{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,4]],"date-time":"2026-01-04T23:18:38Z","timestamp":1767568718947,"version":"3.48.0"},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":["rep.bioscientifica.com"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,10,24]]},"abstract":"<jats:sec>\n                    <jats:title>In brief<\/jats:title>\n                    <jats:p>This study investigates the role of TH2B in pre-implantation embryos and found that TH2B deposition varies between gametes but rapidly redistributes in two-cell embryos after fertilization. Our ultra-low-input native chromatin immunoprecipitation and sequencing (ULI-NChIP-seq) revealed that TH2B is enriched in early chromatin but decreases after the two-cell stage, with strong correlations to key regulatory regions, histone modifications and transposable elements (TEs), indicating its critical role in zygotic genome activation and early developmental processes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Abstract<\/jats:title>\n                    <jats:p>The histone variant TH2B, enriched in oocytes, sperm and early embryos, decreases as embryos differentiate into pre-gastrula stages. Despite its presence, the role of TH2B in epigenetic reprogramming during early embryonic development remains largely under-researched. Our study employed ULI-NChIP-seq to analyze the genome-wide distribution of TH2B in metaphase II (MII) oocytes and early embryos. We found that TH2B is enriched in the chromatin of oocytes and two-cell stage embryos but becomes less prevalent after the two-cell stage. Correlation analysis revealed that the TH2B chromatin patterns in sperm and pre-implantation embryos are more similar to each other than to those in MII oocytes. Gene ontology (GO) analysis of TH2B-occupied loci linked them to various developmental processes including oogenesis, fertilization, chromatin modification and transcription regulation. The study also identified a strong association of TH2B with specific TEs, particularly long terminal repeats, which are known to regulate pre-implantation development. Additionally, early embryos showed H3K9me3 marks at TH2B-bound loci. TH2B exhibited strong correlations with H2A.Z and H3.3 in the two-cell and eight-cell stages, a positive association with H3K27Ac and H3K4me3 and a negative correlation with H3K27me3. Allelic reprogramming analysis of TH2B in embryos from C57BL\/6J and DBA\/2J crosses revealed differential dynamics between maternal and paternal alleles, with a notable paternal bias at the promoter in two-cell embryos. Thus, TH2B\u2019s enrichment in early embryonic stages and its association with key regulatory regions and histone modifications underscore its importance in zygotic genome activation and subsequent developmental processes.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1530\/rep-24-0035","type":"journal-article","created":{"date-parts":[[2024,10,24]],"date-time":"2024-10-24T14:19:51Z","timestamp":1729779591000},"update-policy":"https:\/\/doi.org\/10.1530\/crossmarkpolicy-11","source":"Crossref","is-referenced-by-count":1,"title":["Genome-wide profiling of the epigenetic landscape of histone variant TH2B in murine oocytes and pre-implantation embryos"],"prefix":"10.1093","volume":"169","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-6932-1889","authenticated-orcid":true,"given":"Isha","family":"Singh","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3800-4053","authenticated-orcid":true,"given":"Priyanka","family":"Parte","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","reference":[{"key":"bib1","series-title":"PLoS Genet","first-page":"e1002279","article-title":"Dynamic replacement of histone H3 variants reprograms epigenetic marks in early mouse embryos","volume":"7","author":"Akiyama T","year":"2011","unstructured":"Akiyama T, Suzuki O, Matsuda J, et al. 2011 Dynamic replacement of histone H3 variants reprograms epigenetic marks in early mouse embryos. PLoS Genet 7 e1002279. (https:\/\/doi.org\/10.1371\/journal.pgen.1002279)"},{"key":"bib2","series-title":"Nucleic Acids Res","first-page":"W202","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"Bailey TL","year":"2009","unstructured":"Bailey TL, Boden M, Buske FA, et al. 2009 MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37 W202\u2013W208. (https:\/\/doi.org\/10.1093\/nar\/gkp335)"},{"key":"bib3","series-title":"Dev","first-page":"737","article-title":"Kr\u00fcppel-like factors in mammalian stem cells and development","volume":"144","author":"Bialkowska AB","year":"2017","unstructured":"Bialkowska AB, Yang VW & Mallipattu SK 2017 Kr\u00fcppel-like factors in mammalian stem cells and development. Dev 144 737\u2013754. (https:\/\/doi.org\/10.1242\/dev.145441)"},{"key":"bib4","series-title":"Curr Protoc Mol Biol","first-page":"19.10.11","article-title":"Galaxy: a web-based genome analysis tool for experimentalists","volume":"89","author":"Blankenberg D","year":"2010","unstructured":"Blankenberg D, Von Kuster GV, Coraor N, et al. 2010 Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 89 19.10.11\u201319.10.21. (https:\/\/doi.org\/10.1002\/0471142727.mb1910s89)"},{"key":"bib5","series-title":"Bioinformatics","first-page":"2114","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger AM","year":"2014","unstructured":"Bolger AM, Lohse M & Usadel B 2014 Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30 2114\u20132120. (https:\/\/doi.org\/10.1093\/bioinformatics\/btu170)"},{"key":"bib6","series-title":"Nat Commun","first-page":"6033","article-title":"An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations","volume":"6","author":"Brind\u2019Amour J","year":"2015","unstructured":"Brind\u2019Amour J, Liu S, Hudson M, et al. 2015 An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations. Nat Commun 6 6033. (https:\/\/doi.org\/10.1038\/ncomms7033)"},{"key":"bib7","series-title":"Nat Rev Mol Cell Biol","first-page":"299","article-title":"Variants of core histones and their roles in cell fate decisions, development and cancer","volume":"18","author":"Buschbeck M","year":"2017","unstructured":"Buschbeck M & Hake SB 2017 Variants of core histones and their roles in cell fate decisions, development and cancer. Nat Rev Mol Cell Biol 18 299\u2013314. (https:\/\/doi.org\/10.1038\/nrm.2016.166)"},{"key":"bib8","series-title":"Nat Genet","first-page":"551","article-title":"Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos","volume":"53","author":"Chen Z","year":"2021","unstructured":"Chen Z, Djekidel MN & Zhang Y 2021 Distinct dynamics and functions of H2AK119ub1 and H3K27me3 in mouse preimplantation embryos. Nat Genet 53 551\u2013563. (https:\/\/doi.org\/10.1038\/s41588-021-00821-2)"},{"key":"bib9","series-title":"Nature","first-page":"548","article-title":"Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition","volume":"537","author":"Dahl JA","year":"2016","unstructured":"Dahl JA, Jung I, Aanes H, et al. 2016 Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature 537 548\u2013552. (https:\/\/doi.org\/10.1038\/nature19360)"},{"key":"bib10","series-title":"Birth Defects Res C Embryo Today","first-page":"98","article-title":"DNA methylation in mammalian development and disease","volume":"75","author":"Dean W","year":"2005","unstructured":"Dean W, Lucifero D & Santos F 2005 DNA methylation in mammalian development and disease. Birth Defects Res C Embryo Today 75 98\u2013111. (https:\/\/doi.org\/10.1002\/bdrc.20037)"},{"key":"bib11","series-title":"Curr Opin Genet Dev","first-page":"102086","article-title":"Transposable elements in early human embryo development and embryo models","volume":"81","author":"DiRusso JA","year":"2023","unstructured":"DiRusso JA & Clark AT 2023 Transposable elements in early human embryo development and embryo models. Curr Opin Genet Dev 81 102086. (https:\/\/doi.org\/10.1016\/j.gde.2023.102086)"},{"key":"bib12","series-title":"Biol Reprod","first-page":"654","article-title":"Yin-yang1 is required in the mammalian oocyte for follicle expansion","volume":"84","author":"Griffith GJ","year":"2011","unstructured":"Griffith GJ, Trask MC, Hiller J, et al. 2011 Yin-yang1 is required in the mammalian oocyte for follicle expansion. Biol Reprod 84 654\u2013663. (https:\/\/doi.org\/10.1095\/biolreprod.110.087213)"},{"key":"bib13","series-title":"Nature","first-page":"473","article-title":"Distinctive chromatin in human sperm packages genes for embryo development","volume":"460","author":"Hammoud SS","year":"2009","unstructured":"Hammoud SS, Nix DA, Zhang H, et