Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Export

@article{citeulike:2811350, abstract = {Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and that many functional properties of transcripts are based not on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs. Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output. This transcriptional complexity has been sampled mainly using hybridization-based methods under one or few experimental conditions. Here we applied direct high-throughput sequencing of complementary DNAs (RNA-Seq), supplemented with data from high-density tiling arrays, to globally sample transcripts of the fission yeast Schizosaccharomyces pombe, independently from available gene annotations. We interrogated transcriptomes under multiple conditions, including rapid proliferation, meiotic differentiation and environmental stress, as well as in RNA processing mutants to reveal the dynamic plasticity of the transcriptional landscape as a function of environmental, developmental and genetic factors. High-throughput sequencing proved to be a powerful and quantitative method to sample transcriptomes deeply at maximal resolution. In contrast to hybridization, sequencing showed little, if any, background noise and was sensitive enough to detect widespread transcription in >90\% of the genome, including traces of RNAs that were not robustly transcribed or rapidly degraded. The combined sequencing and strand-specific array data provide rich condition-specific information on novel, mostly non-coding transcripts, untranslated regions and gene structures, thus improving the existing genome annotation. Sequence reads spanning exon-exon or exon-intron junctions give unique insight into a surprising variability in splicing efficiency across introns, genes and conditions. Splicing efficiency was largely coordinated with transcript levels, and increased transcription led to increased splicing in test genes. Hundreds of introns showed such regulated splicing during cellular proliferation or differentiation.}, author = {Wilhelm, Brian T. and Marguerat, Samuel and Watt, Stephen and Schubert, Falk and Wood, Valerie and Goodhead, Ian and Penkett, Christopher J. and Rogers, Jane and B\"{a}hler, J\"{u}rg}, citeulike-article-id = {2811350}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature07002}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature07002}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18488015}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18488015}, day = {26}, doi = {10.1038/nature07002}, issn = {1476-4687}, journal = {Nature}, keywords = {array, cell, dna, exon, gene, genome, intron, pombe, rna, schizosaccharomyces, sequence, transcription, transcriptome, yeast}, month = {June}, number = {7199}, pages = {1239--1243}, posted-at = {2008-06-26 12:17:44}, priority = {2}, publisher = {Nature Publishing Group}, title = {Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.}, url = {http://dx.doi.org/10.1038/nature07002}, volume = {453}, year = {2008} }

TY - JOUR ID - citeulike:2811350 L3 - citeulike-article-id:2811350 N2 - Recent data from several organisms indicate that the transcribed portions of genomes are larger and more complex than expected, and that many functional properties of transcripts are based not on coding sequences but on regulatory sequences in untranslated regions or non-coding RNAs. Alternative start and polyadenylation sites and regulation of intron splicing add additional dimensions to the rich transcriptional output. This transcriptional complexity has been sampled mainly using hybridization-based methods under one or few experimental conditions. Here we applied direct high-throughput sequencing of complementary DNAs (RNA-Seq), supplemented with data from high-density tiling arrays, to globally sample transcripts of the fission yeast Schizosaccharomyces pombe, independently from available gene annotations. We interrogated transcriptomes under multiple conditions, including rapid proliferation, meiotic differentiation and environmental stress, as well as in RNA processing mutants to reveal the dynamic plasticity of the transcriptional landscape as a function of environmental, developmental and genetic factors. High-throughput sequencing proved to be a powerful and quantitative method to sample transcriptomes deeply at maximal resolution. In contrast to hybridization, sequencing showed little, if any, background noise and was sensitive enough to detect widespread transcription in >90% of the genome, including traces of RNAs that were not robustly transcribed or rapidly degraded. The combined sequencing and strand-specific array data provide rich condition-specific information on novel, mostly non-coding transcripts, untranslated regions and gene structures, thus improving the existing genome annotation. Sequence reads spanning exon-exon or exon-intron junctions give unique insight into a surprising variability in splicing efficiency across introns, genes and conditions. Splicing efficiency was largely coordinated with transcript levels, and increased transcription led to increased splicing in test genes. Hundreds of introns showed such regulated splicing during cellular proliferation or differentiation. IS - 7199 JF - Nature SN - 1476-4687 EP - 1243 TI - Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. PB - Nature Publishing Group VL - 453 SP - 1239 KW - array KW - cell KW - dna KW - exon KW - gene KW - genome KW - intron KW - pombe KW - rna KW - schizosaccharomyces KW - sequence KW - transcription KW - transcriptome KW - yeast AU - Wilhelm, Brian AU - Marguerat, Samuel AU - Watt, Stephen AU - Schubert, Falk AU - Wood, Valerie AU - Goodhead, Ian AU - Penkett, Christopher AU - Rogers, Jane AU - Bähler, Jürg PY - 2008/06/26/ UR - http://dx.doi.org/10.1038/nature07002 ER -