Hung Fu-Yu, Chen Chen, Yen Ming-Ren, Hsieh Jo-Wei Allison, Li Chenlong, Shih Yuan-Hsin, Chen Fang-Fang, Chen Pao-Yang, Cui Yuhai, Wu Keqiang
Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan.
Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3 Canada.
NAR Genom Bioinform. 2020 Sep 21;2(3):lqaa066. doi: 10.1093/nargab/lqaa066. eCollection 2020 Sep.
In recent years, eukaryotic long non-coding RNAs (lncRNAs) have been identified as important factors involved in a wide variety of biological processes, including histone modification, alternative splicing and transcription enhancement. The expression of lncRNAs is highly tissue-specific and is regulated by environmental stresses. Recently, a large number of plant lncRNAs have been identified, but very few of them have been studied in detail. Furthermore, the mechanism of lncRNA expression regulation remains largely unknown. HISTONE DEACETYLASE 6 (HDA6) and LSD1-LIKE 1/2 (LDL1/2) can repress gene expression synergistically by regulating H3Ac/H3K4me. In this research, we performed RNA-seq and ChIP-seq analyses to further clarify the function of HDA6-LDL1/2. Our results indicated that the global expression of lncRNAs is increased in and that this increased lncRNA expression is particularly associated with H3Ac/H3K4me2 changes. In addition, we found that HDA6-LDL1/2 is important for repressing lncRNAs that are non-expressed or show low-expression, which may be strongly associated with plant development. GO-enrichment analysis also revealed that the neighboring genes of the lncRNAs that are upregulated in are associated with various developmental processes. Collectively, our results revealed that the expression of lncRNAs is associated with H3Ac/H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex.
近年来，真核生物长链非编码RNA（lncRNAs）已被确认为参与多种生物学过程的重要因素，包括组蛋白修饰、可变剪接和转录增强。lncRNAs的表达具有高度的组织特异性，并受环境胁迫调控。最近，大量植物lncRNAs已被鉴定出来，但对其中很少一部分进行了详细研究。此外，lncRNA表达调控的机制仍 largely未知。组蛋白去乙酰化酶6（HDA6）和类LSD1-1/2（LDL1/2）可通过调节H3Ac/H3K4me协同抑制基因表达。在本研究中，我们进行了RNA测序和染色质免疫沉淀测序分析，以进一步阐明HDA6-LDL1/2的功能。我们的结果表明，lncRNAs的整体表达在 中增加，且这种lncRNA表达的增加与H3Ac/H3K4me2变化特别相关。此外，我们发现HDA6-LDL1/2对于抑制未表达或低表达的lncRNAs很重要，这可能与植物发育密切相关。基因本体富集分析还显示，在 中上调的lncRNAs的邻近基因与各种发育过程相关。总的来说，我们的结果揭示了lncRNAs的表达与由HDA6-LDL1/2组蛋白修饰复合体调控的H3Ac/H3K4me2变化相关。