al. 2009 Distinctive chromatin in human sperm packages genes for embryo development. Nature 460 473\u2013478. (https:\/\/doi.org\/10.1038\/nature08162)"},{"key":"bib14","series-title":"Nat Genet","first-page":"925","article-title":"Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL\/HERVL retrotransposons","volume":"49","author":"Hendrickson PG","year":"2017","unstructured":"Hendrickson PG, Dor\u00e1is JA, Grow EJ, et al. 2017 Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL\/HERVL retrotransposons. Nat Genet 49 925\u2013934. (https:\/\/doi.org\/10.1038\/ng.3844)"},{"key":"bib15","series-title":"Cell Discov","first-page":"28","article-title":"Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity","volume":"4","author":"Hsu CC","year":"2018","unstructured":"Hsu CC, Zhao D, Shi J, et al. 2018 Gas41 links histone acetylation to H2A.Z deposition and maintenance of embryonic stem cell identity. Cell Discov 4 28. (https:\/\/doi.org\/10.1038\/s41421-018-0027-0)"},{"key":"bib16","series-title":"Reprod Fertil Dev","first-page":"1166","article-title":"EZH2 is essential for development of mouse preimplantation embryos","volume":"26","author":"Huang XJ","year":"2014","unstructured":"Huang XJ, Wang X, Ma X, et al. 2014 EZH2 is essential for development of mouse preimplantation embryos. Reprod Fertil Dev 26 1166\u20131175. (https:\/\/doi.org\/10.1071\/RD13169)"},{"key":"bib17","series-title":"Proc Natl Acad Sci USA","article-title":"Steroidogenic factor 1 (SF-1; Nr5a1) regulates the formation of the ovarian reserve","volume":"120","author":"Hughes CHK","year":"2023","unstructured":"Hughes CHK, Smith OE, Meinsohn MC, et al. 2023 Steroidogenic factor 1 (SF-1; Nr5a1) regulates the formation of the ovarian reserve. Proc Natl Acad Sci USA 120 e2220849120. (https:\/\/doi.org\/10.1073\/pnas.2220849120)"},{"key":"bib18","series-title":"Nature","first-page":"419","article-title":"Maternal H3K27me3 controls DNA methylation-independent imprinting","volume":"547","author":"Inoue A","year":"2017","unstructured":"Inoue A, Jiang L, Lu F, et al. 2017 Maternal H3K27me3 controls DNA methylation-independent imprinting. Nature 547 419\u2013424. (https:\/\/doi.org\/10.1038\/nature23262)"},{"key":"bib19","series-title":"Nat Struct and Mol Biol","first-page":"38","article-title":"Reprogramming of the histone H3.3 landscape in the early mouse embryo","volume":"28","author":"Ishiuchi T","year":"2021","unstructured":"Ishiuchi T, Abe S, Inoue K, et al. 2021 Reprogramming of the histone H3.3 landscape in the early mouse embryo. Nat Struct and Mol Biol 28 38\u201349. (https:\/\/doi.org\/10.1038\/s41594-020-00521-1)"},{"key":"bib20","series-title":"Nat Genet","first-page":"1502","article-title":"LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo","volume":"49","author":"Jachowicz JW","year":"2017","unstructured":"Jachowicz JW, Bing X, Pontabry J, et al. 2017 LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo. Nat Genet 49 1502\u20131510. (https:\/\/doi.org\/10.1038\/ng.3945)"},{"key":"bib21","series-title":"F1000Res","first-page":"1479","article-title":"SNPsplit: allele-specific splitting of alignments between genomes with known SNP genotypes","volume":"5","author":"Krueger F","year":"2016","unstructured":"Krueger F & Andrews SR 2016 SNPsplit: allele-specific splitting of alignments between genomes with known SNP genotypes. F1000Res 5 1479. (https:\/\/doi.org\/10.12688\/f1000research.9037.2)"},{"key":"bib22","series-title":"Nat Methods","first-page":"357","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead B","year":"2012","unstructured":"Langmead B & Salzberg SL 2012 Fast gapped-read alignment with Bowtie 2. Nat Methods 9 357\u2013359. (https:\/\/doi.org\/10.1038\/nmeth.1923)"},{"key":"bib23","series-title":"Chromosoma","first-page":"489","article-title":"Evolution of DUX gene macrosatellites in placental mammals","volume":"121","author":"Leidenroth A","year":"2012","unstructured":"Leidenroth A, Clapp J, Mitchell LM, et al. 2012 Evolution of DUX gene macrosatellites in placental mammals. Chromosoma 121 489\u2013497. (https:\/\/doi.org\/10.1007\/s00412-012-0380-y)"},{"key":"bib24","series-title":"Bioinformatics","first-page":"2078","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li H","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, et