State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438, People's Republic of China.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, People's Republic of China.
BMC Biol. 2018 Apr 30;16(1):44. doi: 10.1186/s12915-018-0513-8.
Intron retention (IR), the most prevalent alternative splicing form in plants, plays a critical role in gene expression during plant development and stress response. However, the molecular mechanisms underlying IR regulation remain largely unknown.
Knockdown of SDG725, a histone H3 lysine 36 (H3K36)-specific methyltransferase in rice, leads to alterations of IR in more than 4700 genes. Surprisingly, IR events are globally increased at the 5' region but decreased at the 3' region of the gene body in the SDG725-knockdown mutant. Chromatin immunoprecipitation sequencing analyses reveal that SDG725 depletion results in a genome-wide increase of the H3K36 mono-methylation (H3K36me1) but, unexpectedly, promoter-proximal shifts of H3K36 di- and tri-methylation (H3K36me2 and H3K36me3). Consistent with the results in animals, the levels of H3K36me1/me2/me3 in rice positively correlate with gene expression levels, whereas shifts of H3K36me2/me3 coincide with position-specific alterations of IR. We find that either H3K36me2 or H3K36me3 alone contributes to the positional change of IR caused by SDG725 knockdown, although IR shift is more significant when both H3K36me2 and H3K36me3 modifications are simultaneously shifted.
Our results revealed that SDG725 modulates IR in a position-specific manner, indicating that H3K36 methylation plays a role in RNA splicing, probably by marking the retained introns in plants.
内含子保留（IR）是植物中最普遍的可变剪接形式，在植物发育和应激反应过程中的基因表达中起着关键作用。然而，IR 调控的分子机制在很大程度上仍然未知。
敲低水稻中组蛋白 H3 赖氨酸 36（H3K36）特异性甲基转移酶 SDG725 导致超过 4700 个基因的 IR 改变。令人惊讶的是，SDG725 敲低突变体中基因体的 5'区域的 IR 事件普遍增加，但 3'区域减少。染色质免疫沉淀测序分析显示，SDG725 耗竭导致全基因组 H3K36 单甲基化（H3K36me1）增加，但出乎意料的是，H3K36 二甲基化（H3K36me2）和三甲基化（H3K36me3）在启动子近端发生转移。与动物的结果一致，水稻中 H3K36me1/me2/me3 的水平与基因表达水平呈正相关，而 H3K36me2/me3 的转移与 IR 的位置特异性改变一致。我们发现，H3K36me2 或 H3K36me3 单独作用于 SDG725 敲低引起的 IR 位置改变，尽管当 H3K36me2 和 H3K36me3 修饰同时转移时，IR 转移更为显著。
我们的结果表明，SDG725 以位置特异性方式调节 IR，表明 H3K36 甲基化在 RNA 剪接中发挥作用，可能通过在植物中标记保留的内含子。
