Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.
Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.
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DOI：
10.1016/j.celrep.2015.04.023
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发表时间：
2015-05-19
期刊：
影响因子：
8.8
通讯作者：
Ulitsky I
中科院分区：
文献类型：
--
作者：
Hezroni H;Koppstein D;Schwartz MG;Avrutin A;Bartel DP;Ulitsky I
由于无法从基因组序列中预测长的非编码RNA，因此阻碍了比较基因组学在研究其生物学方面的应用。在这里，我们开发了使用RNA-seq数据来注释16种脊椎动物和海胆的转录组的方法，发现了数千个以前未注释的基因，其中大多数产生长插入非编码RNA（lincRNA）。虽然在每个物种中，>70%的lincRNA不能追溯到> 5000万年前分化的物种中的同源物，但数千种人类lincRNA在其他物种中具有类似表达模式的同源物。这些同源物共享嵌套在外显子结构中的短的、5′偏置的序列保守补丁，这些外显子结构已经被广泛地重新连接，部分地通过转座因子外显子化。因此，超过1000种人类lincRNA可能在哺乳动物中具有保守的功能，而在哺乳动物之外则有数百种，但这些功能只需要很短的特定序列，并且可以容忍基因结构的重大变化。
The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA-seq data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousands of previously unannotated genes, most of which produce long intervening noncoding RNAs (lincRNAs). Although in each species >70% of lincRNAs cannot be traced to homologs in species that diverged >50 million years ago, thousands of human lincRNAs have homologs with similar expression patterns in other species. These homologs share short, 5′-biased patches of sequence conservation nested in exonic architectures that have been extensively rewired, in part by transposable element exonization. Thus, over a thousand human lincRNAs are likely to have conserved functions in mammals, and hundreds beyond mammals, but those functions require only short patches of specific sequences and can tolerate major changes in gene architecture.