Project description:To address co-transcriptional pre-mRNA processing events, Saccharomyces nascent RNA was isolated by chromatin fractionation and analyzed on a genome-wide high density tiling microarray. Co-transcriptional splicing efficiencies were derived by determination of intronic relative to exonic sequence concentrations. Nascent RNA, mRNA and genomic DNA were isolated from wild-type Saccharomyces cells and analyzed on a genome-wide high-density tiling microarry (Saccharomyces Tiling 1.0R Array, Affymetrix). At least 3 independent biological replicates were analyzed (nascent RNA (nRNA): 3 replicates, mRNA: 3 replicates, genomic DNA (gDNA): 4 replicates).
Project description:To address co-transcriptional pre-mRNA processing events, Saccharomyces nascent RNA was isolated by chromatin fractionation and analyzed on a genome-wide high density tiling microarray. Co-transcriptional splicing efficiencies were derived by determination of intronic relative to exonic sequence concentrations.
Project description:We have developed a new genome-wide protocol for nascent transcription analysis at high resolution in the yeast Saccharomyces cerevisiae. This protocol is based in run-on labeling of nascent RNA with a biotinylated precursor. We call it BioGRO for biotin-based genomic run-on.
Project description:We combined the nuclear run-on (NRO) assay which labels and captures nascent transcripts with high throughput DNA sequencing to examine transcriptional activity in Saccharomyces cerevisiae. Examination of nascent transcripts and steady-state transcripts in exponentially growing and heat-shock treated yeast.
Project description:Genome wide mapping of RNA polymearase III binding sites in Saccharomyces cerevisiae under normal growth and nutrient starved condition using ChIP-seq. Chromatin Immuno-precipitation (ChIP) was performed for FLAG tagged version of pol III subunit RPC128 after crosslinking the log-phase cells with formaldehyde. MOCK and IP DNA was sequenced and coverage of pol III was calculated at each base of the genome.
Project description:We combined the nuclear run-on (NRO) assay which labels and captures nascent transcripts with high throughput DNA sequencing to examine transcriptional activity in Saccharomyces cerevisiae.
