Evolutionary epigenomics of retrotransposon-mediated methylation spreading in rice

Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on 5 factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methyla...植物基因组中存在大量转座因子（transposable elements, TEs），学界已提出诸多关于限制转座因子活性的进化驱动力假说。然而，聚焦植物宿主与其转座因子之间的进化表观基因组互作的模型仍较为匮乏。宿主基因组会招募甲基化等表观遗传因子以沉默转座因子，但甲基化作用可扩散至转座因子序列之外，进而影响邻近宿主基因的表达。本研究以水稻（Oryza sativa）为研究对象，通过解析长末端重复序列反转录转座子（long terminal repeat, LTR retrotransposons, RTs）的抑制表观基因组调控机制，探究了转座因子与邻近宿主基因沉默之间的表观遗传权衡效应。研究结果显示，源自长末端重复序列反转录转座子序列的甲基化扩散现象具有显著证据，且扩散程度受五大因素调控：1）长末端重复序列反转录转座子家族类型；2）该转座子的插入时长；3）转座子所在区域的重组速率；4）长末端重复序列反转录转座子序列的甲基化水平；5）染色体位置。甲基化……