Strand‐specific, high‐resolution mapping of modified RNA polymerase II

• Published in: Molecular systems biology Vol. 12; no. 6; pp. 874 - n/a
• Main Authors: Milligan, Laura, Huynh‐Thu, Vân A, Delan‐Forino, Clémentine, Tuck, Alex, Petfalski, Elisabeth, Lombraña, Rodrigo, Sanguinetti, Guido, Kudla, Grzegorz, Tollervey, David
• Format: Journal Article Web Resource
• Language: English
• Published: London Nature Publishing Group UK 01.06.2016; EMBO Press; Wiley-Blackwell; John Wiley and Sons Inc; Springer Nature
• Subjects: Binding Sites; Datasets; Depletion; DNA-directed RNA polymerase; Elongation; EMBO09; EMBO22; EMBO44; Gene expression; Genes; Genetics & genetic processes; Genomes; Génétique & processus génétiques; hidden Markov model; Learning algorithms; Life Sciences; Machine Learning; Mapping; Markov Chains; Non-coding RNA; Nucleotides; Phosphorylation; Polyadenine; polymerase CTD phosphorylation; Proteins; Ribonucleic acid; RNA; RNA modification; RNA polymerase; RNA polymerase II; RNA Polymerase II - chemistry; RNA Polymerase II - metabolism; RNA processing; RNA, Fungal - metabolism; RNA, Messenger - metabolism; Saccharomyces cerevisiae - chemistry; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; Scholarships & fellowships; Sciences du vivant; Surveillance; Termination factors; Transcription; Transcription, Genetic; yeast; polymerase CTD phosphorylation; hidden Markov model; transcription; yeast
• ISSN: 1744-4292; 1744-4292
• DOI: 10.15252/msb.20166869

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. Synopsis A new technique for transcriptome‐wide mapping of RNAPII carrying the five types of CTD phosphorylation is presented. Distinct modification states associated with initiating, early and late elongating RNAPII are identified using a hidden Markov model. Multiple modified forms of RNAPII can be mapped with nucleotide resolution. Machine learning can be used to extract biological insights from these datasets. Initiating RNAPII is associated with a distinct, surveillance‐prone state. Unstable ncRNAs fail to exit this state, potentially linked to rapid degradation. Graphical Abstract A new technique for transcriptome‐wide mapping of RNAPII carrying the five types of CTD phosphorylation is presented. Distinct modification states associated with initiating, early and late elongating RNAPII are identified using a hidden Markov model.