Unknown,Transcriptomics,Genomics,Proteomics

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The Dynamic Transcriptome of Schizosaccharomyces pombe Revealed by RNA/DNA Hybrid Mapping

ABSTRACT: We determined the strand-specific transcriptome of the fission yeast S. pombe under multiple growth conditions using a novel RNA/DNA hybridization mapping (HybMap) technique. HybMap uses an antibody against an RNA/DNA hybrid to detect RNA molecules hybridized to a high density DNA oligonucleotide tiling microarray. HybMap exhibited exceptional dynamic range and reproducibility, and clearly revealed coding, non-coding and structural RNAs, as well as new RNAs conserved in distant yeast species. Virtually the entire euchromatic genome (including intergenics) is transcribed, with heterochromatin dampening intergenic transcription. Transcriptomes of alternative growth conditions reveal changes in both coding and non-coding RNAs. Interestingly, our analysis reveals large numbers of non-coding RNAs, extensive antisense transcription, new properties of antisense transcripts, and induced divergent transcription. Furthermore, HybMap informed the efficiency and locations of RNA splicing genome-wide. Finally, a remarkable feature is observed at heterochromatin boundaries inside centromeres; strand-specific transcription islands around tRNAs. These new features are discussed in terms of organism fitness and transcriptome evolution. Keywords: yeast, gene expression, bioinformatics The dynamic transcriptome of S.pombe was determined using a whole genome tiling array hybridized to total RNA. Transcripts were detected using an antibody specific to RNA/DNA hybrids. This technique, called HybMap, was used across three different growth conditions (Heat shock, MMS treatment, and minimal media) in addtion to standard conditions. To further understand the transcriptome, we isolated PolyA RNA from S.pombe grown in standard conditions and used the HybMap method. Finally, the transcriptome was compared to Pol II, histone, and H3K36me3 ChIP occupancy. NOTE: Processed microarray data values listed in this repository represent only those probes that align to unique genomic positions. Probes that align to multiple genomic locations (reported in the Platform description) may not have values. Please refer to the web link above for a complete genomic data set.

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Timothy Parnell

PROVIDER: E-GEOD-11619 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping.

Dutrow Natalie N Nix David A DA Holt Derick D Milash Brett B Dalley Brian B Westbroek Erick E Parnell Timothy J TJ Cairns Bradley R BR

Nature genetics 20080720 8

We have determined the high-resolution strand-specific transcriptome of the fission yeast S. pombe under multiple growth conditions using a novel RNA-DNA hybridization mapping (HybMap) technique. HybMap uses an antibody against an RNA-DNA hybrid to detect RNA molecules hybridized to a high-density DNA oligonucleotide tiling microarray. HybMap showed exceptional dynamic range and reproducibility, and allowed us to identify strand-specific coding, noncoding and structural RNAs, as well as previous ...[more]

PMID: 18641648

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Dataset Information

The Dynamic Transcriptome of Schizosaccharomyces pombe Revealed by RNA/DNA Hybrid Mapping

Publications

Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping.

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