PXD047023

PXD047023 is an original dataset announced via ProteomeXchange.

Title	Repression of pervasive transcription is the primary role of RNA polymerase II CTD serine 2 phosphorylation in fission yeast
Description	The RNA polymerase II carboxy-terminal domain (CTD) consists of conserved repeats of the consensus sequence Y1-S2-P3-T4-S5-P6-S7, which can be phosphorylated to influence distinct stages of the transcription cycle, including RNA processing. Although affinity purification coupled with mass spectrometry has defined CTD-associated proteins, phospho-dependent CTD interactions have remained largely elusive. Proximity-dependent biotinylation (PDB) provides an alternative approach to identify protein-protein associations in the native cellular environment. Here we present a PDB-based map of the fission yeast RNAPII CTD in live cells. The proteomic screen identified known CTD-associated proteins, but also captured new and unexpected CTD proximal proteins. We also used PDB to identify phospho-dependent CTD interactions by using a mutant in which Ser2 was replaced by alanine in every repeat of the fission yeast CTD. Surprisingly, CTD-mediated biotinylation of most 3’ end processing factors was not affected in the S2A mutant, consistent with RNA-seq and ChIP-seq analysis indicating that CTD Ser2 phosphorylation is not required for 3’ end processing and transcription termination. Conversely, we found that CTD Ser2 phosphorylation is critical for the association between RNAPII and the histone methyltransferase Set2 during transcription elongation. We show that loss of CTD Ser2 phosphorylation disables the Set2-Clr6(II) axis, resulting in a global increase in cryptic antisense transcription that correlates with elevated levels of histone acetylation in gene bodies. Our findings reveal that the fundamental role of CTD Ser2 phosphorylation is to establish a chromatin-based repressive state that prevents cryptic intragenic transcription initiation.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:38:12.861.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nouhou EL Moctar Haidara
SpeciesList	scientific name: Schizosaccharomyces pombe; NCBI TaxID: NCBITaxon:4896; scientific name: Schizosaccharomyces pombe strain SPY73 975 h+; NCBI TaxID: 881122;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-16 07:12:12	ID requested
1	2024-05-06 06:36:32	announced
⏵ 2	2024-10-22 06:38:13	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: TurboID, Set2, antiisense repression, CTD,RNA polymerase II

Francois Bachand
contact affiliation	RNA Group, Dept of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
contact email	f.bachand@usherbrooke.ca
lab head
Nouhou EL Moctar Haidara
contact affiliation	University of Sherbrooke
contact email	nouhou.el.moctar.haidara@usherbrooke.ca
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD047023
     1. Label: PRIDE project
     2. Name: Repression of pervasive transcription is the primary role of RNA polymerase II CTD serine 2 phosphorylation in fission yeast