Noncoding sequences near duplicated genes evolve rapidly.
Noncoding sequences near duplicated genes evolve rapidly.
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DOI：
10.1093/gbe/evq037
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发表时间：
2010
影响因子：
3.3
通讯作者：
Pollard KS
中科院分区：
文献类型：
--
作者：
Kostka D;Hahn MW;Pollard KS
基因表达差异和染色体重排被认为是近缘物种间表型差异的主要原因。还已经确定，重复基因在其氨基酸序列中显示出增强的正选择率。如果功能分化主要是由于基因表达的变化，那么重复基因座中的调控序列也应该迅速进化。为了研究这一假设，我们对人类基因组中每个转录本5 kb内的所有非编码基因座进行了似然比检验（LRT），并确定了自与旧世界猴分化以来人类谱系中取代率增加的序列。与非复制基因相比，在人类和黑猩猩共同祖先中复制的基因附近，快速进化基因座的比例显着较高。我们还进行了一个全基因组扫描预测影响转录因子结合的核苷酸取代。结合位点趋异率在重复基因座的非编码序列中升高，取代率加快。与这些快速进化的基因组元件相关的许多基因属于在先前的氨基酸序列正选择研究中鉴定的功能类别。此外，我们发现富集加速进化附近的基因参与建立和维持怀孕，过程中显着不同的人和猴子。我们的研究结果支持了这样一个假设，即重复基因调节的适应性进化在人类进化中发挥了重要作用。
Gene expression divergence and chromosomal rearrangements have been put forward as major contributors to phenotypic differences between closely related species. It has also been established that duplicated genes show enhanced rates of positive selection in their amino acid sequences. If functional divergence is largely due to changes in gene expression, it follows that regulatory sequences in duplicated loci should also evolve rapidly. To investigate this hypothesis, we performed likelihood ratio tests (LRTs) on all noncoding loci within 5 kb of every transcript in the human genome and identified sequences with increased substitution rates in the human lineage since divergence from Old World Monkeys. The fraction of rapidly evolving loci is significantly higher nearby genes that duplicated in the common ancestor of humans and chimps compared with nonduplicated genes. We also conducted a genome-wide scan for nucleotide substitutions predicted to affect transcription factor binding. Rates of binding site divergence are elevated in noncoding sequences of duplicated loci with accelerated substitution rates. Many of the genes associated with these fast-evolving genomic elements belong to functional categories identified in previous studies of positive selection on amino acid sequences. In addition, we find enrichment for accelerated evolution nearby genes involved in establishment and maintenance of pregnancy, processes that differ significantly between humans and monkeys. Our findings support the hypothesis that adaptive evolution of the regulation of duplicated genes has played a significant role in human evolution.
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影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
DOI：
10.1038/nrg2487
发表时间：
2009-01
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
3.7
作者：
Demuth JP;De Bie T;Stajich JE;Cristianini N;Hahn MW
通讯作者：
Hahn MW
影响因子：
30.8
作者：
Haygood, Ralph;Fedrigo, Olivier;Awray, Gregory
通讯作者：
Awray, Gregory
影响因子：
3.3
作者：
Hahn, Matthew W.;Demuth, Jeffery P.;Han, Sang-Gook
通讯作者：
Han, Sang-Gook