{"doi":"10.1093/nar/gkaf740","title":"Direct histone proteoform profiling of the unannotated, endangered coral <i>Acropora cervicornis</i>","abstract":"Epigenetic modifications directly regulate the patterns of gene expression by altering DNA accessibility and chromatin structure. A knowledge gap is presented by the need to directly measure these modifications, especially for unannotated organisms with unknown primary histone sequences. In the present work, we developed and applied a novel workflow for identifying and annotating histone proteoforms directly from mass spectrometry-based measurements for the endangered Caribbean coral Acropora cervicornis. Combining high-accuracy de novo top-down and bottom-up analysis based on tandem liquid chromatography, trapped ion mobility spectrometry, non-ergodic electron-based fragmentation, and high-resolution mass spectrometry, near complete primary sequence (up to 99%) and over 86 post-translational modification annotations were obtained from pull-down histone fractions. In the absence of reliable genome annotations, H2A, H2B, and H4 histone sequences and the annotation of the post-translational modifications of the stressed A. cervicornis coral allow for a better understanding of chromatin remodeling and new strategies for targeting intervention and restoration of endangered reef corals.","journal":"Nucleic Acids Research","year":2025,"id":553739,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9548,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1451104,"name":"Sabrina Mansoor","orcid":null,"position":1,"is_corresponding":false},{"id":947162,"name":"Kévin Jeanne Dit Fouque","orcid":"0000-0002-2974-1350","position":2,"is_corresponding":false},{"id":1451105,"name":"Lilian Valadares Tose","orcid":null,"position":3,"is_corresponding":false},{"id":1450665,"name":"Javier A. Rodriguez‐Casariego","orcid":"0000-0001-9955-4721","position":4,"is_corresponding":false},{"id":1066738,"name":"Mariangela Kosmopoulou","orcid":"0000-0001-8454-5398","position":5,"is_corresponding":false},{"id":267559,"name":"Detlev Suckau","orcid":"0000-0002-1859-2492","position":6,"is_corresponding":false},{"id":583513,"name":"Francisca N. de Luna Vitorino","orcid":"0000-0001-8543-2299","position":7,"is_corresponding":false},{"id":74960,"name":"Benjamin A. Garcia","orcid":"0000-0003-3596-4750","position":8,"is_corresponding":false},{"id":1294052,"name":"José M. Eirín‐López","orcid":"0000-0002-8041-9770","position":9,"is_corresponding":false},{"id":334166,"name":"Francisco Fernandez‐Lima","orcid":"0000-0002-1283-4390","position":10,"is_corresponding":false},{"id":1451103,"name":"Cassandra N. Fuller","orcid":null,"position":0,"is_corresponding":true}],"reference_count":61,"raw_metadata":null,"created_at":"2026-07-19T02:54:45.872391Z","pmid":"40744498","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":[]}