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

机译：以单核苷酸分辨率调查的真核转录组的动态库

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摘要

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 polyadenyla-tion 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.
机译：来自几种生物的最新数据表明，基因组的转录部分比预期的更大，更复杂，并且转录本的许多功能特性并非基于编码序列，而是基于非翻译区域或非编码RNA中的调控序列。替代的起始和聚腺苷酸化位点以及内含子剪接的调控为丰富的转录输出增加了额外的尺寸。主要在一种或几种实验条件下使用基于杂交的方法对这种转录复杂性进行了采样。在这里，我们将补充性DNA（RNA-Seq）的直接高通量测序（补充来自高密度切片阵列的数据）应用于裂变酵母粟酒裂殖酵母的全球样本转录本，而与可用的基因注释无关。我们询问了多种条件下的转录组，包括快速增殖，减数分裂分化和环境胁迫，以及在RNA加工突变体中，揭示了转录环境的动态可塑性是环境，发育和遗传因素的函数。高通量测序被证明是一种以最大分辨率深度采样转录组的有效且定量的方法。与杂交相反，测序几乎没有背景噪音，并且足够灵敏，可以检测到超过90％的基因组中广泛的转录，包括痕量的RNA，这些RNA未被有效转录或迅速降解。组合的测序和链特异性阵列数据可提供有关新颖的，大多为非编码转录本，未翻译的区域和基因结构的丰富的条件特异性信息，从而改善了现有的基因组注释。跨外显子-外显子或外显子-内含子连接的序列读段提供了独特的洞察力，可了解跨内含子，基因和条件的剪接效率中令人惊讶的可变性。剪接效率在很大程度上与转录本水平协调，转录增加导致测试基因剪接增加。数百个内含子在细胞增殖或分化过程中显示出这种调控的剪接。

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  • 来源
    《Nature》 |2008年第7198期|1239-1243qt0003|共6页
  • 作者

    Brian T. Wilhelm; Samuel Marguerat; Stephen Watt; Falk Schubert; Valerie Wood; Ian Goodhead; Christopher J. Penkett; Jane Rogers; Juerg Baehler;

  • 作者单位

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK Institut de Recherche en Immunologie et en Cancerologie (IRIC), Montreal, H3C 3J7, Canada (B.T.W.) Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK (S.M., S.W., F.S. and J.B) School of Biological Sciences, University of Liverpool, L69 7ZB, UK (I.G.) EMBL-European Bioinformatics Institute, Hinxton, Cambridge, CB101SD, UK (C.J.P.);

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK Institut de Recherche en Immunologie et en Cancerologie (IRIC), Montreal, H3C 3J7, Canada (B.T.W.) Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK (S.M., S.W., F.S. and J.B) School of Biological Sciences, University of Liverpool, L69 7ZB, UK (I.G.) EMBL-European Bioinformatics Institute, Hinxton, Cambridge, CB101SD, UK (C.J.P.);

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK Institut de Recherche en Immunologie et en Cancerologie (IRIC), Montreal, H3C 3J7, Canada (B.T.W.) Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK (S.M., S.W., F.S. and J.B) School of Biological Sciences, University of Liverpool, L69 7ZB, UK (I.G.) EMBL-European Bioinformatics Institute, Hinxton, Cambridge, CB101SD, UK (C.J.P.);

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK Institut de Recherche en Immunologie et en Cancerologie (IRIC), Montreal, H3C 3J7, Canada (B.T.W.) Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK (S.M., S.W., F.S. and J.B) School of Biological Sciences, University of Liverpool, L69 7ZB, UK (I.G.) EMBL-European Bioinformatics Institute, Hinxton, Cambridge, CB101SD, UK (C.J.P.);

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK;

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK Institut de Recherche en Immunologie et en Cancerologie (IRIC), Montreal, H3C 3J7, Canada (B.T.W.) Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK (S.M., S.W., F.S. and J.B) School of Biological Sciences, University of Liverpool, L69 7ZB, UK (I.G.) EMBL-European Bioinformatics Institute, Hinxton, Cambridge, CB101SD, UK (C.J.P.);

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK Institut de Recherche en Immunologie et en Cancerologie (IRIC), Montreal, H3C 3J7, Canada (B.T.W.) Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK (S.M., S.W., F.S. and J.B) School of Biological Sciences, University of Liverpool, L69 7ZB, UK (I.G.) EMBL-European Bioinformatics Institute, Hinxton, Cambridge, CB101SD, UK (C.J.P.);

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK;

    Cancer Research UK Fission Yeast Functional Genomics Group, Wellcome Trust Sanger institute, Hinxton, Cambridge CB1O 1HH, UK Institut de Recherche en Immunologie et en Cancerologie (IRIC), Montreal, H3C 3J7, Canada (B.T.W.) Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK (S.M., S.W., F.S. and J.B) School of Biological Sciences, University of Liverpool, L69 7ZB, UK (I.G.) EMBL-European Bioinformatics Institute, Hinxton, Cambridge, CB101SD, UK (C.J.P.);

  • 收录信息 美国《科学引文索引》(SCI);美国《工程索引》(EI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
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