al. 2009 The sequence alignment\/map format and SAMtools. Bioinformatics 25 2078\u20132079. (https:\/\/doi.org\/10.1093\/bioinformatics\/btp352)"},{"key":"bib25","series-title":"Nucleic Acids Res","first-page":"W126","article-title":"TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms","volume":"52","author":"Li Y","year":"2024","unstructured":"Li Y, Lyu R, Chen S, et al. 2024 TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms. Nucleic Acids Res 52 W126\u2013W131. (https:\/\/doi.org\/10.1093\/nar\/gkae411)"},{"key":"bib26","series-title":"Nat Commun","first-page":"2142","article-title":"Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development","volume":"14","author":"Lismer A","year":"2023","unstructured":"Lismer A & Kimmins S 2023 Emerging evidence that the mammalian sperm epigenome serves as a template for embryo development. Nat Commun 14 2142. (https:\/\/doi.org\/10.1038\/s41467-023-37820-2)"},{"key":"bib27","series-title":"STAR Protoc","first-page":"100602","article-title":"ChIP-seq protocol for sperm cells and embryos to assess environmental impacts and epigenetic inheritance","volume":"2","author":"Lismer A","year":"2021","unstructured":"Lismer A, Lambrot R, Lafleur C, et al. 2021 ChIP-seq protocol for sperm cells and embryos to assess environmental impacts and epigenetic inheritance. STAR Protoc 2 100602. (https:\/\/doi.org\/10.1016\/j.xpro.2021.100602)"},{"key":"bib28","series-title":"Nature","first-page":"558","article-title":"Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos","volume":"537","author":"Liu X","year":"2016","unstructured":"Liu X, Wang C, Liu W, et al. 2016 Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 537 558\u2013562. (https:\/\/doi.org\/10.1038\/nature19362)"},{"key":"bib29","series-title":"Nature","first-page":"139","article-title":"The landscape of RNA Pol II binding reveals a stepwise transition during ZGA","volume":"587","author":"Liu B","year":"2020","unstructured":"Liu B, Xu Q, Wang Q, et al. 2020 The landscape of RNA Pol II binding reveals a stepwise transition during ZGA. Nature 587 139\u2013144. (https:\/\/doi.org\/10.1038\/s41586-020-2847-y)"},{"key":"bib30","series-title":"Adv Sci","first-page":"e2200057","article-title":"Hierarchical accumulation of histone variant H2A.Z regulates transcriptional states and histone modifications in early mammalian embryos","volume":"9","author":"Liu X","year":"2022","unstructured":"Liu X, Zhang J, Zhou J, et al. 2022 Hierarchical accumulation of histone variant H2A.Z regulates transcriptional states and histone modifications in early mammalian embryos. Adv Sci 9 e2200057. (https:\/\/doi.org\/10.1002\/advs.202200057)"},{"key":"bib31","series-title":"Cell","first-page":"1375","article-title":"Establishing chromatin regulatory landscape during mouse preimplantation development","volume":"165","author":"Lu F","year":"2016","unstructured":"Lu F, Liu Y, Inoue A, et al. 2016 Establishing chromatin regulatory landscape during mouse preimplantation development. Cell 165 1375\u20131388. (https:\/\/doi.org\/10.1016\/j.cell.2016.05.050)"},{"key":"bib32","series-title":"Cell Rep","first-page":"3296","article-title":"Genomic repeats categorize genes with distinct functions for orchestrated regulation","volume":"30","author":"Lu JY","year":"2020","unstructured":"Lu JY, Shao W, Chang L, et al. 2020 Genomic repeats categorize genes with distinct functions for orchestrated regulation. Cell Rep 30 3296\u20133311.e5. (https:\/\/doi.org\/10.1016\/j.celrep.2020.02.048)"},{"key":"bib33","series-title":"EMBO J","first-page":"800","article-title":"The profile of repeat-associated histone lysine methylation states in the mouse epigenome","volume":"24","author":"Martens JH","year":"2005","unstructured":"Martens JH, O'Sullivan RJ, Braunschweig U, et al. 2005 The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 24 800\u2013812. (https:\/\/doi.org\/10.1038\/sj.emboj.7600545)"},{"key":"bib34","series-title":"Nat Biotechnol","first-page":"495","article-title":"GREAT improves functional interpretation of cis-regulatory regions","volume":"28","author":"McLean CY","year":"2010","unstructured":"McLean CY, Bristor D, Hiller M, et al. 2010 GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 28 