Song Qingxin, Guan Xueying, Chen Z Jeffrey
Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.
PLoS Genet. 2015 Dec 28;11(12):e1005724. doi: 10.1371/journal.pgen.1005724. eCollection 2015 Dec.
DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites via distinct pathways. Cotton is an allotetraploid consisting of two progenitor genomes. Each cotton fiber is a rapidly-elongating cell derived from the ovule epidermis, but the molecular basis for this developmental transition is unknown. Here we analyzed methylome, transcriptome, and small RNAome and revealed distinct changes in CHH methylation during ovule and fiber development. In ovules, CHH hypermethylation in promoters correlated positively with siRNAs, inducing RNA-dependent DNA methylation (RdDM), and up-regulation of ovule-preferred genes. In fibers, the ovule-derived cells generated additional heterochromatic CHH hypermethylation independent of RdDM, which repressed transposable elements (TEs) and nearby genes including fiber-related genes. Furthermore, CHG and CHH methylation in genic regions contributed to homoeolog expression bias in ovules and fibers. Inhibiting DNA methylation using 5-aza-2'-deoxycytidine in cultured ovules has reduced fiber cell number and length, suggesting a potential role for DNA methylation in fiber development. Thus, RdDM-dependent methylation in promoters and RdDM-independent methylation in TEs and nearby genes could act as a double-lock feedback mechanism to mediate gene and TE expression, potentiating the transition from epidermal to fiber cells during ovule and seed development.
DNA甲基化对于植物和动物的发育至关重要。在植物中，甲基化通过不同途径发生在CG、CHG和CHH（H = A、C或T）位点。棉花是一种异源四倍体，由两个祖先基因组组成。每根棉纤维都是一个从胚珠表皮衍生而来的快速伸长细胞，但这种发育转变的分子基础尚不清楚。在这里，我们分析了甲基化组、转录组和小RNA组，并揭示了胚珠和纤维发育过程中CHH甲基化的明显变化。在胚珠中，启动子中的CHH高甲基化与小干扰RNA（siRNAs）呈正相关，诱导RNA依赖的DNA甲基化（RdDM），并上调胚珠偏好基因。在纤维中，来自胚珠的细胞产生了额外的异染色质CHH高甲基化，独立于RdDM，这抑制了转座元件（TEs）和包括纤维相关基因在内的附近基因。此外，基因区域中的CHG和CHH甲基化导致胚珠和纤维中的同源基因表达偏向。在培养的胚珠中使用5-氮杂-2'-脱氧胞苷抑制DNA甲基化减少了纤维细胞的数量和长度，表明DNA甲基化在纤维发育中具有潜在作用。因此，启动子中依赖RdDM的甲基化以及TEs和附近基因中不依赖RdDM的甲基化可以作为一种双锁反馈机制来介导基因和TEs的表达，在胚珠和种子发育过程中促进从表皮细胞到纤维细胞的转变。
