Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution
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DOI：
10.1101/gr.844103
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发表时间：
2003-01-01
期刊：
影响因子：
7
通讯作者：
Haussler, D
中科院分区：
文献类型：
--
作者：
Hardison, RC;Roskin, KM;Haussler, D
研究了人类基因组中进化变化的六种度量，其中三种来自与小鼠基因组测序联盟联合比对的人类和小鼠基因组，包括（1）编码区中每个四倍简并位点的核苷酸取代，（2）仅在人类-小鼠物种形成之前活跃的转座因子遗迹中每个位点的核苷酸取代，和（3）人类DNA的非重复或祖先重复序列中的非对齐部分;以及三个单独来源于人类基因组数据的部分，包括（4）SNP密度，（5）转座因子插入频率，和（6）重组率。特征1和2是在两类“中性”位点处的核苷酸取代的量度，而4是最近突变的量度。特征3是小鼠中缺失占主导地位的量度，而5代表人类中的插入。结果发现，所有六种基因在全基因组的兆碱基大小的区域中存在显著差异，并且许多基因一起变化。这表明基因组的某些区域在所有改变DNA的过程中变化缓慢，而其他区域变化更快。所有过程中的区域变化与人体中的GC含量以及人和小鼠中GC含量之间的差异相关，但不能完全解释。
Six measures of evolutionary change in the human genome were studied, three derived from the aligned human and mouse genomes in conjunction with the Mouse Genome Sequencing Consortium, consisting of (1) nucleotide substitution per fourfold degenerate site in coding regions, (2) nucleotide substitution per site in relics of transposable elements active only before the human-mouse speciation, and (3) the nonaligning fraction of human DNA that is nonrepetitive or in ancestral repeats; and three derived from human genome data alone, consisting of (4) SNP density, (5) frequency of insertion of transposable elements, and (6) rate of recombination. Features 1 and 2 are measures of nucleotide substitutions at two classes of "neutral" sites, whereas 4 is a measure of recent mutations. Feature 3 is a measure dominated by deletions in mouse, whereas 5 represents insertions in human. It was found that all six vary significantly in megabase-sized regions genome-wide, and many vary together. This indicates that some regions of a genome change slowly by all processes that alter DNA, and others change faster. Regional variation in all processes is correlated with, but not completely accounted for, by GC content in human and the difference between GC content in human and mouse.