{"doi":"10.3390/biom14020176","title":"Mechanisms and Functions of the RNA Polymerase II General Transcription Machinery during the Transcription Cycle","abstract":"<jats:p>Central to the development and survival of all organisms is the regulation of gene expression, which begins with the process of transcription catalyzed by RNA polymerases. During transcription of protein-coding genes, the general transcription factors (GTFs) work alongside RNA polymerase II (Pol II) to assemble the preinitiation complex at the transcription start site, open the promoter DNA, initiate synthesis of the nascent messenger RNA, transition to productive elongation, and ultimately terminate transcription. Through these different stages of transcription, Pol II is dynamically phosphorylated at the C-terminal tail of its largest subunit, serving as a control mechanism for Pol II elongation and a signaling/binding platform for co-transcriptional factors. The large number of core protein factors participating in the fundamental steps of transcription add dense layers of regulation that contribute to the complexity of temporal and spatial control of gene expression within any given cell type. The Pol II transcription system is highly conserved across different levels of eukaryotes; however, most of the information here will focus on the human Pol II system. This review walks through various stages of transcription, from preinitiation complex assembly to termination, highlighting the functions and mechanisms of the core machinery that participates in each stage.</jats:p>","journal":"Biomolecules","year":2024,"id":30862,"datarank":0.6373671939548113,"base_score":3.332204510175204,"endowment":3.332204510175204,"self_citation_contribution":0.49983067652628066,"citation_network_contribution":0.13753651742853068,"self_endowment_contribution":0.49983067652628066,"citer_contribution":0.13753651742853068,"corpus_percentile":null,"corpus_rank":null,"citation_count":27,"citer_count":24,"citers_with_citation_signal":11,"citers_with_endowment":11,"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":166727,"name":"James A. Goodrich","orcid":null,"position":1,"is_corresponding":false},{"id":166728,"name":"Jennifer F. Kugel","orcid":null,"position":2,"is_corresponding":false},{"id":166726,"name":"Stephen R. Archuleta","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":3.295836866004329,"endowment":3.295836866004329,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"38397413","pmcid":"PMC10886972","openalex_id":"https://openalex.org/W4391431841","authors":[],"funders":[{"funder_name":"National Science Foundation","grant_id":"MCB-2242824","title":null},{"funder_name":"National Science Foundation","grant_id":"2242824","title":"Investigating mechanisms of RNA polymerase II transcription and regulation using single molecule fluorescence"}],"total_grants":2,"fwci":5.374,"citation_percentile":0.96517879,"influential_citations":1,"citation_trend":[{"year":2024,"count":3},{"year":2025,"count":17},{"year":2026,"count":6}],"oa_status":"gold","license":"cc-by","oa_locations":[{"url":"https://www.mdpi.com/2218-273X/14/2/176/pdf?version=1706770448","host_type":"journal"},{"url":"https://www.mdpi.com/2218-273X/14/2/176/pdf?version=1706770448","host_type":"GOLD"},{"url":"https://www.mdpi.com/2218-273X/14/2/176/pdf?version=1706770448","host_type":"publisher"},{"url":"https://www.mdpi.com/2218-273X/14/2/176/pdf","host_type":"publisher"},{"url":"https://doi.org/10.3390/biom14020176","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/38397413","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10886972","host_type":"repository"},{"url":"https://doaj.org/article/01179dadc7a847efa3359af3dd82b128","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10886972/pdf/biomolecules-14-00176.pdf","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC10886972","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC10886972?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.3390/biom14020176","host_type":""}],"fields_of_study":["Genomics and Chromatin Dynamics","RNA Research and Splicing","RNA and protein synthesis mechanisms","Medicine","Biology","0301 basic medicine","0303 health sciences","03 medical and health sciences","Humans","RNA Polymerase II","Transcription, Genetic","Transcription Factors","Promoter Regions, Genetic","RNA, Messenger"],"mesh_terms":["Humans","Promoter Regions, Genetic","RNA Polymerase II","RNA, Messenger","Transcription Factors","Transcription, Genetic"],"keywords":["Transcription factor II F","Transcription factor II E","RNA polymerase II","General transcription factor","Transcription factor II D","Transcription preinitiation complex","RNA polymerase II holoenzyme","Transcription factor II A","Biology","Transcription (linguistics)","Eukaryotic transcription","Transcription factor II B","Cell biology","Promoter","Genetics","Gene expression","Gene","Transcription","Preinitiation Complex","Rna Polymerase Ii (Pol Ii)","General Transcription Factors (Gtfs)","Transcription, Genetic","Review","Microbiology","QR1-502","Humans","RNA, Messenger","Promoter Regions, Genetic","Transcription Factors"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-09T05:46:19.874097Z","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":[]}