{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Santana JF"],"funding":["National Institute of General Medical Sciences","NIGMS NIH HHS"],"pagination":["2977-2994"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11014283"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["52(6)"],"pubmed_abstract":["Many factors control the elongation phase of transcription by RNA polymerase II (Pol II), a process that plays an essential role in regulating gene expression. We utilized cells expressing degradation tagged subunits of NELFB, PAF1 and RTF1 to probe the effects of depletion of the factors on nascent transcripts using PRO-Seq and on chromatin architecture using DFF-ChIP. Although NELF is involved in promoter proximal pausing, depletion of NELFB had only a minimal effect on the level of paused transcripts and almost no effect on control of productive elongation. Instead, NELF depletion increased the utilization of downstream transcription start sites and caused a dramatic, genome-wide loss of H3K4me3 marked nucleosomes. Depletion of PAF1 and RTF1 both had major effects on productive transcri"],"journal":["Nucleic acids research"],"pubmed_title":["NELF focuses sites of initiation and maintains promoter architecture."],"pmcid":["PMC11014283"],"funding_grant_id":["R01 GM121428","GM126908","GM121428","R35 GM126908"],"pubmed_authors":["Suarez GA","Luse DS","Price DH","Spector BM","Santana JF"],"additional_accession":[]},"is_claimable":false,"name":"NELF focuses sites of initiation and maintains promoter architecture.","description":"Many factors control the elongation phase of transcription by RNA polymerase II (Pol II), a process that plays an essential role in regulating gene expression. We utilized cells expressing degradation tagged subunits of NELFB, PAF1 and RTF1 to probe the effects of depletion of the factors on nascent transcripts using PRO-Seq and on chromatin architecture using DFF-ChIP. Although NELF is involved in promoter proximal pausing, depletion of NELFB had only a minimal effect on the level of paused transcripts and almost no effect on control of productive elongation. Instead, NELF depletion increased the utilization of downstream transcription start sites and caused a dramatic, genome-wide loss of H3K4me3 marked nucleosomes. Depletion of PAF1 and RTF1 both had major effects on productive transcri","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Apr","modification":"2025-04-26T20:05:27.264Z","creation":"2025-04-06T16:20:44.611Z"},"accession":"S-EPMC11014283","cross_references":{"pubmed":["38197272"],"doi":["10.1093/nar/gkad1253"]}}