495\u2013501. (https:\/\/doi.org\/10.1038\/nbt.1630)"},{"key":"bib35","series-title":"Nucleic Acids Res","first-page":"W566","article-title":"ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap","volume":"43","author":"Metsalu T","year":"2015","unstructured":"Metsalu T & Vilo J 2015 ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. Nucleic Acids Res 43 W566\u2013W570. (https:\/\/doi.org\/10.1093\/nar\/gkv468)"},{"key":"bib36","series-title":"Sci Adv","first-page":"eadg7997","article-title":"Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency","volume":"9","author":"Mirzadeh Azad F","year":"2023","unstructured":"Mirzadeh Azad F, Struys EA, Wingert V, et al. 2023 Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency. Sci Adv 9 eadg7997. (https:\/\/doi.org\/10.1126\/sciadv.adg7997)"},{"key":"bib37","series-title":"Cell","first-page":"5541","article-title":"A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development","volume":"184","author":"Modzelewski AJ","year":"2021","unstructured":"Modzelewski AJ, Shao W, Chen J, et al. 2021 A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell 184 5541\u20135558.e22. (https:\/\/doi.org\/10.1016\/j.cell.2021.09.021)"},{"key":"bib38","series-title":"Genes Dev","first-page":"1680","article-title":"Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B","volume":"27","author":"Montellier E","year":"2013","unstructured":"Montellier E, Boussouar F, Rousseaux S, et al. 2013 Chromatin-to-nucleoprotamine transition is controlled by the histone H2B variant TH2B. Genes Dev 27 1680\u20131692. (https:\/\/doi.org\/10.1101\/gad.220095.113)"},{"key":"bib39","series-title":"Nat Commun","first-page":"5063","article-title":"Genome-wide chromatin accessibility is restricted by ANP32E","volume":"11","author":"Murphy KE","year":"2020","unstructured":"Murphy KE, Meng FW, Makowski CE, et al. 2020 Genome-wide chromatin accessibility is restricted by ANP32E. Nat Commun 11 5063. (https:\/\/doi.org\/10.1038\/s41467-020-18821-x)"},{"key":"bib40","series-title":"Biochem Biophys Res Commun","first-page":"929","article-title":"Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming","volume":"464","author":"Padavattan S","year":"2015","unstructured":"Padavattan S, Shinagawa T, Hasegawa K, et al. 2015 Structural and functional analyses of nucleosome complexes with mouse histone variants TH2a and TH2b, involved in reprogramming. Biochem Biophys Res Commun 464 929\u2013935. (https:\/\/doi.org\/10.1016\/j.bbrc.2015.07.070)"},{"key":"bib41","series-title":"Biophys Chem","first-page":"41","article-title":"Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b","volume":"221","author":"Padavattan S","year":"2017","unstructured":"Padavattan S, Thiruselvam V, Shinagawa T, et al. 2017 Structural analyses of the nucleosome complexes with human testis-specific histone variants, hTh2a and hTh2b. Biophys Chem 221 41\u201348. (https:\/\/doi.org\/10.1016\/j.bpc.2016.11.013)"},{"key":"bib42","series-title":"Nucleic Acids Res","first-page":"D771","article-title":"DBTMEE: a database of transcriptome in mouse early embryos","volume":"43","author":"Park SJ","year":"2015","unstructured":"Park SJ, Shirahige K, Ohsugi M, et al. 2015 DBTMEE: a database of transcriptome in mouse early embryos. Nucleic Acids Res 43 D771\u2013D776. (https:\/\/doi.org\/10.1093\/nar\/gku1001)"},{"key":"bib43","series-title":"Clin epigenetics","first-page":"101","article-title":"Epigenetic landscape of testis specific histone H2B variant and its influence on sperm function","volume":"13","author":"Patankar A","year":"2021","unstructured":"Patankar A, Gajbhiye R, Surve S, et al. 2021 Epigenetic landscape of testis specific histone H2B variant and its influence on sperm function. Clin epigenetics 13 101. (https:\/\/doi.org\/10.1186\/s13148-021-01088-4)"},{"key":"bib44","series-title":"Cell","first-page":"391","article-title":"A LINE1-nucleolin partnership regulates early development and ESC identity","volume":"174","author":"Percharde M","year":"2018","unstructured":"Percharde M, Lin CJ, Yin Y, et al. 2018 A LINE1-nucleolin partnership regulates early development and ESC identity. Cell 174 391\u2013405.e19. (https:\/\/doi.org\/10.1016\/j.cell.2018.05.043)"},{"key":"bib45","series-title":"Dev