Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome.,PLOS Genetics

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Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome.
PLOS Genetics ( IF 4.0 ) Pub Date : 2020-03-18 , DOI: 10.1371/journal.pgen.1008637
Nino A Espinas _{1,

2} , Le Ngoc Tu ₁ , Leonardo Furci ₁ , Yasuka Shimajiri _{1,

3} , Yoshiko Harukawa ₁ , Saori Miura ₁ , Shohei Takuno ₄ , Hidetoshi Saze ₁

Affiliation

Intronic regions of eukaryotic genomes accumulate many Transposable Elements (TEs). Intronic TEs often trigger the formation of transcriptionally repressive heterochromatin, even within transcription-permissive chromatin environments. Although TE-bearing introns are widely observed in eukaryotic genomes, their epigenetic states, impacts on gene regulation and function, and their contributions to genetic diversity and evolution, remain poorly understood. In this study, we investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome, where TEs comprise 35% of the genome. We found that over 10% of 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. On the other hand, introns also accumulate hypomethylated short TEs. Genes with heterochromatic introns are implicated in various biological functions. Transcription of genes bearing intronic heterochromatin is regulated by an epigenetic mechanism involving the conserved factor OsIBM2, mutation of which results in severe developmental and reproductive defects. Furthermore, we found that heterochromatic introns evolve rapidly compared to non-heterochromatic introns. Our study demonstrates that heterochromatin is a common epigenetic feature associated with actively transcribed genes in the rice genome.

中文翻译：

水稻基因组中带有内含子异染色质的基因的转录调控。

真核基因组的内含子区域积累了许多转座元件（TE）。即使在允许转录的染色质环境中，内含子 TE 也经常触发转录抑制性异染色质的形成。尽管携带 TE 的内含子在真核基因组中广泛观察到，但它们的表观遗传状态、对基因调控和功能的影响以及它们对遗传多样性和进化的贡献仍然知之甚少。在这项研究中，我们研究了水稻基因组中内含子 TE 的全基因组分布及其表观遗传状态，其中 TE 占基因组的 35%。我们发现超过10%的水稻基因含有内含子异染色质，其中大部分与TE和重复序列相关。这些异染色质内含子更长并且在启动子近端位置高度富集。另一方面，内含子也会积累低甲基化的短TE。具有异染色质内含子的基因涉及多种生物学功能。带有内含子异染色质的基因的转录受到涉及保守因子 OsIBM2 的表观遗传机制的调节，该因子的突变会导致严重的发育和生殖缺陷。此外，我们发现异染色质内含子比非异染色质内含子进化得更快。我们的研究表明，异染色质是与水稻基因组中活跃转录基因相关的常见表观遗传特征。

更新日期：2020-04-06

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