Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation
Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation
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DOI：
10.1016/j.gene.2014.08.052
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发表时间：
2014-11-10
期刊：
影响因子：
3.5
通讯作者：
Mishra, Rakesh Kumar
中科院分区：
文献类型：
--
作者：
Ramamoorthy, Senthilkumar;Garapati, Hita Sony;Mishra, Rakesh Kumar
简单序列重复 (SSR) 或微卫星是串联重复的短 DNA 序列基序，被发现在高等真核生物中含量丰富。随着基因组复杂性的增加，SSR 的富集表明了正选择及其功能相关性。我们分析了 24 种生物体的基因组，以寻找可能有助于理解 SSR 功能相关性的特征。在 501 个可能的 SSR 中，只有 73 个显示出长度特异性富集。我们还注意到，对于大多数人来说，尤其是在人类基因组中，最佳长度与 45 bp 类似。最后，我们观察到 ACG 和 CCG 的非随机分布，在几个物种的转录起始位点 (TSS) 周围富集。综上所述，这些结果表明 SSR 在功能上与潜在的监管作用相关。我们认为，像基因组中的任何其他功能元件一样，此类重复是在正选择压力下进化的。 (C) 2014 Elsevier B.V. 保留所有权利。
Simple sequence repeats (SSRs) or microsatellites are tandemly repeated short DNA sequence motifs found to be abundant in higher eukaryotes. Enrichment of SSRs with increasing genome complexity points to a positive selection and their functional relevance. We analyzed genomes of 24 organisms to find features that may help understand the functional relevance of SSRs. Of the 501 possible SSRs, only 73 show length specific enrichment. We also noticed that similar to 45 bp is the optimum length for a majority of them particularly in the human genome. Finally, we observed non-random distribution of ACG and CCG, enriched around transcriptional start sites (TSSs) in several species. Taken together, these results suggest that SSRs are functionally relevant with potential regulatory role. We propose that such repeats are evolving under positive selection pressure like any other functional element in the genome. (C) 2014 Elsevier B.V. All rights reserved.