Zea mays Epigenomics

Methylation of chromosomal DNA in animals and plants is a fundamental mechanism of epigenetic regulation, and the maize genome, with its diverse complement of transposons and repeats, is a paradigm for transgenerational mechanisms such as paramutation and imprinting. We have determined the genome-wide cytosine methylation map of two maize inbred lines, B73 and Mo17, at high coverage and at single nucleotide resolution. Transposon methylation is highest in CG (65%) and CHG (50%) contexts (where H = A, C or T), while methylation in CHH (5%) contexts is guided by 24nt small interfering RNA (siRNA), and not by 21-22nt siRNA. We have found that CG (8%) methylation seems to deter insertion of Mutator transposons into exons, while CHH and CHG methylation at splice donor and acceptor sites strongly inhibits RNA splicing. Methylation differences between parents are inherited in recombinant inbred lines, but methylation switches, guided by siRNA, are widespread and persist for up to 8 generations. These differences influence splicing, and recurrent switching suggest that paramutation is much more common than previously supposed, and may contribute to heterosis. Our results provide a comprehensive high resolution resource for maize genome methylation, as well as a map of recurrent transgenerational epigenetic shifts (paramutation) in the two most commonly used inbred maize lines. Overall design: Genome-wide cytosine methylation map in 2 maize strains by bisulfite sequencing, and RNA and small RNA profiles in the same tissue using Illumina platform.动植物染色体DNA的甲基化是表观遗传调控的核心机制之一；玉米基因组因富含转座子与重复序列，是副突变（paramutation）、基因组印记（imprinting）等跨代表观调控机制的经典研究范式。本研究以高覆盖度、单碱基分辨率绘制了两个玉米自交系B73与Mo17的全基因组胞嘧啶甲基化图谱。转座子的甲基化水平在CG（65%）与CHG（50%）序列语境中最高（其中H代表A、C或T），而CHH（5%）序列语境的甲基化则由24nt小干扰RNA（small interfering RNA, siRNA）介导，而非21-22nt siRNA。研究发现，CG位点（8%）的甲基化可抑制Mutator转座子插入外显子区域；而剪接供体与受体位点处的CHH与CHG甲基化，则会显著抑制RNA剪接过程。亲本间的甲基化差异可在重组自交系中稳定遗传，但受siRNA介导的甲基化转换现象广泛存在，且可延续至多8代。这类甲基化差异会影响RNA剪接，反复出现的甲基化转换提示副突变的发生频率远高于此前预期，或对杂种优势（heterosis）的形成具有重要贡献。本研究成果为玉米基因组甲基化研究提供了一套高分辨率的综合性资源，同时也绘制了当前最常用的两个玉米自交系中跨代反复出现的表观遗传偏移（副突变）图谱。整体实验设计：通过亚硫酸氢盐测序获取两个玉米品系的全基因组胞嘧啶甲基化图谱，并利用Illumina测序平台对同一组织的转录组与小RNA组进行测序分析。