Genomic signatures of germline gene expression
Genomic signatures of germline gene expression
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DOI：
10.1101/gr.106666.110
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发表时间：
2010-11-01
期刊：
影响因子：
7
通讯作者：
Green, Phil
中科院分区：
文献类型：
--
作者：
McVicker, Graham;Green, Phil
人类基因组中的转录区域在转座元件密度、交叉率、不对称替换和序列组成模式方面与相邻的基因间区不同。我们使用各种生殖系和体细胞组织的公开基因表达数据，测试了这些差异是反映了选择，还是生殖系转录的副产品。在减数分裂组织中，互换速率与基因表达呈显著负相关，表明互换受转录抑制。链偏向成分(G+T含量)和A->；G与T->；C替换不对称均与生殖系基因表达呈正相关。我们在等位基因频率数据中没有发现链偏向的证据，这意味着替代不对称反映了突变而不是固定偏向。转座元件的密度与生殖系表达呈正相关，表明这些元件优先插入到活跃转录的区域。对于所考察的每个特征，我们的分析倾向于对观察到的趋势做出非选择性的解释，并指出生殖系基因表达在塑造哺乳动物基因组中的作用。[补充材料可在http://www.genome.org.]在线获得。
Transcribed regions in the human genome differ from adjacent intergenic regions in transposable element density, crossover rates, and asymmetric substitution and sequence composition patterns. We tested whether these differences reflect selection or are instead a byproduct of germline transcription, using publicly available gene expression data from a variety of germline and somatic tissues. Crossover rate shows a strong negative correlation with gene expression in meiotic tissues, suggesting that crossover is inhibited by transcription. Strand-biased composition (G+T content) and A -> G versus T -> C substitution asymmetry are both positively correlated with germline gene expression. We find no evidence for a strand bias in allele frequency data, implying that the substitution asymmetry reflects a mutation rather than a fixation bias. The density of transposable elements is positively correlated with germline expression, suggesting that such elements preferentially insert into regions that are actively transcribed. For each of the features examined, our analyses favor a nonselective explanation for the observed trends and point to the role of germline gene expression in shaping the mammalian genome.[Supplemental material is available online at http://www.genome.org.]