Retrocopy contributions to the evolution of the human genome.
Retrocopy contributions to the evolution of the human genome.
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DOI：
10.1186/1471-2164-9-466
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发表时间：
2008-10-08
期刊：
影响因子：
4.4
通讯作者：
Brosius J
中科院分区：
文献类型：
--
作者：
Baertsch R;Diekhans M;Kent WJ;Haussler D;Brosius J
通过点突变的进化是一个相对缓慢的过程，不太可能完全解释灵长类动物和其他哺乳动物之间的差异。相比之下，人类基因组的45%由反转录元素组成，其中许多是在灵长类谱系中插入的。逆转录mrna的一个子集（逆转录拷贝）在灵长类动物中表现出强烈的表达，通常产生功能性逆转录基因。为了鉴定和分析相对较新进化的逆转录基因，我们将所有人类mrna与人类基因组进行了BLASTZ比对，并获得了一组表明逆转录的特征。在主要出现在灵长类谱系的12,000多个假定的逆转录衍生基因中，726个具有转录表达的有力证据被详细检查。这些mRNA逆转录事件分为三类：1)34个逆转录和反义逆转录，增加了现有基因的潜在蛋白质编码空间和utr；II)插入新基因座的682个完整的反向复制副本；III)一组意想不到的13个逆转录，与其他类型的转置元件（sin, LINEs, LTRs），甚至未注释的序列结合，形成潜在的新基因，在灵长类动物之外没有同源物。除了在人类中存在外，一些候选基因在黑猩猩、猩猩和恒河猴中也有潜在的存活的orf，强调了它们的潜在功能。mrna衍生的逆转录以多种方式为基因的进化提供了原料，复制和修改现有基因的蛋白质编码区，并产生新的蛋白质编码空间或非蛋白质编码rna的潜力，通过框外，反向或先前的非蛋白质编码序列的意外贡献。
Evolution via point mutations is a relatively slow process and is unlikely to completely explain the differences between primates and other mammals. By contrast, 45% of the human genome is composed of retroposed elements, many of which were inserted in the primate lineage. A subset of retroposed mRNAs (retrocopies) shows strong evidence of expression in primates, often yielding functional retrogenes. To identify and analyze the relatively recently evolved retrogenes, we carried out BLASTZ alignments of all human mRNAs against the human genome and scored a set of features indicative of retroposition. Of over 12,000 putative retrocopy-derived genes that arose mainly in the primate lineage, 726 with strong evidence of transcript expression were examined in detail. These mRNA retroposition events fall into three categories: I) 34 retrocopies and antisense retrocopies that added potential protein coding space and UTRs to existing genes; II) 682 complete retrocopy duplications inserted into new loci; and III) an unexpected set of 13 retrocopies that contributed out-of-frame, or antisense sequences in combination with other types of transposed elements (SINEs, LINEs, LTRs), even unannotated sequence to form potentially novel genes with no homologs outside primates. In addition to their presence in human, several of the gene candidates also had potentially viable ORFs in chimpanzee, orangutan, and rhesus macaque, underscoring their potential of function. mRNA-derived retrocopies provide raw material for the evolution of genes in a wide variety of ways, duplicating and amending the protein coding region of existing genes as well as generating the potential for new protein coding space, or non-protein coding RNAs, by unexpected contributions out of frame, in reverse orientation, or from previously non-protein coding sequence.
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影响因子：
12.3
作者：
Bailey JA;Baertsch R;Kent WJ;Haussler D;Eichler EE
通讯作者：
Eichler EE
影响因子：
3.7
作者：
Chen, YT;Iseli, C;Jongeneel, CV
通讯作者：
Jongeneel, CV
影响因子：
3.9
作者：
Hayashi, Y;Sakata, H;Yomo, T
通讯作者：
Yomo, T
影响因子：
3.3
作者：
Begun, David J.;Lindfors, Heather A.;Jones, Corbin D.
通讯作者：
Jones, Corbin D.
影响因子：
56.9
作者：
Bailey, JA;Gu, ZP;Eichler, EE
通讯作者：
Eichler, EE