COMPASS complexes redundantly regulate gene expression and DNA methylation in Arabidopsis [ChIP-seq]

The evolutionally conserved COMPASS complexes are responsible for the catalyzation of H3K4 methylations. Recently, three types of COMPASS complexes which contains histone methyltransferases ATX1/2, ATX3, or ATX4/5 were identified in Arabidopsis. Here, we report the ATX proteins are essential for the survival of Arabidopsis. By RNA-seq and chromatin immunoprecipitation (ChIP-seq) analysis, we found ATX1/2-, ATX3-, and ATX4/5-containing COMPASS complex redundantly regulate gene expression and H3K4me3 modifications. In addition to the developmental-related genes, we found the expression of DNA methylation-related genes were also regulated by the COMPASS complexes. The transcript and H3K4me3 levels at the RdDM pathway genes (NRPE1, DCL3, IDN2, FDM2) and at the DNA demethylase encoding genes (ROS1, DML2, DML3) were down-regulated in atx1/2/4/5 mutants. Via bisulfate sequencing, we found the atx1/2/4/5 showed hypermethylation at CG and CHG contexts whereas the hypomethylation at CHH contexts. By comparing the differentially methylated regions (DMRs) in atx1/2/4/5 with that in ros1;dml2;dml3 (rdd) and in nrpe1, a large part of overlapping DMRs were identified. Based on these results and other findings, we propose that the hypermethylation in CG and CHG is partially caused by the down-regulation of ROS1/DML2/DML3, and the hypomethylation in CHH is mainly caused by the down-regulation of NRPE1. Furthermore, we revealed that the COMPASS complexes also play a redundant role in regulating the transcription of transposable elements (TEs). This study extends our knowledge about the function of COMPASS in plant development and illustrate the important roles for COMPASS complexes in the regulation of DNA methylation and TEs transcription. Examination of H3K4me3 levels in wild type and the COMPASS complex mutants grown under long day conditions.

进化保守的COMPASS复合物负责催化H3K4甲基化修饰。近期，研究人员在拟南芥中鉴定出三类分别含有组蛋白甲基转移酶ATX1/2、ATX3或ATX4/5的COMPASS复合物。本研究证实ATX蛋白对拟南芥的存活至关重要。通过RNA测序（RNA-seq）与染色质免疫共沉淀测序（ChIP-seq）分析，我们发现含有ATX1/2、ATX3以及ATX4/5的COMPASS复合物可冗余调控基因表达与H3K4me3修饰。除发育相关基因外，本研究还发现COMPASS复合物亦可调控DNA甲基化相关基因的表达。在atx1/2/4/5突变体中，RNA指导的DNA甲基化（RdDM）途径基因（NRPE1、DCL3、IDN2、FDM2）以及DNA去甲基化酶编码基因（ROS1、DML2、DML3）的转录本水平与H3K4me3修饰水平均出现下调。通过亚硫酸氢盐测序分析，我们发现atx1/2/4/5突变体在CG与CHG序列背景下呈现高甲基化，而在CHH序列背景下则呈现低甲基化。通过比对atx1/2/4/5突变体与ros1;dml2;dml3（rdd）以及nrpe1突变体中的差异甲基化区域（DMRs），我们鉴定出大量重叠的DMRs。基于上述结果与其他相关研究发现，我们提出CG与CHG背景下的高甲基化部分源于ROS1/DML2/DML3的表达下调，而CHH背景下的低甲基化则主要由NRPE1的表达下调所致。此外，本研究还揭示COMPASS复合物在调控转座因子（TEs）的转录过程中同样发挥冗余功能。本研究拓展了我们对COMPASS复合物在植物发育中功能的认知，并阐明了COMPASS复合物在调控DNA甲基化与转座因子转录过程中的重要作用。本研究还检测了长日照培养条件下野生型及COMPASS复合物突变体的H3K4me3水平。