title: Genome-wide analysis of KAP1, the 7SK snRNP complex, and RNA polymerase II.
abstract: The transition of RNA polymerase II (Pol II) from transcription initiation into productive elongation in eukaryotic cells is regulated by the P-TEFb kinase, which phosphorylates the C-terminal domain of paused Pol II at promoter-proximal regions. Our recent study found that P-TEFb (in an inhibited state bound to the 7SK snRNP complex) interacts with the KAP1/TRIM28 transcriptional regulator, and that KAP1 and the 7SK snRNP co-occupy most gene promoters containing paused Pol II. Here we provide a detailed experimental description and analysis of the ChIP-seq datasets that have been deposited into Gene Expression Omnibus (GEO): GS72622, so that independent groups can replicate and expand upon these findings. We propose these datasets would provide valuable information for researchers studying mechanisms of transcriptional regulation including Pol II pausing and pause release.
authors.affiliation: Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Ryan P
authors.initials: RP
authors.lastname: McNamara
authors.affiliation: Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Carlos
authors.initials: C
authors.lastname: Guzman
authors.affiliation: The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Reeder
authors.affiliation: Department of Microbiology, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
authors.forename: Iván
authors.initials: I
authors.lastname: D'Orso
keywords: Bp, base pairs; Cdk9, cyclin-dependent kinase 9; ChIP, chromatin immunoprecipitation; ChIP-seq; ChIP-seq, chromatin immunoprecipitation sequencing; CycT1, cyclin T1; GRO-seq, Global run on sequencing; Hexim1, hexamethylene bis-acetamide inducible protein 1; KAP1; KAP1, Kruppel-associated protein; KEC, KAP1-7SK snRNP early elongation complex; Larp7, La-related protein 7; MePCE, methyl phosphate capping enzyme; P-TEFb, positive transcription elongation factor b; P-TEFb/7SK snRNP; Pol II, RNA polymerase II; RNA polymerase II; TSS, transcription start site; Transcription elongation; qPCR, quantitative PCR; snRNP, small nuclear ribonucleoprotein