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Nature:亲缘关系远的物种之间转录组的差异

摘要 : “modENCODE consortium”报告了对人类、蠕虫和果蝇的转录组数据所做的一项比较分析,揭示了一些古老的、保守的特征,如在发育基因中富集的共享的共表达模块。相关文章发表于2014年8月27日的《Nature》杂志上。

 Nature:亲缘关系远的物种之间转录组的差异

在这篇论文中,“modENCODE consortium”报告了对人类、蠕虫和果蝇的转录组数据所做的一项比较分析,揭示了一些古老的、保守的特征,如在发育基因中富集的共享的共表达模块。

表达模式被用来排列蠕虫和果蝇发育的不同阶段。所有三种生物的基因表达水平(包括编码基因和非编码基因)都可以利用一个模型、基于仅仅一组独立于生物的参数来从启动子上的染色质特征定量预测。

原文摘要:

Comparative analysis of the transcriptome across distant species

Mark B. Gerstein, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B. Brown, Carrie A. Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li, Baikang Pei, Arif O. Harmanci, Michael O. Duff, Sarah Djebali, Roger P. Alexander, Burak H. Alver, Raymond Auerbach, Kimberly Bell, Peter J. Bickel, Max E. Boeck, Nathan P. Boley, Benjamin W. Booth, Lucy Cherbas, Peter Cherbas, Chao Di et al.

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a ‘universal model’ based on a single set of organism-independent parameters.

对应none杂志: 2014年8月28日Nature杂志精选

来源: Nature 浏览次数:208

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