TY - JOUR
T1 - Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast
AU - Booth, Gregory T.
AU - Parua, Pabitra K.
AU - Sansó, Miriam
AU - Fisher, Robert P.
AU - Lis, John T.
N1 - Funding Information:
Research reported in this publication was supported by NIH grant GM104291 to R.P.F. and GM25232 to J.T.L. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. We thank Cornell Genomics Facility for overseeing the sequencing of our libraries. We thank Chao Zhang (Department of Chemistry, University of Southern California), who originally advised us to make the N84T mutation for the generation of the mcs6as5 strain. We are grateful for valuable discussions with Charles Danko and Hojoong Kwak regarding transcription wave calling and other computational methods.
Publisher Copyright:
© 2018 The Author(s).
PY - 2018/12/1
Y1 - 2018/12/1
N2 - Post-translational modifications of the transcription elongation complex provide mechanisms to fine-tune gene expression, yet their specific impacts on RNA polymerase II regulation remain difficult to ascertain. Here, in Schizosaccharomyces pombe, we examine the role of Cdk9, and related Mcs6/Cdk7 and Lsk1/Cdk12 kinases, on transcription at base-pair resolution with Precision Run-On sequencing (PRO-seq). Within a minute of Cdk9 inhibition, phosphorylation of Pol II-associated factor, Spt5 is undetectable. The effects of Cdk9 inhibition are more severe than inhibition of Cdk7 and Cdk12, resulting in a shift of Pol II toward the transcription start site (TSS). A time course of Cdk9 inhibition reveals that early transcribing Pol II can escape promoter-proximal regions, but with a severely reduced elongation rate of only ~400 bp/min. Our results in fission yeast suggest the existence of a conserved global regulatory checkpoint that requires Cdk9 kinase activity.
AB - Post-translational modifications of the transcription elongation complex provide mechanisms to fine-tune gene expression, yet their specific impacts on RNA polymerase II regulation remain difficult to ascertain. Here, in Schizosaccharomyces pombe, we examine the role of Cdk9, and related Mcs6/Cdk7 and Lsk1/Cdk12 kinases, on transcription at base-pair resolution with Precision Run-On sequencing (PRO-seq). Within a minute of Cdk9 inhibition, phosphorylation of Pol II-associated factor, Spt5 is undetectable. The effects of Cdk9 inhibition are more severe than inhibition of Cdk7 and Cdk12, resulting in a shift of Pol II toward the transcription start site (TSS). A time course of Cdk9 inhibition reveals that early transcribing Pol II can escape promoter-proximal regions, but with a severely reduced elongation rate of only ~400 bp/min. Our results in fission yeast suggest the existence of a conserved global regulatory checkpoint that requires Cdk9 kinase activity.
UR - http://www.scopus.com/inward/record.url?scp=85041511518&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85041511518&partnerID=8YFLogxK
U2 - 10.1038/s41467-018-03006-4
DO - 10.1038/s41467-018-03006-4
M3 - Article
C2 - 29416031
AN - SCOPUS:85041511518
SN - 2041-1723
VL - 9
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 543
ER -