchestrates human oocyte-to-embryo transition. Nat Struct Mol Biol. 2023;30:200\u201315.","journal-title":"Nat Struct Mol Biol"},{"key":"2250_CR15","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1038\/s41576-019-0150-2","volume":"20","author":"R Stark","year":"2019","unstructured":"Stark R, Grzelak M, Hadfield J. RNA sequencing: the teenage years. Nat Rev Genet. 2019;20:631\u201356.","journal-title":"Nat Rev Genet"},{"key":"2250_CR16","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1038\/s41592-018-0014-2","volume":"15","author":"X Adiconis","year":"2018","unstructured":"Adiconis X, Haber AL, Simmons SK, Moonshine AL, Ji Z, Busby MA, et al. Comprehensive comparative analysis of 5\u2032-end RNA-sequencing methods. Nat Methods. 2018;15:505\u201311.","journal-title":"Nat Methods"},{"key":"2250_CR17","doi-asserted-by":"publisher","first-page":"e1737","DOI":"10.1002\/wrna.1737","volume":"14","author":"A Brouze","year":"2022","unstructured":"Brouze A, Krawczyk PS, Dziembowski A, Mroczek S. Measuring the tail: methods for poly(A) tail profiling. WIREs RNA. 2022;14:e1737.","journal-title":"WIREs RNA"},{"key":"2250_CR18","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/nmeth0306-211","volume":"3","author":"R Kodzius","year":"2006","unstructured":"Kodzius R, Kojima M, Nishiyori H, Nakamura M, Fukuda S, Tagami M, et al. CAGE: cap analysis of gene expression. Nat Methods. 2006;3:211\u201322.","journal-title":"Nat Methods"},{"key":"2250_CR19","doi-asserted-by":"publisher","first-page":"e0234696","DOI":"10.1371\/journal.pone.0234696","volume":"15","author":"F Yu","year":"2020","unstructured":"Yu F, Zhang Y, Cheng C, Wang W, Zhou Z, Rang W, et al. Poly(A)-seq: a method for direct sequencing and analysis of the transcriptomic poly(A)-tails. PLoS ONE. 2020;15:e0234696.","journal-title":"PLoS ONE"},{"key":"2250_CR20","doi-asserted-by":"publisher","first-page":"708","DOI":"10.1038\/s41587-020-0497-0","volume":"38","author":"M Hagemann-Jensen","year":"2020","unstructured":"Hagemann-Jensen M, Ziegenhain C, Chen P, Ramsk\u00f6ld D, Hendriks G-J, Larsson AJM, et al. Single-cell RNA counting at allele and isoform resolution using Smart-seq3. Nat Biotechnol. 2020;38:708\u201314.","journal-title":"Nat Biotechnol"},{"key":"2250_CR21","doi-asserted-by":"publisher","first-page":"e694","DOI":"10.1002\/ctm2.694","volume":"12","author":"D Jovic","year":"2022","unstructured":"Jovic D, Liang X, Zeng H, Lin L, Xu F, Luo Y. Single-cell RNA sequencing technologies and applications: a brief overview. Clin Transl Med. 2022;12:e694.","journal-title":"Clin Transl Med"},{"key":"2250_CR22","doi-asserted-by":"publisher","first-page":"5148","DOI":"10.1038\/s41467-020-18976-7","volume":"11","author":"Y Hu","year":"2020","unstructured":"Hu Y, Zhong J, Xiao Y, Xing Z, Sheu K, Fan S, et al. Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation. Nat Commun. 2020;11:5148.","journal-title":"Nat Commun"},{"key":"2250_CR23","doi-asserted-by":"publisher","first-page":"5292","DOI":"10.1038\/s41467-019-13228-9","volume":"10","author":"Y Liu","year":"2019","unstructured":"Liu Y, Nie H, Liu H, Lu F. Poly(A) inclusive RNA isoform sequencing (PAIso-seq) reveals wide-spread non-adenosine residues within RNA poly(A) tails. Nat Commun. 2019;10:5292.","journal-title":"Nat Commun"},{"key":"2250_CR24","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1002\/jez.1402150209","volume":"215","author":"AL Sternlicht","year":"1981","unstructured":"Sternlicht AL, Schultz RM. Biochemical studies of mammalian oogenesis: kinetics of accumulation of total and poly(A)-containing RNA during growth of the mouse oocyte. J Of Experimental Zoology. 1981;215:191\u2013200.","journal-title":"J Of Experimental Zoology"},{"key":"2250_CR25","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1093\/biolre\/ioac014","volume":"107","author":"Z-Y Jiang","year":"2022","unstructured":"Jiang Z-Y, Fan H-Y. Five questions toward mRNA degradation in oocytes and preimplantation embryos: when, who, to whom, how, and why? Biol Reprod. 