Eichten Steven R, Stuart Tim, Srivastava Akanksha, Lister Ryan, Borevitz Justin O
ARC Centre of Excellence in Plant Energy Biology, The Australian National University, Canberra, Australia, 2601.
ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Perth, Australia, 6009.
Genome Res. 2016 Nov;26(11):1520-1531. doi: 10.1101/gr.205468.116. Epub 2016 Sep 9.
DNA methylation, a common modification of genomic DNA, is known to influence the expression of transposable elements as well as some genes. Although commonly viewed as an epigenetic mark, evidence has shown that underlying genetic variation, such as transposable element polymorphisms, often associate with differential DNA methylation states. To investigate the role of DNA methylation variation, transposable element polymorphism, and genomic diversity, whole-genome bisulfite sequencing was performed on genetically diverse lines of the model cereal Brachypodium distachyon Although DNA methylation profiles are broadly similar, thousands of differentially methylated regions are observed between lines. An analysis of novel transposable element indel variation highlighted hundreds of new polymorphisms not seen in the reference sequence. DNA methylation and transposable element variation is correlated with the genome-wide amount of genetic variation present between samples. However, there was minimal evidence that novel transposon insertions or deletions are associated with nearby differential methylation. This study highlights unique relationships between genetic variation and DNA methylation variation within Brachypodium and provides a valuable map of DNA methylation across diverse resequenced accessions of this model cereal species.
DNA甲基化是基因组DNA的一种常见修饰，已知其会影响转座元件以及一些基因的表达。尽管通常被视为一种表观遗传标记，但有证据表明，潜在的遗传变异，如转座元件多态性，常常与不同的DNA甲基化状态相关。为了研究DNA甲基化变异、转座元件多态性和基因组多样性的作用，对模式禾本科植物二穗短柄草的不同遗传品系进行了全基因组亚硫酸氢盐测序。尽管DNA甲基化图谱大致相似，但品系间观察到了数千个差异甲基化区域。对新型转座元件插入缺失变异的分析突出了数百个在参考序列中未出现的新多态性。DNA甲基化和转座元件变异与样本间全基因组的遗传变异量相关。然而，几乎没有证据表明新型转座子插入或缺失与附近的差异甲基化有关。这项研究突出了二穗短柄草内遗传变异与DNA甲基化变异之间的独特关系，并提供了该模式禾本科物种不同重测序种质的宝贵DNA甲基化图谱。
