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The evolution of IncRNA repertoires and expression patterns in tetrapods

机译:四足动物中IncRNA库的演变和表达模式

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摘要

我们对“长非编码RNA”(IncRNAs)的演化史rn知之甚少,但这方面的信息可帮助了解它们的rn功能。为此,Henrik Kaessmann及同事发表了rn对l1种四足动物的全部IncRNA及表达模式所rn做的首次大规模演化研究。%Only a very small fraction of long noncoding RNAs (IncRNAs) are well characterized. The evolutionary history of IncRNAs can provide insights into their functionality, but the absence of IncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of IncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific IncRNAs and 2,500 highly conserved IncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that IncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most IncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous IncRNA and protein -coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for IncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.
机译:我们对“长非编码RNA”(IncRNAs)的演化史rn知之甚少,但这方面的信息可帮助了解它们的rn功能。为此,Henrik Kaessmann及同事发表了rn对l1种四足动物的全部IncRNA及表达模式所rn做的首次大规模演化研究。%Only a very small fraction of long noncoding RNAs (IncRNAs) are well characterized. The evolutionary history of IncRNAs can provide insights into their functionality, but the absence of IncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of IncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific IncRNAs and 2,500 highly conserved IncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that IncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most IncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous IncRNA and protein -coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for IncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.

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  • 来源
    《Nature》 |2014年第7485期|635-640a11|共7页
  • 作者单位

    Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland,Laboratory of Developmental Genomics, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland (A.N.) Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA, and Broad Institute, Cambridge, Massachusetts 02142, USA (M.S.);

    Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland,Laboratory of Developmental Genomics, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland (A.N.) Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA, and Broad Institute, Cambridge, Massachusetts 02142, USA (M.S.);

    Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;

    Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;

    The Robinson Institute, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia;

    Department of Systematic Zoology, Faculty of Agriculture and Horticulture, Humboldt University Berlin, 10099 Bertin, Germany;

    Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA;

    The Robinson Institute, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia;

    Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland;

  • 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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