2022;107:62\u201375.","journal-title":"Biol Reprod"},{"key":"2250_CR26","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1093\/biolre\/ioz012","volume":"101","author":"Q-Q Sha","year":"2019","unstructured":"Sha Q-Q, Zhang J, Fan H-Y. A story of birth and death: mRNA translation and clearance at the onset of maternal-to-zygotic transition in mammals\u2020. Biol Reprod. 2019;101:579\u201390.","journal-title":"Biol Reprod"},{"key":"2250_CR27","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1038\/s41594-023-00969-x","volume":"30","author":"Y Wang","year":"2023","unstructured":"Wang Y, Li Y, Skuland T, Zhou C, Li A, Hashim A, et al. The RNA m6A landscape of mouse oocytes and preimplantation embryos. Nat Struct Mol Biol. 2023;30:703\u20139.","journal-title":"Nat Struct Mol Biol"},{"key":"2250_CR28","doi-asserted-by":"publisher","first-page":"7239","DOI":"10.1093\/nar\/gkab378","volume":"49","author":"S Oerum","year":"2021","unstructured":"Oerum S, Meynier V, Catala M, Tisn\u00e9 C. A comprehensive review of m6A\/m6Am RNA methyltransferase structures. Nucleic Acids Res. 2021;49:7239\u201355.","journal-title":"Nucleic Acids Res"},{"key":"2250_CR29","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1016\/j.molcel.2019.06.006","volume":"75","author":"K Boulias","year":"2019","unstructured":"Boulias K, Toczyd\u0142owska-Socha D, Hawley BR, Liberman N, Takashima K, Zaccara S, et al. Identification of the m6Am methyltransferase PCIF1 reveals the location and functions of m6Am in the transcriptome. Mol Cell. 2019;75:631-643.e8.","journal-title":"Mol Cell"},{"key":"2250_CR30","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1016\/j.molcel.2019.05.030","volume":"75","author":"E Sendinc","year":"2019","unstructured":"Sendinc E, Valle-Garcia D, Dhall A, Chen H, Henriques T, Navarrete-Perea J, et al. PCIF1 catalyzes m6Am mRNA methylation to regulate gene expression. Mol Cell. 2019;75:620-630.e9.","journal-title":"Mol Cell"},{"key":"2250_CR31","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 Y-S, Yang Y-G. Dynamic transcriptomic m6A decoration: writers, erasers, readers and functions in RNA metabolism. Cell Res. 2018;28:616\u201324.","journal-title":"Cell Res"},{"key":"2250_CR32","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1038\/s41422-018-0117-4","volume":"29","author":"H Sun","year":"2018","unstructured":"Sun H, Zhang M, Li K, Bai D, Yi C. Cap-specific, terminal N6-methylation by a mammalian m6Am methyltransferase. Cell Res. 2018;29:80\u20132.","journal-title":"Cell Res"},{"key":"2250_CR33","doi-asserted-by":"crossref","unstructured":"Isakova A, Neff N, Quake SR. Single cell profiling of total RNA using Smart-seq-total. 2020.","DOI":"10.1101\/2020.06.02.131060"},{"key":"2250_CR34","doi-asserted-by":"publisher","first-page":"18220","DOI":"10.1074\/jbc.RA119.010676","volume":"294","author":"MG Wulf","year":"2019","unstructured":"Wulf MG, Maguire S, Humbert P, Dai N, Bei Y, Nichols NM, et al. Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other. J Chem Biol. 2019;294:18220\u201331.","journal-title":"J Chem Biol"},{"key":"2250_CR35","doi-asserted-by":"publisher","first-page":"e2","DOI":"10.1093\/nar\/gkab861","volume":"50","author":"MG Wulf","year":"2021","unstructured":"Wulf MG, Maguire S, Dai N, Blondel A, Posfai D, Krishnan K, et al. Chemical capping improves template switching and enhances sequencing of small RNAs. Nucleic Acids Res. 2021;50:e2\u2013e2.","journal-title":"Nucleic Acids Res"},{"key":"2250_CR36","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1038\/s41556-023-01328-0","volume":"26","author":"T Wang","year":"2024","unstructured":"Wang T, Peng J, Fan J, Tang N, Hua R, Zhou X, et al. Single-cell multi-omics profiling of human preimplantation embryos identifies cytoskeletal defects during embryonic arrest. Nat Cell Biol. 2024;26:263\u201377.","journal-title":"Nat Cell Biol"},{"key":"2250_CR37","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1016\/j.cell.2024.12.028","volume":"188","author":"W Zhu","year":"2025","unstructured":"Zhu W, Meng J, Li Y, Gu L, Liu W, Li Z, et al. Comparative proteomic landscapes elucidate human preimplantation development and failure. Cell. 2025;188:814-831.e21.","journal-title":"Cell"},{"key":"2250_CR38","doi-asserted-by":"publisher","first-page":"843","DOI":"10.1038\/nrg2438","volume":"9","author":"WF Marzluff","year":"2008","unstructured":"Marzluff WF, Wagner EJ, Duronio RJ. Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail. Nat Rev Genet. 2008;9:843\u201354.","journal-title":"Nat Rev Genet"},{"key":"2250_CR39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-018-2579-2","volume":"19","author":"JM Gaspar","year":"2018","unstructured":"Gaspar JM. NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors. Bmc Bioinform. 2018;19:1\u20139.","journal-title":"Bmc Bioinform"},{"key":"2250_CR40","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/257251a0","volume":"257","author":"CM Wei","year":"1975","unstructured":"Wei CM, Gershowitz A, Moss B. N6, O2\u2032-dimethyladenosine a novel methylated ribonucleoside next to the 5\u2032 terminal of animal cell and virus mRNAs. Nature. 1975;257:251\u20133.","journal-title":"Nature"},{"key":"2250_CR41","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1038\/nmeth.3453","volume":"12","author":"B Linder","year":"2015","unstructured":"Linder B, Grozhik AV, Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat Methods. 2015;12:767\u201372.","journal-title":"Nat Methods"},{"key":"2250_CR42","doi-asserted-by":"publisher","first-page":"eaav0080","DOI":"10.1126\/science.aav0080","volume":"363","author":"S Akichika","year":"2019","unstructured":"Akichika S, Hirano S, Shichino Y, Suzuki T, Nishimasu H, Ishitani R, et al. Cap-specific terminal N6-methylation of RNA by an RNA polymerase II\u2013associated methyltransferase. Science. 2019;363:eaav0080.","journal-title":"Science"},{"key":"2250_CR43","doi-asserted-by":"publisher","first-page":"4778","DOI":"10.1038\/s41467-021-25105-5","volume":"12","author":"H Sun","year":"2021","unstructured":"Sun H, Li K, Zhang X, Liu J, Zhang M, Meng H, et al. m6Am-seq reveals the dynamic m6Am methylation in the human transcriptome. Nat Commun. 2021;12:4778.","journal-title":"Nat Commun"},{"key":"2250_CR44","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/nrm2838","volume":"11","author":"RJ Jackson","year":"2010","unstructured":"Jackson RJ, Hellen CUT, Pestova TV. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol. 2010;11:113\u201327.","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2250_CR45","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.bbagrm.2018.09.011","volume":"1862","author":"A Galloway","year":"2019","unstructured":"Galloway A, Cowling VH. mRNA cap regulation in mammalian cell function and fate. Biochim Biophys Acta Gene Regul Mech. 2019;1862:270\u20139.","journal-title":"Biochim Biophys Acta Gene Regul Mech"},{"key":"2250_CR46","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1093\/nass\/nrp065","volume":"53","author":"M Ishikawa","year":"2009","unstructured":"Ishikawa M, Murai R, Hagiwara H, Hoshino T, Suyama K. Preparation of eukaryotic mRNA having differently methylated adenosine at the 5\u2032-terminus and the effect of the methyl group in translation. Nucleic Acids Symp Ser (Oxf). 2009;53:129\u201330.","journal-title":"Nucleic Acids Symp Ser (Oxf)"},{"key":"2250_CR47","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1038\/s41580-023-00582-2","volume":"24","author":"H Zhang","year":"2023","unstructured":"Zhang H, Ji S, Zhang K, Chen Y, Ming J, Kong F, et al. Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition. Nat Cell Biol. 2023;24:166.","journal-title":"Nat Cell Biol"},{"key":"2250_CR48","doi-asserted-by":"publisher","first-page":"1047","DOI":"10.1038\/s41586-023-06428-3","volume":"620","author":"S Ji","year":"2023","unstructured":"Ji S, Chen F, Stein P, Wang J, Zhou Z, Wang L, et al. OBOX regulates mouse zygotic genome activation and early development. Nature. 