Do Alu repeats drive the evolution of the primate transcriptome?
Do Alu repeats drive the evolution of the primate transcriptome?
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DOI：
10.1186/gb-2008-9-2-r25
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发表时间：
2008
期刊：
影响因子：
12.3
通讯作者：
Hurst LD
中科院分区：
文献类型：
--
作者：
Urrutia AO;Ocaña LB;Hurst LD
Alu元素丰富的广泛表达的基因附近的最好的解释是他们的优先保护管家基因附近。 在人类基因组中的所有重复元件中，Alus在广泛组织中表达的基因附近富集是不寻常的。这导致了Alus可能通过提供CpG岛、修饰转录因子结合或改变染色质结构来修饰相邻基因的表达宽度的提议。在这里，我们考虑是否Alus增加了其附近基因的表达宽度。与修饰假说相反，我们发现那些一直具有广泛表达的基因在Alus中最丰富，而那些更有可能变得更广泛表达的基因富集程度较低。这一发现与Alus在广泛表达的基因附近积累但不影响其表达宽度的模型一致。此外，该模型与小鼠基因的表达宽度预测其人类直系同源物附近的Alu密度的发现一致。然而，发现Alus与转录谱分歧的一些替代措施有关，尽管关于Alus是否与低或高分歧基因相关的证据是矛盾的。如果Alu有任何影响，它不是通过提供CpG岛，因为它们在转录起始位点附近特别罕见。先前报道的Alu富集某些细胞功能的基因，被认为是Alus功能重要性的证据，似乎部分是与广泛表达的基因相关的副产品。Alu在广泛表达的基因附近的丰度更好地解释了它们在管家基因附近的优先保存，而不是对基因表达的修饰作用。
The abundance of Alu elements near broadly expressed genes is best explained by their preferential preservation near housekeeping genes. Of all repetitive elements in the human genome, Alus are unusual in being enriched near to genes that are expressed across a broad range of tissues. This has led to the proposal that Alus might be modifying the expression breadth of neighboring genes, possibly by providing CpG islands, modifying transcription factor binding, or altering chromatin structure. Here we consider whether Alus have increased expression breadth of genes in their vicinity. Contrary to the modification hypothesis, we find that those genes that have always had broad expression are richest in Alus, whereas those that are more likely to have become more broadly expressed have lower enrichment. This finding is consistent with a model in which Alus accumulate near broadly expressed genes but do not affect their expression breadth. Furthermore, this model is consistent with the finding that expression breadth of mouse genes predicts Alu density near their human orthologs. However, Alus were found to be related to some alternative measures of transcription profile divergence, although evidence is contradictory as to whether Alus associate with lowly or highly diverged genes. If Alu have any effect it is not by provision of CpG islands, because they are especially rare near to transcriptional start sites. Previously reported Alu enrichment for genes serving certain cellular functions, suggested to be evidence of functional importance of Alus, appears to be partly a byproduct of the association with broadly expressed genes. The abundance of Alu near broadly expressed genes is better explained by their preferential preservation near to housekeeping genes rather than by a modifying effect on expression of genes.
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