Interpreting mammalian evolution using Fugu genome comparisons
Interpreting mammalian evolution using Fugu genome comparisons
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DOI：
10.1016/j.ygeno.2004.07.011
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发表时间：
2004-11-01
期刊：
影响因子：
4.4
通讯作者：
Loots, GG
中科院分区：
文献类型：
--
作者：
Ovcharenko, I;Stubbs, L;Loots, GG
最近，它已被证明，大量的进化保守的人，河豚非编码元件的功能作为组织特异性的转录增强子在体内，这表明远距离比较能够确定一个特定类别的调控元件。因此，我们假设，通过并列的人/河豚和人/小鼠的保护模式，我们可以定义保护标准，发现转录调控元件特定于哺乳动物。非编码人类/河豚进化保守元件（ECRs）和它们的人类/小鼠对应物的基因组规模比较揭示了人类/小鼠ECRs的共同特征（大于或等于350 bp长，大于或等于77%的同一性），其在鱼类中也是保守的。这个新定义的阈值识别90%的所有人类/河豚非编码ECR，而无需人类-河豚基因组比对的帮助，并提供了一个非常有效的过滤器，用于识别功能性人类/小鼠ECR。爱思唯尔公司出版
Recently, it has been shown that a significant number of evolutionarily conserved human-Fugu noncoding elements function as tissue-specific transcriptional enhancers in vivo, suggesting that distant comparisons are capable of identifying a particular class of regulatory elements. We therefore hypothesized that by juxtaposing human/Fugu and human/mouse conservation patterns we can define conservation criteria for discovering transcriptional regulatory elements specific to mammals. Genome-scale comparisons of noncoding human/Fugu evolutionary conserved elements (ECRs) and their humans/mouse counterparts revealed a particular signature common to human/mouse ECRs (greater than or equal to350 bp long, greater than or equal to77% identity) that are also conserved in fishes. This newly defined threshold identifies 90% of all human/Fugu noncoding ECRs without the assistance of human-Fugu genome alignments and provides a very efficient filter for identifying functional human/mouse ECRs. Published by Elsevier Inc.