DNA Methylome and LncRNAome Analysis Provide Insights Into Mechanisms of Genome-Dosage Effects in Autotetraploid Cassava.
DNA Methylome and LncRNAome Analysis Provide Insights Into Mechanisms of Genome-Dosage Effects in Autotetraploid Cassava.
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DOI：
10.3389/fpls.2022.915056
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发表时间：
2022
影响因子：
5.6
通讯作者：
Yan, Huabing
中科院分区：
文献类型：
--
作者：
Xiao, Liang;Lu, Liuying;Zeng, Wendan;Shang, Xiaohong;Cao, Sheng;Yan, Huabing
关键词：
全基因组复制(WGD)增加了所有编码和非编码基因的剂量，但基因组剂量效应的分子含义仍然难以捉摸。在本研究中，我们构建了二倍体和人工产生的同源四倍体木薯(Manihotesculenta Crantz)的甲基组和IncRNA组的整合图谱。我们发现转座元件(TES)抑制了邻近蛋白编码基因(PCG)的表达水平，而TES则激活了邻近的长非编码RNA(LncRNAs)的表达。在同源四倍体木薯中，mCG和mCHH位点上DNA转座子的高甲基化可能是抑制邻近PCGs表达的有效途径，导致同源四倍体和二倍体木薯中大多数PCGs的表达水平相似。在同源四倍体中，MCHG和mCHH位点反转录转座子甲基化水平的降低有助于减少吉普赛相邻的长基因间非编码RNA的甲基化，潜在地保持了大部分lncRNAs的二倍体表达模式。总之，我们的研究强调了WGD诱导的DNA转座子和反转录转座子中的DNA甲基化变化可能分别是对所有编码基因和lncRNAs剂量的直接适应性反应。
Whole genome duplication (WGD) increases the dosage of all coding and non-coding genes, yet the molecular implications of genome-dosage effects remain elusive. In this study, we generated integrated maps of the methylomes and lncRNAomes for diploid and artificially generated autotetraploid cassava (Manihot esculenta Crantz). We found that transposable elements (TEs) suppressed adjacent protein coding gene (PCG)-expression levels, while TEs activated the expression of nearby long non-coding RNAs (lncRNAs) in the cassava genome. The hypermethylation of DNA transposons in mCG and mCHH sites may be an effective way to suppress the expression of nearby PCGs in autotetraploid cassava, resulting in similar expression levels for most of PCGs between autotetraploid and diploid cassava. In the autotetraploid, decreased methylation levels of retrotransposons at mCHG and mCHH sites contributed to reduced methylation of Gypsy-neighboring long intergenic non-coding RNAs, potentially preserving diploid-like expression patterns in the major of lncRNAs. Collectively, our study highlighted that WGD-induced DNA methylation variation in DNA transposons and retrotransposons may be as direct adaptive responses to dosage of all coding-genes and lncRNAs, respectively.
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影响因子：
4.5
作者：
Kapusta A;Kronenberg Z;Lynch VJ;Zhuo X;Ramsay L;Bourque G;Yandell M;Feschotte C
通讯作者：
Feschotte C
影响因子：
5.4
作者：
Fregene, MA;Suarez, M;Kresovich, S
通讯作者：
Kresovich, S
影响因子：
46.9
作者：
Bredeson, Jessen V.;Lyons, Jessica B.;Rokhsar, Daniel S.
通讯作者：
Rokhsar, Daniel S.
DOI：
10.1126/science.1224839
发表时间：
2012-09-14
期刊：
Science (New York, N.Y.)
影响因子：
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作者：
Ibarra CA;Feng X;Schoft VK;Hsieh TF;Uzawa R;Rodrigues JA;Zemach A;Chumak N;Machlicova A;Nishimura T;Rojas D;Fischer RL;Tamaru H;Zilberman D
通讯作者：
Zilberman D
DOI：
10.1038/nrg2719
发表时间：
2010-03
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
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