{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T06:08:54Z","timestamp":1791266934177,"version":"4.1.0"},"reference-count":52,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T00:00:00Z","timestamp":1680134400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009609","name":"Hospital Infantil de M\u00e9xico Federico G\u00f3mez","doi-asserted-by":"publisher","award":["HIM\/2018\/079 SSA 1518 HIM 2021\/061"],"award-info":[{"award-number":["HIM\/2018\/079 SSA 1518 HIM 2021\/061"]}],"id":[{"id":"10.13039\/501100009609","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005739","name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","doi-asserted-by":"publisher","award":["IN225917"],"award-info":[{"award-number":["IN225917"]}],"id":[{"id":"10.13039\/501100005739","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013394","name":"Instituto Nacional de Medicina Gen\u00f3mica","doi-asserted-by":"publisher","award":["ID348"],"award-info":[{"award-number":["ID348"]}],"id":[{"id":"10.13039\/501100013394","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell Dev. Biol."],"abstract":"<jats:p>CTCF is an architectonic protein that organizes the genome inside the nucleus in almost all eukaryotic cells. There is evidence that CTCF plays a critical role during spermatogenesis as its depletion produces abnormal sperm and infertility. However, defects produced by its depletion throughout spermatogenesis have not been fully characterized. In this work, we performed single cell RNA sequencing in spermatogenic cells with and without CTCF. We uncovered defects in transcriptional programs that explain the severity of the damage in the produced sperm. In the early stages of spermatogenesis, transcriptional alterations are mild. As germ cells go through the specialization stage or spermiogenesis, transcriptional profiles become more altered. We found morphology defects in spermatids that support the alterations in their transcriptional profiles. Altogether, our study sheds light on the contribution of CTCF to the phenotype of male gametes and provides a fundamental description of its role at different stages of spermiogenesis.<\/jats:p>","DOI":"10.3389\/fcell.2023.1119514","type":"journal-article","created":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T05:00:40Z","timestamp":1680152440000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Spermiogenesis alterations in the absence of CTCF revealed by single cell RNA sequencing"],"prefix":"10.3389","volume":"11","author":[{"given":"Ulises","family":"Torres-Flores","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernanda","family":"D\u00edaz-Espinosa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tayde","family":"L\u00f3pez-Santaella","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosa","family":"Rebollar-Vega","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aar\u00f3n","family":"V\u00e1zquez-Jim\u00e9nez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ian J.","family":"Taylor","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosario","family":"Ortiz-Hern\u00e1ndez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga M.","family":"Echeverr\u00eda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gerardo H.","family":"V\u00e1zquez-Nin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mar\u00eda Concepci\u00f3n","family":"Gutierrez-Ruiz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inti Alberto","family":"De la Rosa-Vel\u00e1zquez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osbaldo","family":"Resendis-Antonio","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abrahan","family":"Hern\u00e1ndez-Hernandez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,3,30]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"dev137729","DOI":"10.1242\/dev.137729","article-title":"Developing in 3D: The role of CTCF in cell differentiation","volume":"145","author":"Arzate-Mej\u00eda","year":"2018","journal-title":"Development"},{"key":"B2","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/s13059-016-0927-y","article-title":"Design and computational analysis of single-cell RNA-sequencing experiments","volume":"17","author":"Bacher","year":"2016","journal-title":"Genome Biol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"e127807","DOI":"10.1172\/jci.insight.127807","article-title":"Early alterations in stem-like\/marrow-resident T cells and innate and myeloid cells in preneoplastic gammopathy","volume":"4","author":"Bailur","year":"2019","journal-title":"JCI Insight"},{"key":"B4","doi-asserted-by":"publisher","first-page":"173","DOI":"10.3389\/fcvm.2019.00173","article-title":"Single-cell RNA sequencing of the cardiovascular system: New looks for old diseases","volume":"6","author":"Chaudhry","year":"2019","journal-title":"Front. Cardiovasc Med."