Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition.
Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition.
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DOI：
10.1186/s12915-021-00985-7
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发表时间：
2021-03-09
期刊：
影响因子：
5.4
通讯作者：
Liu B
中科院分区：
文献类型：
--
作者：
Lv Z;Li Z;Wang M;Zhao F;Zhang W;Li C;Gong L;Zhang Y;Mason AS;Liu B
多倍体在植物和许多其他真核生物谱系的进化中起着突出的作用。然而，多倍体基因组如何通过基因组调控来适应两组或多组染色体的突然出现仍然知之甚少。本研究分析了多倍体小麦A和B亚基因组中与驯化和倍性转变相关的组蛋白修饰和基因表达谱。研究发现，A和B亚基因组中绝大多数同源三联体基因的常染色质组蛋白标记H3K4me3和H3K27me3的表观遗传修饰模式在野生小麦和驯化小麦四倍体之间高度保守，并在六倍体到提取四倍体再到再合成六倍体的倍性转变过程中保持稳定。然而，在四倍体和六倍体小麦驯化过程中，以及在倍性转变过程中，有一部分基因被不同地修饰，这些基因在特定的基因本体（GO）术语中被富集。提取的四倍体小麦总体组蛋白修饰水平高于其六倍体供体，并且在重新合成的六倍体中是可逆的并恢复到正常水平。此外，H3K4me3标记沿每条染色体远端分布，与预期的亚基因组表达显著相关，而H3K27me3标记仅表现出微弱的远端偏倚，与基因表达没有显著相关性。我们的研究结果揭示了多倍体小麦在驯化和倍性转变过程中A和B亚基因组组蛋白修饰模式的总体高稳定性。然而，在六倍体小麦中，a和B基因组中一些功能相关基因的修饰水平受到D基因组的反式调控。在线版本包含补充材料，可在10.1186/s12915-021-00985-7获得。
Polyploidy has played a prominent role in the evolution of plants and many other eukaryotic lineages. However, how polyploid genomes adapt to the abrupt presence of two or more sets of chromosomes via genome regulation remains poorly understood. Here, we analyzed genome-wide histone modification and gene expression profiles in relation to domestication and ploidy transition in the A and B subgenomes of polyploid wheat. We found that epigenetic modification patterns by two typical euchromatin histone markers, H3K4me3 and H3K27me3, for the great majority of homoeologous triad genes in A and B subgenomes were highly conserved between wild and domesticated tetraploid wheats and remained stable in the process of ploidy transitions from hexaploid to extracted tetraploid and then back to resynthesized hexaploid. However, a subset of genes was differentially modified during tetraploid and hexaploid wheat domestication and in response to ploidy transitions, and these genes were enriched for particular gene ontology (GO) terms. The extracted tetraploid wheat manifested higher overall histone modification levels than its hexaploid donor, and which were reversible and restored to normal levels in the resynthesized hexaploid. Further, while H3K4me3 marks were distally distributed along each chromosome and significantly correlated with subgenome expression as expected, H3K27me3 marks showed only a weak distal bias and did not show a significant correlation with gene expression. Our results reveal overall high stability of histone modification patterns in the A and B subgenomes of polyploid wheat during domestication and in the process of ploidy transitions. However, modification levels of a subset of functionally relevant genes in the A and B genomes were trans-regulated by the D genome in hexaploid wheat. The online version contains supplementary material available at 10.1186/s12915-021-00985-7.
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影响因子：
1.7
作者：
Feldman, M;Levy, AA
通讯作者：
Levy, AA
影响因子：
12.3
作者：
Gardiner LJ;Quinton-Tulloch M;Olohan L;Price J;Hall N;Hall A
通讯作者：
Hall A
影响因子：
13.8
作者：
He Z;Wang L;Harper AL;Havlickova L;Pradhan AK;Parkin IAP;Bancroft I
通讯作者：
Bancroft I
影响因子：
7
作者：
Gardiner LJ;Joynson R;Omony J;Rusholme-Pilcher R;Olohan L;Lang D;Bai C;Hawkesford M;Salt D;Spannagl M;Mayer KFX;Kenny J;Bevan M;Hall N;Hall A
通讯作者：
Hall A
影响因子：
48
作者：
Kim D;Langmead B;Salzberg SL
通讯作者：
Salzberg SL