2023;620:1047\u201353.","journal-title":"Nature"},{"key":"2250_CR49","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/s41587-023-01831-7","volume":"42","author":"Y Li","year":"2023","unstructured":"Li Y, Wang Y, Vera-Rodriguez M, Lindeman LC, Skuggen LE, Rasmussen EMK, et al. Single-cell m6A mapping in vivo using picoMeRIP\u2013seq. Nat Biotechnol. 2023;42:591\u20136.","journal-title":"Nat Biotechnol"},{"issue":"12","key":"2250_CR50","doi-asserted-by":"publisher","first-page":"1909","DOI":"10.1038\/s41587-023-02109-8","volume":"42","author":"T Wu","year":"2024","unstructured":"Wu T, Cheng AY, Zhang Y, Xu J, Wu J, Wen L, et al. KARR-seq reveals cellular higher-order RNA structures and RNA\u2013RNA interactions. Nat Biotechnol. 2024;42(12):1909\u201320.","journal-title":"Nat Biotechnol"},{"key":"2250_CR51","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1016\/j.molcel.2023.01.013","volume":"83","author":"P Dave","year":"2023","unstructured":"Dave P, Roth G, Griesbach E, Mateju D, Hochstoeger T, Chao JA. Single-molecule imaging reveals translation-dependent destabilization of mRNAs. Mol Cell. 2023;83:589-606.e6.","journal-title":"Mol Cell"},{"key":"2250_CR52","doi-asserted-by":"publisher","first-page":"114077","DOI":"10.1016\/j.celrep.2024.114077","volume":"43","author":"H Yu","year":"2024","unstructured":"Yu H, Zhao J, Shen Y, Qiao L, Liu Y, Xie G, et al. The dynamic landscape of enhancer-derived RNA during mouse early embryo development. Cell Rep. 2024;43:114077.","journal-title":"Cell Rep"},{"key":"2250_CR53","doi-asserted-by":"crossref","unstructured":"Cvetesic N, Borkowska M, Hatanaka Y, Yu C, Vincent SD, M\u00fcller F, et al. Global regulatory transitions at core promoters demarcate the mammalian germline cycle. bioRxiv. 2020. Available from: https:\/\/www.biorxiv.org\/content\/10.1101\/2020.10.30.361865v1.full.pdf.","DOI":"10.1101\/2020.10.30.361865"},{"key":"2250_CR54","first-page":"1943","volume":"28","author":"N Cvetesic","year":"2018","unstructured":"Cvetesic N, Leitch HG, Borkowska M, M\u00fcller F, Carninci P, Hajkova P, et al. SLIC-CAGE: high-resolution transcription start site mapping using nanogram-levels of total RNA. Nucleic Acids Res. 2018;28:1943\u201356.","journal-title":"Nucleic Acids Res"},{"key":"2250_CR55","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1016\/j.molcel.2019.09.032","volume":"77","author":"J Liu","year":"2020","unstructured":"Liu J, Li K, Cai J, Zhang M, Zhang X, Xiong X, et al. Landscape and regulation of m6A and m6Am methylome across human and mouse tissues. Mol Cell. 2020;77:426-440.e6.","journal-title":"Mol Cell"},{"key":"2250_CR56","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, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, et al. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5\u2032 sites. Cell Rep. 2014;8:284\u201396.","journal-title":"Cell Rep"},{"key":"2250_CR57","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.3317","volume":"12","author":"D Kim","year":"2015","unstructured":"Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357\u201360.","journal-title":"Nat Methods"},{"key":"2250_CR58","first-page":"1","volume":"18","author":"MC Frith","year":"2007","unstructured":"Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A. A code for transcription initiation in mammalian genomes. Nucleic Acids Res. 2007;18:1\u201312.","journal-title":"Nucleic Acids Res"},{"key":"2250_CR59","doi-asserted-by":"crossref","unstructured":"Rozewicki J, Li S, Amada KM, Standley DM, Katoh K. MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Res. 2019.","DOI":"10.1093\/nar\/gkz342"},{"key":"2250_CR60","doi-asserted-by":"publisher","first-page":"W39","DOI":"10.1093\/nar\/gkv416","volume":"43","author":"TL Bailey","year":"2015","unstructured":"Bailey TL, Johnson J, Grant CE, Noble WS. The MEME Suite. Nucleic Acids Res. 2015;43:W39-49.","journal-title":"Nucleic Acids Res"},{"key":"2250_CR61","unstructured":"Huan Yao, Chun-Chun Gao, Danru Zhang, Jiawei Xu, Gege Song, Xiu Fan, Dao-Bo Liang, Yu-Sheng Chen, Qian Li, Yanjie Guo, Yu-Ting Cai, Lulu Hu, Yong-Liang Zhao, Ying-Pu Sun, Ying Yang, Jianyong Han, Yun-Gui Yang. BioProject. https:\/\/ngdc.cncb.ac.cn\/bioproject\/browse\/PRJCA008779."