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1459","DOI":"10.1098\/rstb.2010.0024","article-title":"The biology of spermatogenesis: The past, present and future","volume":"365","author":"Cheng","year":"2010","journal-title":"Philos. Trans. R. Soc. Lond B Biol. Sci."},{"key":"B6","doi-asserted-by":"publisher","first-page":"56","DOI":"10.1002\/jemt.10317","article-title":"Expression of mammalian spermatozoal nucleoproteins","volume":"61","author":"Dadoune","year":"2003","journal-title":"Microsc. Res. Tech."},{"key":"B7","doi-asserted-by":"publisher","first-page":"12483","DOI":"10.1074\/jbc.M110.164574","article-title":"CTCF promotes muscle differentiation by modulating the activity of myogenic regulatory factors","volume":"286","author":"Delgado-Olgu\u00edn","year":"2011","journal-title":"J. Biol. Chem."},{"key":"B8","doi-asserted-by":"publisher","first-page":"1950","DOI":"10.1093\/gbe\/evw136","article-title":"Mitochondria, the cell cycle, and the origin of sex via a syncytial eukaryote common ancestor","volume":"8","author":"Garg","year":"2016","journal-title":"Genome Biol. Evol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"e1006985","DOI":"10.1371\/journal.pgen.1006985","article-title":"CTCF counter-regulates cardiomyocyte development and maturation programs in the embryonic heart","volume":"13","author":"Gomez-Velazquez","year":"2017","journal-title":"PLOS Genet."},{"key":"B10","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1016\/j.devcel.2018.07.025","article-title":"A comprehensive roadmap of murine spermatogenesis defined by single-cell RNA-seq","volume":"46","author":"Green","year":"2018","journal-title":"Dev. Cell"},{"key":"B11","doi-asserted-by":"publisher","first-page":"17507","DOI":"10.1073\/pnas.1111941109","article-title":"The chromatin insulator CTCF and the emergence of metazoan diversity","volume":"109","author":"Heger","year":"2012","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1016\/j.celrep.2018.10.026","article-title":"The mammalian spermatogenesis single-cell transcriptome, from spermatogonial stem cells to spermatids","volume":"25","author":"Hermann","year":"2018","journal-title":"Cell Rep."},{"key":"B13","doi-asserted-by":"publisher","first-page":"28355","DOI":"10.1038\/srep28355","article-title":"CTCF contributes in a critical way to spermatogenesis and male fertility","volume":"6","author":"Hern\u00e1ndez-Hern\u00e1ndez","year":"2016","journal-title":"Sci. Rep."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/nar\/gkn923","article-title":"Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists","volume":"37","author":"Huang","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"B15","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc."},{"key":"B16","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.molcel.2019.04.014","article-title":"Maintenance of CTCF- and transcription factor-mediated interactions from the gametes to the early mouse embryo","volume":"75","author":"Jung","year":"2019","journal-title":"Mol. Cell"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1366","DOI":"10.1016\/j.celrep.2017.01.034","article-title":"Chromatin states in mouse sperm correlate with embryonic and adult regulatory landscapes","volume":"18","author":"Jung","year":"2017","journal-title":"Cell Rep."},{"key":"B18","doi-asserted-by":"publisher","first-page":"4628","DOI":"10.1091\/mbc.e03-04-0226","article-title":"Acroplaxome, an F-actin-keratin-containing plate, anchors the acrosome to the nucleus during shaping of the spermatid head","volume":"14","author":"Kierszenbaum","year":"2003","journal-title":"Mol. Biol. Cell"},{"key":"B19","doi-asserted-by":"publisher","first-page":"461954","DOI":"10.1101\/461954v2","article-title":"Fast, sensitive, and accurate integration of single cell data with Harmony [Internet]","volume":"14","author":"Korsunsky","year":"2018","journal-title":"bioRxiv"},{"key":"B20","doi-asserted-by":"publisher","first-page":"3012","DOI":"10.1093\/humrep\/det336","article-title":"A combined approach facilitates the reliable detection of human spermatogonia in vitro","volume":"28","author":"Kossack","year":"2013","journal-title":"Hum. Reprod."