{"doi":"10.1093/pnasnexus/pgad062","title":"Relationship between lysine methyltransferase levels and heterochromatin gene repression in living cells and in silico","abstract":"Abstract Gene regulation plays essential roles in all multicellular organisms, allowing for different specialized tissue types to be generated from a complex genome. Heterochromatin-driven gene repression, associated with a physical compaction of the genome, is a pathway involving core components that are conserved from yeast to human. Posttranslational modification of chromatin is a critical component of gene regulation. Specifically, tri-methylation of the nucleosome component histone 3 at lysine 9 (H3K9me3) is a key feature of this pathway along with the hallmark heterochromatin protein 1 (HP1). Histone methyltransferases are recruited by HP1 to deposit H3K9me3 marks which nucleate and recruit more HP1 in a process that spreads from the targeting site to signal for gene repression. One of the enzymes recruited is SETDB1, a methyltransferase which putatively catalyzes posttranslational methylation marks on H3K9. To better understand the contribution of SETDB1 in heterochromatin formation, we downregulated SETDB1 through knockdown by a dCas9-KRAB system and examined heterochromatin formation in a chromatin in vivo assay (CiA-Oct4). We studied the contribution of SETDB1 to heterochromatin formation kinetics in a developmentally crucial locus, Oct4. Our data demonstrate that SETDB1 reduction led to a delay in both gene silencing and in H3K9me3 accumulation. Importantly, SETDB1 knockdown to a ∼50% level did not stop heterochromatin formation completely. Particle-based Monte Carlo simulations in 3D space with explicit representation of key molecular processes enabled the elucidation of how SETDB1 downregulation affects the individual molecular processes underlying heterochromatin formation.","journal":"PNAS Nexus","year":2023,"id":374378,"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":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9569,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":795225,"name":"Michael R. Williams","orcid":"0000-0003-3310-7181","position":1,"is_corresponding":false},{"id":1136357,"name":"Ameriks D Barboza Castillo","orcid":null,"position":2,"is_corresponding":false},{"id":36749,"name":"Dmitri Kireev","orcid":"0000-0001-8479-8555","position":3,"is_corresponding":false},{"id":266824,"name":"Nathaniel A. Hathaway","orcid":"0000-0002-9807-0167","position":4,"is_corresponding":false},{"id":269185,"name":"Xiaokang Yan","orcid":null,"position":0,"is_corresponding":true}],"reference_count":98,"raw_metadata":null,"created_at":"2026-07-19T01:16:11.341687Z","pmid":"37020498","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":[]}