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PMID: 31391587 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.

Nature ·Vol. 572 ·No. 7770 ·2019-00-00 ·Pages 543-548

Guo YE, Manteiga JC, Henninger JE, Sabari BR, Dall'Agnese A, Hannett NM, Spille JH, Afeyan LK, Zamudio AV, Shrinivas K, Abraham BJ, Boija A, Decker TM, Rimel JK, Fant CB, Lee TI, Cisse II, Sharp PA, Taatjes DJ, Young RA

Abstract

The synthesis of pre-mRNA by RNA polymerase II (Pol II) involves the formation of a transcription initiation complex, and a transition to an elongation complex1-4. The large subunit of Pol II contains an intrinsically disordered C-terminal domain that is phosphorylated by cyclin-dependent kinases during the transition from initiation to elongation, thus influencing the interaction of the C-terminal domain with different components of the initiation or the RNA-splicing apparatus5,6. Recent observations suggest that this model provides only a partial picture of the effects of phosphorylation of the C-terminal domain7-12. Both the transcription-initiation machinery and the splicing machinery can form phase-separated condensates that contain large numbers of component molecules: hundreds of molecules of Pol II and mediator are concentrated in condensates at super-enhancers7,8, and large numbers of splicing factors are concentrated in nuclear speckles, some of which occur at highly active transcription sites9-12. Here we investigate whether the phosphorylation of the Pol II C-terminal domain regulates the incorporation of Pol II into phase-separated condensates that are associated with transcription initiation and splicing. We find that the hypophosphorylated C-terminal domain of Pol II is incorporated into mediator condensates and that phosphorylation by regulatory cyclin-dependent kinases reduces this incorporation. We also find that the hyperphosphorylated C-terminal domain is preferentially incorporated into condensates that are formed by splicing factors. These results suggest that phosphorylation of the Pol II C-terminal domain drives an exchange from condensates that are involved in transcription initiation to those that are involved in RNA processing, and implicates phosphorylation as a mechanism that regulates condensate preference.

MeSH Terms
Animals Cell Line Enhancer Elements, Genetic/genetics Gene Expression Regulation/genetics Humans Mediator Complex/chemistry,genetics,metabolism Mice Phosphorylation Protein Domains RNA Polymerase II/chemistry,genetics,metabolism RNA Splicing RNA Splicing Factors/chemistry,genetics,metabolism Transcription, Genetic
Chemicals
Mediator Complex RNA Splicing Factors RNA Polymerase II
Authors & Affiliations
20 authors, click to expand affiliations / ORCID
Guo Yang Eric
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Manteiga John C
Whitehead Institute for Biomedical Research, Cambridge, MA, USA. | Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Henninger Jonathan E
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Sabari Benjamin R
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Dall'Agnese Alessandra
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Hannett Nancy M
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Spille Jan-Hendrik
Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA. | Department of Physics, University of Illinois at Chicago, Chicago, IL, USA.
Afeyan Lena K
Whitehead Institute for Biomedical Research, Cambridge, MA, USA. | Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Zamudio Alicia V
Whitehead Institute for Biomedical Research, Cambridge, MA, USA. | Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Shrinivas Krishna
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA. | Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
Abraham Brian J
Whitehead Institute for Biomedical Research, Cambridge, MA, USA. | Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA.
Boija Ann
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Decker Tim-Michael
Department of Biochemistry, University of Colorado, Boulder, CO, USA.
Rimel Jenna K
Department of Biochemistry, University of Colorado, Boulder, CO, USA.
Fant Charli B
Department of Biochemistry, University of Colorado, Boulder, CO, USA.
Lee Tong Ihn
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Cisse Ibrahim I
Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
Sharp Phillip A
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. | Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
Taatjes Dylan J
Department of Biochemistry, University of Colorado, Boulder, CO, USA.
Young Richard A
Whitehead Institute for Biomedical Research, Cambridge, MA, USA. young@wi.mit.edu. | Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. young@wi.mit.edu.
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Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
DOI
10.1038/s41586-019-1464-0
Email
young@wi.mit.edu
Published
2019-00-00
Epub
2019-00-07
Pages
543-548
Language
English
Region
England
NLM ID
0410462
PMCID
PMC6706314
Subset
IM
Grants
NIGMS NIH HHS · R01 GM034277 · United States
NIGMS NIH HHS · R01 GM123511 · United States
NIGMS NIH HHS · T32 GM007287 · United States
Corrections
CommentIn
PMID: 31734037
External Links
PubMed source DOI: 10.1038/s41586-019-1464-0 PMC Full Text View journal details
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