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标题：Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora
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作者：Kim A. Steige ; Benjamin Laenen ; Johan Reimegård 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2017
卷号：114
期号：5
页码：1087-1092
DOI：10.1073/pnas.1612561114
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Understanding the causes of cis- regulatory variation is a long-standing aim in evolutionary biology. Although cis -regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis- regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis- regulatory variation in the outcrossing plant Capsella grandiflora . We first identified a set of 1,010 genes with common cis- regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis- regulatory variation ( i ) are under weaker purifying selection and ( ii ) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis- regulatory variation. Gene body methylation (gbM) was a major factor constraining cis- regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis- regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis- regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis- regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis- regulatory variation in a wide range of plant species.
关键词：allele-specific expression ; fitness effects ; purifying selection ; positive selection ; gene body methylation