},{"key":"B21","doi-asserted-by":"publisher","first-page":"082511","DOI":"10.1101\/082511v1","article-title":"Gskb: A gene set database for pathway analysis in mouse","volume":"28","author":"Lai","year":"2016","journal-title":"bioRxiv"},{"key":"B22","doi-asserted-by":"publisher","first-page":"27575","DOI":"10.1074\/jbc.M313942200","article-title":"Regulation of eye development by transcription control of CCCTC binding factor (CTCF)","volume":"279","author":"Li","year":"2004","journal-title":"J. Biol. Chem."},{"key":"B23","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1038\/s41586-019-1910-z","article-title":"The structural basis for cohesin\u2013CTCF-anchored loops","volume":"578","author":"Li","year":"2020","journal-title":"Nature"},{"key":"B24","doi-asserted-by":"publisher","first-page":"6521","DOI":"10.1038\/s41598-018-24725-0","article-title":"Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencing","volume":"8","author":"Lukassen","year":"2018","journal-title":"Sci. Rep."},{"key":"B25","doi-asserted-by":"publisher","first-page":"101034","DOI":"10.1016\/j.isci.2020.101034","article-title":"Reorganized 3D genome structures support transcriptional regulation in mouse spermatogenesis","volume":"23","author":"Luo","year":"2020","journal-title":"iScience"},{"key":"B26","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1095\/biolreprod.109.078907","article-title":"Claudin 11 deficiency in mice results in loss of the Sertoli cell epithelial phenotype in the testis","volume":"82","author":"Mazaud-Guittot","year":"2010","journal-title":"Biol. Reprod."},{"key":"B27","doi-asserted-by":"publisher","first-page":"R9","DOI":"10.1530\/REP-18-0009","article-title":"Epigenetic reprogramming during spermatogenesis and male factor infertility","volume":"156","author":"McSwiggin","year":"2018","journal-title":"Reproduction"},{"key":"B28","doi-asserted-by":"publisher","first-page":"e34915","DOI":"10.1371\/journal.pone.0034915","article-title":"Loss of maternal CTCF is associated with peri-implantation lethality of Ctcf null embryos","volume":"7","author":"Moore","year":"2012","journal-title":"PLOS ONE"},{"key":"B29","doi-asserted-by":"publisher","first-page":"R988","DOI":"10.1016\/j.cub.2017.07.067","article-title":"spermatogenesis","volume":"27","author":"Nishimura","year":"2017","journal-title":"Curr. Biol."},{"key":"B30","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1038\/s10038-021-00989-9","article-title":"Data-driven comparison of multiple high-dimensional single-cell expression profiles","volume":"67","author":"Okada","year":"2022","journal-title":"J. Hum. Genet."},{"key":"B31","doi-asserted-by":"publisher","first-page":"5795","DOI":"10.1038\/ncomms6795","article-title":"MORC1 represses transposable elements in the mouse male germline","volume":"5","author":"Pastor","year":"2014","journal-title":"Nat. Commun."},{"key":"B32","doi-asserted-by":"publisher","first-page":"161","DOI":"10.1186\/s13059-015-0736-8","article-title":"Comparative analyses of CTCF and BORIS occupancies uncover two distinct classes of CTCF binding genomic regions","volume":"16","author":"Pugacheva","year":"2015","journal-title":"Genome Biol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"1089","DOI":"10.1126\/science.1063443","article-title":"Epigenetic reprogramming in mammalian development","volume":"293","author":"Reik","year":"2001","journal-title":"Science"},{"key":"B34","doi-asserted-by":"publisher","first-page":"3846","DOI":"10.1038\/s41467-021-24140-6","article-title":"The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis","volume":"12","author":"Rivero-Hinojosa","year":"2021","journal-title":"Nat. Commun."