Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response.
Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response.
复制标题
与干旱对比和盐度应激反应的水稻品种中与基因表达相关的不同DNA甲基化模式。
DOI：
10.1038/srep14922
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发表时间：
2015-10-09
影响因子：
4.6
通讯作者：
Jain M
中科院分区：
文献类型：
--
作者：
Garg R;Narayana Chevala V;Shankar R;Jain M
DNA甲基化是一种表观遗传机制，在基因调控中对环境条件的响应起着重要作用。在全基因组水平上理解DNA甲基化可以为深入了解非生物应激反应/适应的调控机制提供帮助。我们通过对全基因组亚硫酸盐测序和RNA测序的综合分析，报道了三个水稻品种(IR64，胁迫敏感；Nagina 22，耐旱；Pokkali，耐盐)的DNA甲基化模式及其对转录的影响。我们在水稻品种中发现了广泛的单碱基分辨的DNA甲基化，确定了每个位点的序列背景和甲基化程度。总体而言，三个水稻品种的甲基化水平存在显著差异。在不同品种中发现了大量差异甲基化区域，其中许多与非生物胁迫反应重要基因的差异表达有关。转座子相关的DMR被发现与邻近的蛋白编码基因(S)的转录丰度偶联。小RNA(SmRNA)丰度与高甲基化区域呈正相关。这些结果为了解DNA甲基化、基因表达和smRNA丰度之间的相互作用提供了深入的见解，并暗示了在水稻非生物胁迫适应中的作用。
DNA methylation is an epigenetic mechanism that play an important role in gene regulation in response to environmental conditions. The understanding of DNA methylation at the whole genome level can provide insights into the regulatory mechanisms underlying abiotic stress response/adaptation. We report DNA methylation patterns and their influence on transcription in three rice (Oryza sativa) cultivars (IR64, stress-sensitive; Nagina 22, drought-tolerant; Pokkali, salinity-tolerant) via an integrated analysis of whole genome bisulphite sequencing and RNA sequencing. We discovered extensive DNA methylation at single-base resolution in rice cultivars, identified the sequence context and extent of methylation at each site. Overall, methylation levels were significantly different in the three rice cultivars. Numerous differentially methylated regions (DMRs) among different cultivars were identified and many of which were associated with differential expression of genes important for abiotic stress response. Transposon-associated DMRs were found coupled to the transcript abundance of nearby protein-coding gene(s). Small RNA (smRNA) abundance was found to be positively correlated with hypermethylated regions. These results provide insights into interplay among DNA methylation, gene expression and smRNA abundance, and suggest a role in abiotic stress adaptation in rice.