Max Planck Institute for Plant Breeding Research, Carl-von-Linné weg 10, 50829 Cologne, Germany.
Mol Biol Evol. 2012 Nov;29(11):3385-95. doi: 10.1093/molbev/mss146. Epub 2012 May 28.
Cis-regulatory DNA has been suspected to play a preeminent role in adaptive evolution, but understanding the role of cis-regulatory mutations in gene expression divergence first requires an accurate analysis of the functional differences associated with these regions. We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species Arabidopsis thaliana and A. lyrata with a whole-genome SNP (single nucleotide polymorphism) tiling array. We observed 2,205 genes showing ASE pattern in at least one tissue. Nearly 90% of genes displaying ASE preferentially expressed the allele of A. lyrata. Genome-wide comparison of sequence divergence revealed that genes displaying ASE had a higher ratio of nonsynonymous to synonymous substitutions in coding regions. We further observe that the epigenetic landscape of histone methylation in A. thaliana genome associate with ASE. The asymmetry in the direction of allele-specific expression suggests interspecific differences in the efficiency of gene silencing in F1 hybrids.
顺式调控 DNA 被怀疑在适应性进化中起着突出的作用，但要了解顺式调控突变在基因表达分歧中的作用，首先需要对这些区域相关的功能差异进行准确分析。我们利用全基因组 SNP（单核苷酸多态性）平铺阵列分析了在两个密切相关的物种拟南芥和 A. lyrata 之间产生的 F1 种间杂种的叶和花组织中的等位基因特异性表达（ASE）。我们观察到至少有一个组织中存在 2205 个表现出 ASE 模式的基因。近 90%表现出 ASE 的基因优先表达 A. lyrata 的等位基因。全基因组序列差异比较表明，表现出 ASE 的基因在编码区具有更高的非同义替换与同义替换比值。我们进一步观察到，组蛋白甲基化的表观遗传景观与 ASE 相关。等位基因特异性表达方向的不对称表明，F1 杂种中基因沉默的效率存在种间差异。
