State Key Laboratory of Cotton Bio-breeding and Integrated, Chinese Academy of Agricultural Sciences, Institute of Cotton Research, Anyang 455000, China.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Agricultural Genomics Institute at Shenzhen, Shenzhen 518120, China.
Mol Biol Evol. 2024 May 3;41(5). doi: 10.1093/molbev/msae095.
Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings of duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern gene regulatory control. Here, we characterized genome-wide nucleosome organization and chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X = 52), relative to its two diploid parents (AA or DD genome) and their synthetic diploid hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average nucleosome spacing in diploids, and this intergenomic difference diminished in the allopolyploid but not hybrid. Allopolyploidization also exhibited increased accessibility at promoters genome-wide and synchronized cis-regulatory motifs between subgenomes. A prominent cis-acting control was inferred for chromatin dynamics and demonstrated by transposable element removal from promoters. Linking accessibility to gene expression patterns, we found distinct regulatory effects for hybridization and later allopolyploid stages, including nuanced establishment of homoeolog expression bias and expression level dominance. Histone gene expression and nucleosome organization are coordinated through chromatin accessibility. Our study demonstrates the capability to track high-resolution chromatin structure dynamics and reveals their role in the evolution of cis-regulatory landscapes and duplicate gene expression in polyploids, illuminating regulatory ties to subgenomic asymmetry and dominance.
多倍体是植物物种形成和适应的主要机制，但对重复基因调控的机制理解仍不清楚。染色质结构动力学被认为可以控制基因调控。在这里，我们使用 DNS-seq 技术，对异源四倍体棉花（Gossypium hirsutum，AADD，2n = 4X = 52）相对于其两个二倍体亲本（AA 或 DD 基因组）及其人工合成的二倍体杂种（AD）的全基因组核小体组织和染色质可及性进行了表征。较大的 A 基因组在二倍体中表现出更宽的平均核小体间距，这种种间差异在异源多倍体中减小，但在杂种中没有减小。异源多倍体化还表现出全基因组启动子处可及性的增加，以及亚基因组之间顺式调控基序的同步化。推断出染色质动力学的一个主要顺式作用控制，并通过从启动子中去除转座元件进行了证明。将可及性与基因表达模式联系起来，我们发现杂交和随后的异源多倍体阶段有明显的调控效应，包括同源基因表达偏倚和表达水平优势的细微建立。组蛋白基因表达和核小体组织通过染色质可及性进行协调。我们的研究表明了跟踪高分辨率染色质结构动力学的能力，并揭示了它们在顺式调控景观和多倍体中重复基因表达进化中的作用，阐明了与亚基因组不对称性和优势的调控联系。
