The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants.
The evolution of CHROMOMETHYLASES and gene body DNA methylation in plants.
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DOI：
10.1186/s13059-017-1195-1
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发表时间：
2017-05-01
期刊：
影响因子：
12.3
通讯作者：
Schmitz RJ
中科院分区：
文献类型：
--
作者：
Bewick AJ;Niederhuth CE;Ji L;Rohr NA;Griffin PT;Leebens-Mack J;Schmitz RJ
基因体甲基化（gbM）的进化，其起源及其功能后果知之甚少。通过配对Viridiplantae中最大的转录组（>1000）和甲基化组（77），我们对gbM的进化及其与色甲基化酶（CMT）蛋白的关系提供了新的见解。CMT是绿色植物门中进化保守的DNA甲基转移酶。重复事件导致了现在所谓的CMT 1、2和3。CMT 1，2和3在真双子叶植物中的独立丢失，CMT 2和ZMET在单子叶植物和单子叶植物/鸭茅科植物中的独立丢失，拷贝数的变化和非中性进化表明该基因家族的重叠或流体功能进化。基因内的DNA甲基化是普遍存在的，并发现在所有主要的分类组Viridiplantae调查。在被子植物的姐妹物种中也发现了富含甲基化CG（mCG）的基因。与gbM相关的基因和DNA甲基化模式的比例仅限于具有功能性CMT 3或直系同源物的被子植物。然而，mCG富集基因在裸子植物火炬松共享一些相似性gbM基因在Amborella spanipoda。此外，裸子植物和蕨类植物共享与CMT 2和3密切相关的CMT同系物。因此，gbM对CMT的依赖性很可能扩展到所有被子植物，也可能扩展到裸子植物和蕨类植物。由此产生的基因家族的CMT成绩单，从最多样化的采样植物到目前为止，重新定义了我们的理解CMT的进化及其对DNA甲基化的进化后果。未来，同源和旁系同源CMT的功能测试将揭示表观基因组的新作用和后果。本文的在线版本（doi：10.1186/s13059-017-1195-1）包含补充材料，可供授权用户使用。
The evolution of gene body methylation (gbM), its origins, and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridiplantae, we provide novel insights into the evolution of gbM and its relationship to CHROMOMETHYLASE (CMT) proteins. CMTs are evolutionary conserved DNA methyltransferases in Viridiplantae. Duplication events gave rise to what are now referred to as CMT1, 2 and 3. Independent losses of CMT1, 2, and 3 in eudicots, CMT2 and ZMET in monocots and monocots/commelinids, variation in copy number, and non-neutral evolution suggests overlapping or fluid functional evolution of this gene family. DNA methylation within genes is widespread and is found in all major taxonomic groups of Viridiplantae investigated. Genes enriched with methylated CGs (mCG) were also identified in species sister to angiosperms. The proportion of genes and DNA methylation patterns associated with gbM are restricted to angiosperms with a functional CMT3 or ortholog. However, mCG-enriched genes in the gymnosperm Pinus taeda shared some similarities with gbM genes in Amborella trichopoda. Additionally, gymnosperms and ferns share a CMT homolog closely related to CMT2 and 3. Hence, the dependency of gbM on a CMT most likely extends to all angiosperms and possibly gymnosperms and ferns. The resulting gene family phylogeny of CMT transcripts from the most diverse sampling of plants to date redefines our understanding of CMT evolution and its evolutionary consequences on DNA methylation. Future, functional tests of homologous and paralogous CMTs will uncover novel roles and consequences to the epigenome. The online version of this article (doi:10.1186/s13059-017-1195-1) contains supplementary material, which is available to authorized users.