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Measurement of Isoform Specific Turnover using sequencing (MIST-Seq) after transcriptional arrest in rpb1-1 strain of budding yeast

ABSTRACT: Transcriptional arrest is performed in the rpb1-1 strain grown at 24C in two independent biological replicates by raising the temperature instantly to 37C. Total RNA was collected at fixed time points after the arrest and sequenced using the 3' T-filling protocol as described by Wilkening et al 2013 to obtain accurate quantification of 3' isoforms. The decaying library size is corrected for the by reads mapping to the S.pombe spike-in control RNA. The decay rates are estimated on fitting a single parameter exponential decay curve after taking the technical reproducibility of low counts for every time point into account.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Charles Girardot

PROVIDER: E-MTAB-2123 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions.

Gupta Ishaan I Clauder-Münster Sandra S Klaus Bernd B Järvelin Aino I AI Aiyar Raeka S RS Benes Vladimir V Wilkening Stefan S Huber Wolfgang W Pelechano Vicent V Steinmetz Lars M LM

Molecular systems biology 20140225

Recent research has uncovered extensive variability in the boundaries of transcript isoforms, yet the functional consequences of this variation remain largely unexplored. Here, we systematically discriminate between the molecular phenotypes of overlapping coding and non-coding transcriptional events from each genic locus using a novel genome-wide, nucleotide-resolution technique to quantify the half-lives of 3' transcript isoforms in yeast. Our results reveal widespread differences in stability ...[more]

PMID: 24569168

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