A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.
A subset of conserved mammalian long non-coding RNAs are fossils of ancestral protein-coding genes.
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保守的哺乳动物长的非编码RNA的子集是祖先蛋白质编码基因的化石。
DOI：
10.1186/s13059-017-1293-0
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发表时间：
2017-08-30
期刊：
影响因子：
12.3
通讯作者：
Ulitsky I
中科院分区：
文献类型：
--
作者：
Hezroni H;Ben-Tov Perry R;Meir Z;Housman G;Lubelsky Y;Ulitsky I
只有一小部分人类长链非编码RNA（lncRNA）在哺乳动物外是保守的，但哺乳动物中新lncRNA诞生的基础事件在很大程度上仍然未知。一个潜在的来源是转化为lncRNA的蛋白质编码基因的残余物。我们系统地比较了脊椎动物中lncRNA和蛋白质编码基因座，并估计高达5%的保守哺乳动物lncRNA来自丢失的蛋白质编码基因。这些lncRNA具有特定的特征，例如更广泛的表达结构域，使它们与其他lncRNA区分开来。14个lncRNA与丢失的蛋白质编码基因的当代同源物的位点具有序列相似性。我们建议，选择作用于增强子序列是主要负责保留这些地区。作为保留在lncRNA中的来自蛋白质编码祖先的RNA元件的一个例子，我们详细描述了JPX lncRNA中的一个短翻译ORF，该ORF来自蛋白质编码基因中的上游ORF，并保留了其一些功能。我们估计约55个注释的保守人类lncRNA来自祖先蛋白质编码基因的部分，因此编码潜力的丧失是新lncRNA的不可忽视的来源。一些lncRNA从其蛋白质编码祖先遗传了影响转录和翻译的调控元件，并且这些元件可以影响这些lncRNA的表达宽度和功能。本文的在线版本（doi：10.1186/s13059-017-1293-0）包含补充材料，可供授权用户使用。
Only a small portion of human long non-coding RNAs (lncRNAs) appear to be conserved outside of mammals, but the events underlying the birth of new lncRNAs in mammals remain largely unknown. One potential source is remnants of protein-coding genes that transitioned into lncRNAs. We systematically compare lncRNA and protein-coding loci across vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are derived from lost protein-coding genes. These lncRNAs have specific characteristics, such as broader expression domains, that set them apart from other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the contemporary homologs of the lost protein-coding genes. We propose that selection acting on enhancer sequences is mostly responsible for retention of these regions. As an example of an RNA element from a protein-coding ancestor that was retained in the lncRNA, we describe in detail a short translated ORF in the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene and retains some of its functionality. We estimate that ~ 55 annotated conserved human lncRNAs are derived from parts of ancestral protein-coding genes, and loss of coding potential is thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory elements influencing transcription and translation from their protein-coding ancestors and those elements can influence the expression breadth and functionality of these lncRNAs. The online version of this article (doi:10.1186/s13059-017-1293-0) contains supplementary material, which is available to authorized users.
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