Cell","first-page":"625","article-title":"A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development","volume":"19","author":"Probst AV","year":"2010","unstructured":"Probst AV, Okamoto I, Casanova M, et al. 2010 A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development. Dev Cell 19 625\u2013638. (https:\/\/doi.org\/10.1016\/j.devcel.2010.09.002)"},{"key":"bib46","series-title":"Bioinformatics","first-page":"841","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan AR","year":"2010","unstructured":"Quinlan AR & Hall IM 2010 BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26 841\u2013842. (https:\/\/doi.org\/10.1093\/bioinformatics\/btq033)"},{"key":"bib47","series-title":"Nucleic Acids Res","first-page":"W160","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez F","year":"2016","unstructured":"Ram\u00edrez F, Ryan DP, Gr\u00fcning B, et al. 2016 deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res 44 W160\u2013W165. (https:\/\/doi.org\/10.1093\/nar\/gkw257)"},{"key":"bib48","series-title":"Nat Biotechnol","first-page":"24","article-title":"Integrative genomics viewer","volume":"29","author":"Robinson JT","year":"2011","unstructured":"Robinson JT, Thorvaldsd\u00f3ttir H, Winckler W, et al. 2011 Integrative genomics viewer. Nat Biotechnol 29 24\u201326. (https:\/\/doi.org\/10.1038\/nbt.1754)"},{"key":"bib49","series-title":"Nucleic Acids Res","first-page":"5599","article-title":"USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation","volume":"50","author":"Rong Y","year":"2022","unstructured":"Rong Y, Zhu YZ, Yu JL, et al. 2022 USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation. Nucleic Acids Res 50 5599\u20135616. (https:\/\/doi.org\/10.1093\/nar\/gkac468)"},{"key":"bib50","series-title":"Genes Dev","first-page":"590","article-title":"Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development","volume":"37","author":"Sakamoto M","year":"2023","unstructured":"Sakamoto M, Abe S, Miki Y, et al. 2023 Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development. Genes Dev 37 590\u2013604. (https:\/\/doi.org\/10.1101\/gad.350376.122)"},{"key":"bib51","series-title":"Cells","first-page":"858","article-title":"The transcription factor Elf3 is essential for a successful mesenchymal to epithelial transition","volume":"8","author":"Sengez B","year":"2019","unstructured":"Sengez B, Ayg\u00fcn I, Shehwana H, et al. 2019 The transcription factor Elf3 is essential for a successful mesenchymal to epithelial transition. Cells 8 858. (https:\/\/doi.org\/10.3390\/cells8080858)"},{"key":"bib53","series-title":"Cell Stem Cell","first-page":"217","article-title":"Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells","volume":"14","author":"Shinagawa T","year":"2014","unstructured":"Shinagawa T, Takagi T, Tsukamoto D, et al. 2014 Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells. Cell Stem Cell 14 217\u2013227. (https:\/\/doi.org\/10.1016\/j.stem.2013.12.015)"},{"key":"bib52","series-title":"Development","first-page":"1287","article-title":"Disruption of Th2a and Th2b genes causes defects in spermatogenesis","volume":"142","author":"Shinagawa T","year":"2015","unstructured":"Shinagawa T, Huynh LM, Takagi T, et al. 2015 Disruption of Th2a and Th2b genes causes defects in spermatogenesis. Development 142 1287\u20131292. (https:\/\/doi.org\/10.1242\/dev.121830)"},{"key":"bib74","series-title":"J Biol Chem","first-page":"4155","article-title":"A cysteine-containing H2B-like histone found in mature mammalian testis.","volume":"251","author":"Shires A","year":"1976","unstructured":"Shires A, Carpenter MP & Chalkley R 1976 A cysteine-containing H2B-like histone found in mature mammalian testis. J Biol Chem 251 4155\u20134158."