Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

Harlen, Kevin M.; Trotta, Kristine L.; Smith, Erin E.; Mosaheb, Mohammad M.; Fuchs, Stephen M.; Churchman, L. Stirling

doi:10.1016/j.celrep.2016.05.010

Cited by 153RNA Research and SplicingGenomics and Chromatin DynamicsNuclear Structure and Function

Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

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Harlen, Kevin M., Trotta, Kristine L., Smith, Erin E., Mosaheb, Mohammad M., Fuchs, Stephen M., Churchman, L. Stirling·2016·Cell Reports

DOI 10.1016/j.celrep.2016.05.010PMC PMC4966903

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Abstract

Transcription controls splicing and other gene regulatory processes, yet mechanisms remain obscure due to our fragmented knowledge of the molecular connections between the dynamically phosphorylated RNA polymerase II (Pol II) C-terminal domain (CTD) and regulatory factors. By systematically isolating phosphorylation states of the CTD heptapeptide repeat (Y1S2P3T4S5P6S7), we identify hundreds of protein factors that are differentially enriched, revealing unappreciated connections between the Pol II CTD and co-transcriptional processes. These data uncover a role for threonine-4 in 3' end processing through control of the transition between cleavage and termination. Furthermore, serine-5 phosphorylation seeds spliceosomal assembly immediately downstream of 3' splice sites through a direct interaction with spliceosomal subcomplex U1. Strikingly, threonine-4 phosphorylation also impacts splicing by serving as a mark of co-transcriptional spliceosome release and ensuring efficient post-transcriptional splicing genome-wide. Thus, comprehensive Pol II interactomes identify the complex and functional connections between transcription machinery and other gene regulatory complexes.

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PRO-seq and NET-seq confirmed a pause at the 3′ splice site in budding yeast and Drosophila, at the 3′ and 5′ splice sites in human cells, and at the 5′ splice site in plants.
“These methods also confirmed the existence of a pause at the 3′ splice site in budding yeast (Harlen et al, 2016) and Drosophila (Kwak et al, 2013), at the 3′ and 5′ splice sites in human cells (Mayer et al, 2015; Nojima et al, 2015) and at the 5′ splice site in plants (Kindgren et al, 2020).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Harlen et al, 2016

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Authors: Harlen, K. M., Trotta, K. L., Smith, E. E., Mosaheb, M. M., Fuchs, S. M., & Churchman, L. S.
Affiliations: Harvard University (US)
Tufts University (US)
Corresponding author: Churchman, L. Stirling
ORCID: Harlen, Kevin M.
Trotta, Kristine L.
Fuchs, Stephen M.
Churchman, L. Stirling
Venue: Cell Reports
Publisher: Elsevier BV
Published: 2016-06
Volume: 15
Issue: 10
Pages: 2147-2158
ISSN: 2211-1247 (ISSN-L)
DOI: 10.1016/j.celrep.2016.05.010
PMC: PMC4966903
OpenAlex: W2399619985
Cited by: 150
References: 50
Citations by year: 2026: 8 · 2025: 7 · 2024: 19 · 2023: 11 · 2022: 10 · 2021: 25 · 2020: 11 · 2019: 22 · 2018: 10 · 2017: 23 · 2016: 4
FWCI: 10.22
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc-nd
www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)
Locations: Cell Reports (publishedVersion, cc-by-nc-nd)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: U.S. National Institutes of Health NHGRI (R01HG007173)
Damon Runyon Dale F. Frey Award
Burroughs Wellcome Fund Career Award
U.S. National Science Foundation Graduate Research Fellowship (DGE1144152)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
Keywords: RNA polymerase II, C-terminal domain phosphorylation, protein-protein interaction network, 3' end processing, spliceosome assembly, U1 snRNP, co-transcriptional splicing, transcriptional regulation
MeSH terms: Protein Domains, Amino Acid Sequence, Amino Acids, Models, Genetic, Phosphorylation, RNA Polymerase II, RNA Splicing, Saccharomyces cerevisiae, Structure-Activity Relationship, Genome, Fungal, Spliceosomes, Proteomics, Protein Interaction Maps, Transcription Termination, Genetic

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Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

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