title: Genetic and genomic analyses of RNA polymerase II-pausing factor in regulation of mammalian transcription and cell growth.
abstract: Many mammalian genes are occupied by paused RNA polymerase II (pol II) in the promoter-proximal region on both sides of the transcription start site. However, the impact of pol II pausing on gene expression and cell biology is not fully understood. In this study, we used a Cre-Lox system to conditionally knock out the b subunit of mouse negative elongation factor (Nelf-b), a key pol II-pausing factor, in mouse embryonic fibroblasts. We found that Nelf-b was associated with the promoter-proximal region of the majority of expressed genes, yet genetic ablation of Nelf-b only affected the steady-state mRNA levels of a small percentage of the Nelf-b-associated genes. Interestingly, Nelf-b deletion also increased levels of transcription start site upstream transcripts at multiple negative elongation factor-associated genes. The direct target genes of Nelf-b were highly enriched with those involved in the control of cell growth and cell death. Correspondingly, Nelf-b knock-out mouse embryonic fibroblasts exhibited slower progression from quiescence to proliferation, as well as in a cycling cell population. Furthermore, Nelf-b deletion also resulted in increased apoptosis. Thus, the genetic and genomic studies provide new physiological and molecular insight into Nelf-mediated pol II pausing.
authors.affiliation: Department of Molecular Medicine/Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78245, USA.
authors.forename: Jianlong
authors.initials: J
authors.lastname: Sun
authors.forename: Haihui
authors.initials: H
authors.lastname: Pan
authors.forename: Chengwei
authors.initials: C
authors.lastname: Lei
authors.forename: Bin
authors.initials: B
authors.lastname: Yuan
authors.forename: Sreejith J
authors.initials: SJ
authors.lastname: Nair
authors.forename: Craig
authors.initials: C
authors.lastname: April
authors.forename: Balaji
authors.initials: B
authors.lastname: Parameswaran
authors.forename: Brandy
authors.initials: B
authors.lastname: Klotzle
authors.forename: Jian-Bing
authors.initials: JB
authors.lastname: Fan
authors.forename: Jianhua
authors.initials: J
authors.lastname: Ruan
authors.forename: Rong
authors.initials: R
authors.lastname: Li
mesh_terms: D000818:Animals; D017209:Apoptosis / Q000235:genetics; D002460:Cell Line; D049109:Cell Proliferation; D004622:Embryo, Mammalian / Q000166:cytology / Q000378:metabolism*; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism*; D017353:Gene Deletion; D016678:Genome / Q000502:physiology; D051379:Mice; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics; D016601:RNA-Binding Proteins
chemical_list: C541978:Cobra1 protein, mouse; D009687:Nuclear Proteins; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D012319:RNA Polymerase II