title: CDK9 inhibitors define elongation checkpoints at both ends of RNA polymerase II-transcribed genes.
abstract: Transcription through early-elongation checkpoints requires phosphorylation of negative transcription elongation factors (NTEFs) by the cyclin-dependent kinase (CDK) 9. Using CDK9 inhibitors and global run-on sequencing (GRO-seq), we have mapped CDK9 inhibitor-sensitive checkpoints genome wide in human cells. Our data indicate that early-elongation checkpoints are a general feature of RNA polymerase (pol) II-transcribed human genes and occur independently of polymerase stalling. Pol II that has negotiated the early-elongation checkpoint can elongate in the presence of inhibitors but, remarkably, terminates transcription prematurely close to the terminal polyadenylation (poly(A)) site. Our analysis has revealed an unexpected poly(A)-associated elongation checkpoint, which has major implications for the regulation of gene expression. Interestingly, the pattern of modification of the C-terminal domain of pol II terminated at this new checkpoint largely mirrors the pattern normally found downstream of the poly(A) site, thus suggesting common mechanisms of termination.
authors: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
authors: Clélia
authors: C
authors: Laitem
authors: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
authors: Justyna
authors: J
authors: Zaborowska
authors: 1] Sir William Dunn School of Pathology, University of Oxford, Oxford, UK. [2] Department of Biotechnology, International Islamic University Malaysia, Pahang, Malaysia.
authors: Nur F
authors: NF
authors: Isa
authors: Faculty of Science, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany.
authors: Johann
authors: J
authors: Kufs
authors: Computational Genomics Analysis and Training Programme, Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
authors: Martin
authors: 0000000151400002
authors: M
authors: Dienstbier
authors: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
authors: Shona
authors: S
authors: Murphy
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D042863:Cyclin-Dependent Kinase 9 / Q000037:antagonists & inhibitors* / Q000235:genetics / Q000378:metabolism; D024581:Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating) / Q000096:biosynthesis*; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D010441:Peptide Chain Elongation, Translational / Q000187:drug effects* / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D034622:RNA Interference; D012319:RNA Polymerase II; D034741:RNA, Small Interfering; D017422:Sequence Analysis, DNA; D014158:Transcription, Genetic / Q000187:drug effects*
chemical_list: D034741:RNA, Small Interfering; D024581:Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating); C467969:CDK9 protein, human; D042863:Cyclin-Dependent Kinase 9; D012319:RNA Polymerase II