},{"key":"bib54","series-title":"Front Cell Dev Biol","first-page":"755751","article-title":"Heterogeneity in the epigenetic landscape of murine testis-specific histone variants TH2A and TH2B sharing the same Bi-directional promoter","volume":"9","author":"Singh I","year":"2021","unstructured":"Singh I & Parte P 2021 Heterogeneity in the epigenetic landscape of murine testis-specific histone variants TH2A and TH2B sharing the same Bi-directional promoter. Front Cell Dev Biol 9 755751. (https:\/\/doi.org\/10.3389\/fcell.2021.755751)"},{"key":"bib55","series-title":"Reproduction","first-page":"697","article-title":"HIRA contributes to zygote formation in mice and is implicated in human 1PN zygote phenotype","volume":"161","author":"Smith R","year":"2021","unstructured":"Smith R, Pickering SJ, Kopakaki A, et al. 2021 HIRA contributes to zygote formation in mice and is implicated in human 1PN zygote phenotype. Reproduction 161 697\u2013707. (https:\/\/doi.org\/10.1530\/REP-20-0636)"},{"key":"bib56","series-title":"Int J Mol Sci","first-page":"1459","article-title":"The dynamics of histone modifications during mammalian zygotic genome activation","volume":"25","author":"Sotomayor-Lugo F","year":"2024","unstructured":"Sotomayor-Lugo F, Iglesias-Barrameda N, Castillo-Aleman YM, et al. 2024 The dynamics of histone modifications during mammalian zygotic genome activation. Int J Mol Sci 25 1459. (https:\/\/doi.org\/10.3390\/ijms25031459)"},{"key":"bib57","series-title":"Nat Methods","first-page":"121","article-title":"BoxPlotR: a web tool for generation of box plots","volume":"11","author":"Spitzer M","year":"2014","unstructured":"Spitzer M, Wildenhain J, Rappsilber J, et al. 2014 BoxPlotR: a web tool for generation of box plots. Nat Methods 11 121\u2013122. (https:\/\/doi.org\/10.1038\/nmeth.2811)"},{"key":"bib58","series-title":"J Biol Chem","first-page":"5560","article-title":"Isolation and characterization of TH2A, a germ cell-specific variant of histone 2A in rat testis","volume":"257","author":"Trostle-Weige PK","year":"1982","unstructured":"Trostle-Weige PK, Meistrich ML, Brock WA, et al. 1982 Isolation and characterization of TH2A, a germ cell-specific variant of histone 2A in rat testis. J Biol Chem 257 5560\u20135567. (https:\/\/doi.org\/10.1016\/s0021-9258(19)83813-9)"},{"key":"bib59","series-title":"Nat Cell Biol","first-page":"620","article-title":"Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development","volume":"20","author":"Wang C","year":"2018","unstructured":"Wang C, Liu X, Gao Y, et al. 2018 Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat Cell Biol 20 620\u2013631. (https:\/\/doi.org\/10.1038\/s41556-018-0093-4)"},{"key":"bib60","series-title":"EMBO J","first-page":"e112012","article-title":"CBP\/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos","volume":"41","author":"Wang M","year":"2022","unstructured":"Wang M, Chen Z & Zhang Y 2022 CBP\/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. EMBO J 41 e112012. (https:\/\/doi.org\/10.15252\/embj.2022112012)"},{"key":"bib61","series-title":"Nature","first-page":"652","article-title":"The landscape of accessible chromatin in mammalian preimplantation embryos","volume":"534","author":"Wu J","year":"2016","unstructured":"Wu J, Huang B, Chen H, et al. 2016 The landscape of accessible chromatin in mammalian preimplantation embryos. Nature 534 652\u2013657. (https:\/\/doi.org\/10.1038\/nature18606)"},{"key":"bib62","series-title":"Cell","first-page":"816","article-title":"Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome","volume":"148","author":"Xie W","year":"2012","unstructured":"Xie W, Barr CL, Kim A, et al. 2012 Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148 816\u2013831. (https:\/\/doi.org\/10.1016\/j.cell.2011.12.035)"},{"key":"bib63","series-title":"Trends Cell Biol","first-page":"237","article-title":"Epigenome in early mammalian development: inheritance, reprogramming and establishment","volume":"28","author":"Xu Q","year":"2018","unstructured":"Xu Q & Xie W 2018 Epigenome in early mammalian development: inheritance, reprogramming and establishment. Trends Cell Biol 28 237\u2013253. (https:\/\/doi.org\/10.1016\/j.tcb.2017.10.008)"},{"key":"bib64","series-title":"Protein and Cell","first-page":"7","article-title":"Insights into epigenetic patterns in mammalian early embryos","volume":"12","author":"Xu R","year":"2021","unstructured":"Xu R, Li C, Liu X, et al. 2021 Insights into epigenetic patterns in mammalian early embryos. Protein and Cell 12 7\u201328. (https:\/\/doi.org\/10.1007\/s13238-020-00757-z)"},{"key":"bib65","series-title":"Cell Stem Cell","first-page":"1051","article-title":"Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos","volume":"29","author":"Xu R","year":"2022","unstructured":"Xu R, Li S, Wu Q, et al. 2022 Stage-specific H3K9me3 occupancy ensures retrotransposon silencing in human