{"doi":"10.1101/2020.10.30.361865","title":"Global regulatory transitions at core promoters demarcate the mammalian germline cycle","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>\n                  Core promoters integrate regulatory inputs of genes\n                  <jats:sup>1–3</jats:sup>\n                  . Global dynamics of promoter usage can reveal systemic changes in how genomic sequence is interpreted by the cell\n                  <jats:sup>4</jats:sup>\n                  Here we report the first analysis of promoter dynamics and code switching in the mammalian germ line, characterising the full cycle of transitions from embryonic stem cells through germline, oogenesis, and zygotic genome activation. Using Super Low Input Carrier-CAGE\n                  <jats:sup>5,6</jats:sup>\n                  (SLIC-CAGE) we show that mouse germline development starts with the somatic promoter code, followed by a prominent switch to the maternal code during follicular oogenesis. The sequence features underlying the shift from somatic to maternal code are conserved across vertebrates, despite large differences in promoter nucleotide compositions. In addition, we show that, prior to this major shift, the promoters of gonadal germ cells diverge from the canonical somatic transcription initiation. This divergence is distinct from the promoter code used later by developing oocytes and reveals genome-wide promoter remodelling associated with alternative nucleosome positioning during early female and male germline development. Collectively, our findings establish promoter-level regulatory transitions as a central, conserved feature of the vertebrate life cycle.\n                </jats:p>","journal":null,"year":null,"id":635707,"datarank":0.3453877639491069,"base_score":2.302585092994046,"endowment":2.302585092994046,"self_citation_contribution":0.3453877639491069,"citation_network_contribution":0.0,"self_endowment_contribution":0.3453877639491069,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":9,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1649388,"name":"Malgorzata Borkowska","orcid":"0000-0002-8567-7218","position":1,"is_corresponding":false},{"id":1234817,"name":"Yuki Hatanaka","orcid":"0000-0003-3365-8506","position":2,"is_corresponding":false},{"id":828555,"name":"Changwei Yu","orcid":"0000-0002-0119-8616","position":3,"is_corresponding":false},{"id":715777,"name":"Stéphane D. Vincent","orcid":"0000-0003-1638-9615","position":4,"is_corresponding":false},{"id":551117,"name":"Ferenc Müller","orcid":"0000-0002-0996-774X","position":5,"is_corresponding":false},{"id":168650,"name":"Làszlò Tora","orcid":"0000-0001-7398-2250","position":6,"is_corresponding":false},{"id":893015,"name":"Harry G. Leitch","orcid":"0000-0002-3486-8962","position":7,"is_corresponding":false},{"id":257938,"name":"Petra Hájková","orcid":"0000-0003-4145-1468","position":8,"is_corresponding":false},{"id":11666,"name":"Boris Lenhard","orcid":"0000-0002-1114-1509","position":9,"is_corresponding":false},{"id":574902,"name":"Nevena Cvetešić","orcid":"0000-0002-1575-5612","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Global regulatory transitions at core promoters demarcate the mammalian germline cycle","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>\n                  Core promoters integrate regulatory inputs of genes\n                  <jats:sup>1–3</jats:sup>\n                  . Global dynamics of promoter usage can reveal systemic changes in how genomic sequence is interpreted by the cell\n                  <jats:sup>4</jats:sup>\n                  Here we report the first analysis of promoter dynamics and code switching in the mammalian germ line, characterising the full cycle of transitions from embryonic stem cells through germline, oogenesis, and zygotic genome activation. Using Super Low Input Carrier-CAGE\n                  <jats:sup>5,6</jats:sup>\n                  (SLIC-CAGE) we show that mouse germline development starts with the somatic promoter code, followed by a prominent switch to the maternal code during follicular oogenesis. The sequence features underlying the shift from somatic to maternal code are conserved across vertebrates, despite large differences in promoter nucleotide compositions. In addition, we show that, prior to this major shift, the promoters of gonadal germ cells diverge from the canonical somatic transcription initiation. This divergence is distinct from the promoter code used later by developing oocytes and reveals genome-wide promoter remodelling associated with alternative nucleosome positioning during early female and male germline development. Collectively, our findings establish promoter-level regulatory transitions as a central, conserved feature of the vertebrate life cycle.\n                </jats:p>","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19767382","pmcid":null,"openalex_id":null,"authors":[],"funders":[{"funder_name":"European Commission","grant_id":"648879","title":"Complexity and dynamics of nucleic acids modifications in vivo"},{"funder_name":"French National Research Agency (ANR)","grant_id":"ANR-10-IDEX-0002","title":null},{"funder_name":"European Commission","grant_id":"340551","title":"From birth to action: regulation of gene expression through transcription complex biogenesis"},{"funder_name":"Wellcome Trust","grant_id":"106954","title":"The core promoter: an unexplored regulatory level of transcription during vertebrate development."},{"funder_name":"Wellcome Trust","grant_id":"217309","title":"Deciphering germline-specific transcription initiation codes"}],"total_grants":5,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"green","license":"cc-by-nc-nd","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2020/11/20/2020.10.30.361865.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2020.10.30.361865","host_type":"publisher"},{"url":"https://doi.org/10.1101/2020.10.30.361865","host_type":""},{"url":"https://dx.doi.org/10.1101/2020.10.30.361865","host_type":""},{"url":"https://hal.science/hal-02990943v1","host_type":""},{"url":"https://hal.science/hal-02990943v1/document","host_type":""},{"url":"http://dx.doi.org/10.1101/2020.10.30.361865","host_type":""}],"fields_of_study":["0301 basic medicine","0303 health sciences","03 medical and health sciences"],"mesh_terms":[],"keywords":["[SDV] Life Sciences [q-bio]"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-06T15:28:46.738581Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}