},{"key":"2250_CR62","unstructured":"You Wu, Xiaocui Xu, Meijie Qi, Chuan Chen, Mengying Li, Rushuang Yan, Xiaochen Kou, Yanhong Zhao, Wenqiang Liu, Yanhe Li, Xuelian Liu, Meiling Zhang, Chengqi Yi, Hongbin Liu, Junhong Xiang, Hong Wang, Bin Shen, Yawei Gao, Shaorong Gao. Genome Sequence Archive. https:\/\/ngdc.cncb.ac.cn\/gsa\/browse\/CRA003985\/CRR274750."},{"key":"2250_CR63","unstructured":"Lloret-Llinares M, Karadoulama E, Chen Y, Wojenski LA, Villafano GJ, Bornholdt J, Andersson R, Core L, Sandelin A, Jensen TH. Sequence Read Archive. https:\/\/identifiers.org\/insdc.sra:SRR7300113."},{"key":"2250_CR64","unstructured":"Lloret-Llinares M, Karadoulama E, Chen Y, Wojenski LA, Villafano GJ, Bornholdt J, Andersson R, Core L, Sandelin A, Jensen TH. Sequence Read Archive. https:\/\/identifiers.org\/insdc.sra:SRR7300114."},{"key":"2250_CR65","unstructured":"Oomen ME, Rodriguez-Terrones D, Kurome M, Zakhartchenko V, Mottes L, Simmet K, Noll C, Nakatani T, Mourra-Diaz CM, Aksoy I, Savatier P, G\u00f6ke J, Wolf E, Kaessmann H, Torres-Padilla ME. Sequence Read Archive. https:\/\/identifiers.org\/insdc.sra:SRR23403774."},{"key":"2250_CR66","unstructured":"Oomen ME, Rodriguez-Terrones D, Kurome M, Zakhartchenko V, Mottes L, Simmet K, Noll C, Nakatani T, Mourra-Diaz CM, Aksoy I, Savatier P, G\u00f6ke J, Wolf E, Kaessmann H, Torres-Padilla ME. Sequence Read Archive. https:\/\/identifiers.org\/insdc.sra:SRR23403777."},{"key":"2250_CR67","unstructured":"Zhuqing Xiong, Kai Xu, Zili Lin, Feng Kong, Qiujun Wang, Yujun Quan, Qian-Qian Sha, Fajin Li, Zhuoning Zou, Ling Liu, Shuyan Ji, Yuling Chen, Hongmei Zhang, Jianhuo Fang, Guang Yu, Bofeng Liu, Lijuan Wang, Huili Wang, Haiteng Deng, Xuerui Yang, Heng-Yu Fan, Lei Li, Wei Xie. Sequence Read Archive. https:\/\/identifiers.org\/insdc.sra:SRP303825."},{"key":"2250_CR68","unstructured":"Hongmei Zhang, Shuyan Ji, Ke Zhang, Yuling Chen, Jia Ming, Feng Kong, Lijuan Wang, Shun Wang, Zhuoning Zou, Zhuqing Xiong, Kai Xu, Zili Lin, Bo Huang, Ling Liu, Qiang Fan, Suoqin Jin, Haiteng Deng & Wei Xie. Additional file 2: Table S1. https:\/\/static-content.springer.com\/esm\/art%3A10.1186%2Fs13059-023-02997-8\/MediaObjects\/13059_2023_2997_MOESM2_ESM.xlsx."}],"container-title":["BMC Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-025-02250-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12915-025-02250-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12915-025-02250-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,29]],"date-time":"2025-05-29T10:02:24Z","timestamp":1748512944000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbiol.biomedcentral.com\/articles\/10.1186\/s12915-025-02250-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,28]]},"references-count":68,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["2250"],"URL":"https:\/\/doi.org\/10.1186\/s12915-025-02250-7","relation":{},"ISSN":["1741-7007"],"issn-type":[{"value":"1741-7007","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,5,28]]},"assertion":[{"value":"6 October 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 May 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"28 May 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"All donated oocytes and embryos were collected after the consent and approval of the patients based on the guidelines of the ethical committee of the First Affiliated Hospital of Zhengzhou University guidelines of the People\u2019s Republic of China on the ethical principles of the Human Assisted Reproductive Technology and the Helsinki Declaration (IRB approval number: 2023-KY-0465). All donors agreed that their unmatured oocytes would be used for basic research to understand the mechanism of in vitro oocyte maturation and that the donation would not affect their clinical treatment.","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 no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"147"}}