Study of intronic heterochromatin in the rice genome

Intronic regions of eukaryotic genomes accumulate a large number of Transposable Elements (TEs). Although TE-bearing introns are widely observed among eukaryotic genomes, their epigenetic states, impacts on gene regulation and function, and their contributions to genetic diversity and evolution, are yet to be fully understood. In this study, we investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome. We found that over 10% of the rice genes contain intronic heterochromatin, most of which are associated with TEs and repetitive sequences. These heterochromatic introns are longer and highly enriched in promoter-proximal positions. The genes with heterochromatic intron tend to show tissue-specific expression pattern, and are also implicated in basal functions in developmental processes as well as in responses to environmental stimuli. Furthermore, we found that heterochromatic introns evolve rapidly compared to non-heterochromatic introns. Our study highlights regulatory roles of intronic heterochromatin on gene transcription and its impacts on diversification of genome sequence and gene functions in plants.

真核生物基因组的内含子区域会累积大量转座因子（Transposable Elements，TEs）。尽管携带转座因子的内含子在真核生物基因组中已被广泛观测到，但目前学界对其表观遗传状态、对基因调控与功能的影响，以及其对遗传多样性和进化的贡献仍未完全阐明。本研究针对水稻（Oryza sativa）基因组中内含子区转座因子的全基因组分布特征及其表观遗传状态展开了系统探究。研究发现，超过10%的水稻基因携带有内含子异染色质，其中绝大多数与转座因子及重复序列相关联。这类异染色质内含子长度更长，且在启动子近端区域高度富集。携带有异染色质内含子的基因往往呈现组织特异性表达模式，同时参与发育过程中的基础功能以及对环境刺激的应答。此外，相较于非异染色质内含子，异染色质内含子的进化速率更快。本研究揭示了内含子异染色质对基因转录的调控作用，及其对植物基因组序列多样性与基因功能分化的影响。