Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions.
Phytophthora methylomes are modulated by 6mA methyltransferases and associated with adaptive genome regions.
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疫霉甲基化组由 6mA 甲基转移酶调节并与适应性基因组区域相关
DOI：
10.1186/s13059-018-1564-4
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发表时间：
2018-10-31
期刊：
影响因子：
12.3
通讯作者：
Dong S
中科院分区：
文献类型：
--
作者：
Chen H;Shu H;Wang L;Zhang F;Li X;Ochola SO;Mao F;Ma H;Ye W;Gu T;Jiang L;Wu Y;Wang Y;Kamoun S;Dong S
丝状真菌植物病原体基因组通常显示出一个二分结构，基因稀疏，重复丰富的隔间作为适应性进化的摇篮。这种双速基因组结构与全基因组DNA修饰相关的程度尚不清楚。我们表明，卵菌致病疫霉和大豆疫霉具有功能性腺嘌呤N6-甲基化（6 mA）甲基转移酶，调节模式的6 mA标记的基因组。与此相反，5-甲基胞嘧啶不能检测到这些物种。每个物种的甲基化DNA IP测序（MeDIP-seq）揭示6 mA在转录起始位点（TSS）周围耗尽，并且与低表达基因，特别是转座因子相关。占据基因稀疏区域的基因在两个基因组中都具有较高水平的6 mA，这可能暗示了适应性进化中的甲基化。来自致病疫霉和大豆疫霉的所有六种推定的腺嘌呤甲基转移酶（除了PsDAMT 2）均显示出稳健的酶活性。令人惊讶的是，大豆疫霉中的单敲除显著降低了体内6 mA水平，表明这三种酶不是完全冗余的。Psdamt 3突变体的MeDIP-seq揭示了基因间不均匀的6 mA甲基化减少，表明PsDAMT 3可能在TSS后偏好基因体甲基化。此外，转座因子如DNA因子在psdamt 3突变体中更活跃。大量基因，特别是来自适应性基因组区室的基因，差异表达。我们的研究结果提供的证据表明，6 mA修饰可能是疫霉基因组中的表观遗传标记，6 mA甲基化的复杂模式可能与这些重要植物病原体的适应性进化有关。
Filamentous plant pathogen genomes often display a bipartite architecture with gene-sparse, repeat-rich compartments serving as a cradle for adaptive evolution. The extent to which this two-speed genome architecture is associated with genome-wide DNA modifications is unknown. We show that the oomycetes Phytophthora infestans and Phytophthora sojae possess functional adenine N6-methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine could not be detected in these species. Methylated DNA IP sequencing (MeDIP-seq) of each species reveals 6mA is depleted around the transcription start sites (TSSs) and is associated with lowly expressed genes, particularly transposable elements. Genes occupying the gene-sparse regions have higher levels of 6mA in both genomes, possibly implicating the methylome in adaptive evolution. All six putative adenine methyltransferases from P. infestans and P. sojae, except PsDAMT2, display robust enzymatic activities. Surprisingly, single knockouts in P. sojae significantly reduce in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the psdamt3 mutant reveals uneven 6mA methylation reduction across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Furthermore, transposable elements such as DNA elements are more active in the psdamt3 mutant. A large number of genes, particularly those from the adaptive genomic compartment, are differentially expressed. Our findings provide evidence that 6mA modification is potentially an epigenetic mark in Phytophthora genomes, and complex patterns of 6mA methylation may be associated with adaptive evolution in these important plant pathogens.
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N6-甲基脱氧腺苷标记了衣原体中的主动转录起始位点。
影响因子：
64.5
作者：
Fu Y;Luo GZ;Chen K;Deng X;Yu M;Han D;Hao Z;Liu J;Lu X;Dore LC;Weng X;Ji Q;Mets L;He C
通讯作者：
He C
影响因子：
5.6
作者：
ARBER, W;DUSSOIX, D
通讯作者：
DUSSOIX, D
影响因子：
4
作者：
Dong, Suomeng;Raffaele, Sylvain;Kamoun, Sophien
通讯作者：
Kamoun, Sophien
影响因子：
64.5
作者：
Liu, Fange;Clark, Wesley;Luo, Guanzheng;Wang, Xiaoyun;Fu, Ye;Wei, Jiangbo;Wang, Xiao;Hao, Ziyang;Dai, Qing;Zheng, Guanqun;Ma, Honghui;Han, Dali;Evans, Molly;Klungland, Arne;Pan, Tao;He, Chuan
通讯作者：
He, Chuan
影响因子：
14.9
作者：
KOSSYKH, VG;SCHLAGMAN, SL;HATTMAN, S
通讯作者：
HATTMAN, S