},{"key":"B35","doi-asserted-by":"publisher","first-page":"960","DOI":"10.1186\/s12864-018-5249-x","article-title":"ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data","volume":"19","author":"Romagnoli","year":"2018","journal-title":"BMC Genomics"},{"key":"B36","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Satija","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"B37","doi-asserted-by":"publisher","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"B38","doi-asserted-by":"publisher","first-page":"aab2006","DOI":"10.1126\/science.aab2006","article-title":"Disruption of histone methylation in developing sperm impairs offspring health transgenerationally","volume":"350","author":"Siklenka","year":"2015","journal-title":"Science"},{"key":"B39","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1530\/rep.1.00997","article-title":"Gene expression profiles of Spo11-\/- mouse testes with spermatocytes arrested in meiotic prophase I","volume":"132","author":"Smirnova","year":"2006","journal-title":"Reproduction"},{"key":"B40","doi-asserted-by":"publisher","first-page":"1399","DOI":"10.2217\/epi-2016-0056","article-title":"Establishment and functions of DNA methylation in the germline","volume":"8","author":"Stewart","year":"2016","journal-title":"Epigenomics"},{"key":"B41","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B42","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.3390\/genes13081383","article-title":"CTCF and its partners: Shaper of 3D genome during development","volume":"13","author":"Sun","year":"2022","journal-title":"Genes"},{"key":"B43","doi-asserted-by":"publisher","first-page":"2473","DOI":"10.1128\/MCB.01093-09","article-title":"Expression of a testis-specific form of Gal3st1 (CST), a gene essential for spermatogenesis, is regulated by the CTCF paralogous gene BORIS","volume":"30","author":"Suzuki","year":"2010","journal-title":"Mol. Cell. Biol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"e1006361","DOI":"10.1371\/journal.pcbi.1006361","article-title":"scPipe: A flexible R\/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data","volume":"14","author":"Tian","year":"2018","journal-title":"PLoS Comput. Biol."},{"key":"B45","doi-asserted-by":"publisher","first-page":"780","DOI":"10.3389\/fgene.2020.00780","article-title":"The interplay between replacement and retention of histones in the sperm genome","volume":"11","author":"Torres-Flores","year":"2020","journal-title":"Front. Genet."},{"key":"B46","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol."},{"key":"B47","doi-asserted-by":"publisher","first-page":"5868","DOI":"10.1038\/ncomms6868","article-title":"Paternal heterochromatin formation in human embryos is H3K9\/HP1 directed and primed by sperm-derived histone modifications","volume":"5","author":"van de Werken","year":"2014","journal-title":"Nat. Commun."},{"key":"B48","doi-asserted-by":"publisher","first-page":"3595","DOI":"10.1128\/MCB.26.9.3595-3609.2006","article-title":"Loss of TSLC1 causes male infertility due to a defect at the spermatid stage of spermatogenesis","volume":"26","author":"van der Weyden","year":"2006","journal-title":"Mol. Cell Biol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"2729","DOI":"10.1242\/dev.024539","article-title":"Maternal depletion of CTCF reveals multiple functions during oocyte and preimplantation embryo development","volume":"135","author":"Wan","year":"2008","journal-title":"Development"},{"key":"B50","doi-asserted-by":"publisher","first-page":"2860","DOI":"10.1523\/JNEUROSCI.3769-13.2014","article-title":"Dual effect of CTCF loss on neuroprogenitor differentiation and survival","volume":"34","author":"Watson","year":"2014","journal-title":"J. Neurosci."},{"key":"B51","doi-asserted-by":"publisher","first-page":"1465","DOI":"10.1098\/rstb.2009.0323","article-title":"Evolution and spermatogenesis","volume":"365","author":"White-Cooper","year":"2010","journal-title":"Philos. Trans. R. Soc. Lond B Biol. Sci."},{"key":"B52","doi-asserted-by":"publisher","first-page":"774","DOI":"10.1038\/s41467-020-14482-y","article-title":"Determining sequencing depth in a single-cell RNA-seq experiment","volume":"11","author":"Zhang","year":"2020","journal-title":"Nat. Commun."}],"container-title":["Frontiers in Cell and Developmental Biology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcell.2023.1119514\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,30]],"date-time":"2023-03-30T05:00:45Z","timestamp":1680152445000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcell.2023.1119514\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,30]]},"references-count":52,"alternative-id":["10.3389\/fcell.2023.1119514"],"URL":"https:\/\/doi.org\/10.3389\/fcell.2023.1119514","relation":{},"ISSN":["2296-634X"],"issn-type":[{"value":"2296-634X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,3,30]]},"article-number":"1119514"}}