pre-implantation embryos. Cell Stem Cell 29 1051\u20131066.e8. (https:\/\/doi.org\/10.1016\/j.stem.2022.06.001)"},{"key":"bib66","series-title":"Cell Rep","first-page":"113775","article-title":"Systematic evaluation of retroviral LTRs as cis-regulatory elements in mouse embryos","volume":"43","author":"Yang J","year":"2024","unstructured":"Yang J, Cook L & Chen Z 2024 Systematic evaluation of retroviral LTRs as cis-regulatory elements in mouse embryos. Cell Rep 43 113775. (https:\/\/doi.org\/10.1016\/j.celrep.2024.113775)"},{"key":"bib67","series-title":"Nat Commun","first-page":"4440","article-title":"Histone H3K36me2 and H3K36me3 form a chromatin platform essential for DNMT3A-dependent DNA methylation in mouse oocytes","volume":"13","author":"Yano S","year":"2022","unstructured":"Yano S, Ishiuchi T, Abe S, et al. 2022 Histone H3K36me2 and H3K36me3 form a chromatin platform essential for DNMT3A-dependent DNA methylation in mouse oocytes. Nat Commun 13 4440. (https:\/\/doi.org\/10.1038\/s41467-022-32141-2)"},{"key":"bib68","series-title":"Bioinformatics","first-page":"2382","article-title":"ChIPseeker: an R\/Bioconductor package for ChIP peak annotation, comparison and visualization","volume":"31","author":"Yu G","year":"2015","unstructured":"Yu G, Wang LG & He QY 2015 ChIPseeker: an R\/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31 2382\u20132383. (https:\/\/doi.org\/10.1093\/bioinformatics\/btv145)"},{"key":"bib69","series-title":"Cell Discov","first-page":"13","article-title":"Human zygotic genome activation is initiated from paternal genome","volume":"9","author":"Yuan S","year":"2023","unstructured":"Yuan S, Zhan J, Zhang J, et al. 2023 Human zygotic genome activation is initiated from paternal genome. Cell Discov 9 13. (https:\/\/doi.org\/10.1038\/s41421-022-00494-z)"},{"key":"bib70","series-title":"Genome Biol","first-page":"R137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang Y","year":"2008","unstructured":"Zhang Y, Liu T, Meyer CA, et al. 2008 Model-based analysis of ChIP-Seq (MACS). Genome Biol 9 R137. (https:\/\/doi.org\/10.1186\/gb-2008-9-9-r137)"},{"key":"bib71","series-title":"Nature","first-page":"553","article-title":"Allelic reprogramming of the histone modification H3K4me3 in early mammalian development","volume":"537","author":"Zhang B","year":"2016","unstructured":"Zhang B, Zheng H, Huang B, et al. 2016 Allelic reprogramming of the histone modification H3K4me3 in early mammalian development. Nature 537 553\u2013557. (https:\/\/doi.org\/10.1038\/nature19361)"},{"key":"bib72","series-title":"Nat Commun","first-page":"1523","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou Y","year":"2019","unstructured":"Zhou Y, Zhou B, Pache L, et al. 2019 Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 10 1523. (https:\/\/doi.org\/10.1038\/s41467-019-09234-6)"},{"key":"bib73","series-title":"Sci Bull","first-page":"2489","article-title":"Genomewide decoupling of H2AK119ub1 and H3K27me3 in early mouse development","volume":"66","author":"Zhu Y","year":"2021","unstructured":"Zhu Y, Yu J, Rong Y, et al. 2021 Genomewide decoupling of H2AK119ub1 and H3K27me3 in early mouse development. Sci Bull 66 2489\u20132497. (https:\/\/doi.org\/10.1016\/j.scib.2021.06.010)"}],"container-title":["Reproduction"],"original-title":[],"link":[{"URL":"https:\/\/rep.bioscientifica.com\/view\/journals\/rep\/169\/1\/REP-24-0035.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/rep.bioscientifica.com\/downloadpdf\/journals\/rep\/169\/1\/REP-24-0035.xml","content-type":"text\/html","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/rep.bioscientifica.com\/downloadpdf\/journals\/rep\/169\/1\/REP-24-0035.xml","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,4]],"date-time":"2026-01-04T23:03:34Z","timestamp":1767567814000},"score":1,"resource":{"primary":{"URL":"https:\/\/rep.bioscientifica.com\/view\/journals\/rep\/169\/1\/REP-24-0035.xml"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,10,24]]},"references-count":74,"journal-issue":{"issue":"1"},"URL":"https:\/\/doi.org\/10.1530\/rep-24-0035","relation":{},"ISSN":["1470-1626","1741-7899"],"issn-type":[{"type":"print","value":"1470-1626"},{"type":"electronic","value":"1741-7899"}],"subject":[],"published":{"date-parts":[[2024,10,24]]}}}