Strand-specific, high-resolution mapping of modified RNA polymerase II.
Reversible modification of the RNAPII C-terminal domain links transcription with RNA processing and surveillance activities. To better understand this, we mapped the location of RNAPII carrying the five types of CTD phosphorylation on the RNA transcript, providing strand-specific, nucleotide-resolution information, and we used a machine learning-based approach to define RNAPII states. This revealed enrichment of Ser5P, and depletion of Tyr1P, Ser2P, Thr4P, and Ser7P in the transcription start site (TSS) proximal ~150 nt of most genes, with depletion of all modifications close to the poly(A) site. The TSS region also showed elevated RNAPII relative to regions further 3', with high recruitment of RNA surveillance and termination factors, and correlated with the previously mapped 3' ends of short, unstable ncRNA transcripts. A hidden Markov model identified distinct modification states associated with initiating, early elongating and later elongating RNAPII. The initiation state was enriched near the TSS of protein-coding genes and persisted throughout exon 1 of intron-containing genes. Notably, unstable ncRNAs apparently failed to transition into the elongation states seen on protein-coding genes.
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
Laura
L
Milligan
School of Informatics, University of Edinburgh, Edinburgh, UK Department of Electrical Engineering and Computer Science, University of Liège, Liège, Belgium.
Vân A
VA
Huynh-Thu
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
Clémentine
C
Delan-Forino
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Cambridge, UK.
Alex
A
Tuck
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.
Elisabeth
E
Petfalski
MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.
Rodrigo
R
Lombraña
School of Informatics, University of Edinburgh, Edinburgh, UK d.tollervey@ed.ac.uk gkudla@gmail.com gsanguin@inf.ed.ac.uk.
Guido
G
Sanguinetti
MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK d.tollervey@ed.ac.uk gkudla@gmail.com gsanguin@inf.ed.ac.uk.
Grzegorz
0000-0002-7924-2744
G
Kudla
Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK d.tollervey@ed.ac.uk gkudla@gmail.com gsanguin@inf.ed.ac.uk.
David
0000-0003-2894-2772
D
Tollervey
D001665:Binding Sites; D000069550:Machine Learning; D008390:Markov Chains; D010766:Phosphorylation; D012319:RNA Polymerase II / Q000737:chemistry / Q000378:metabolism*; D012331:RNA, Fungal / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic
D012331:RNA, Fungal; D012333:RNA, Messenger; D029701:Saccharomyces cerevisiae Proteins; D012319:RNA Polymerase II
hidden Markov model; polymerase CTD phosphorylation; transcription; yeast