RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids
RNAi of met1 reduces DNA methylation and induces genome-specific changes in gene expression and centromeric small RNA accumulation in Arabidopsis allopolyploids
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DOI：
10.1534/genetics.107.086272
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发表时间：
2008-04-01
期刊：
影响因子：
3.3
通讯作者：
Chen, Z. Jeffrey
中科院分区：
文献类型：
--
作者：
Chen, Meng;Ha, Misook;Chen, Z. Jeffrey
基因组结构和基因表达的变化已经在含有两个或多个不同基因组的再合成和天然异源多倍体中被证明。基因表达的快速和随机变化的潜在机制是未知的。拟南芥（Arabidopsis suecica）是一种天然异源四倍体，来源于现存的拟南芥A.和拟南芥A.在异源四倍体中同源的arenosa基因组。在这里，我们报告说，RNAi的met 1减少DNA甲基化，改变了类似的表达200个基因，其中许多编码转座子，预测蛋白质，着丝粒和异染色质RNA。DNA甲基化减少经常发生在上调基因的启动子区域，并且En/Spm样转座子在met 1-RNAi A中被重新激活。苏西卡线。转座子、异染色质重复序列和着丝粒小RNA的去阻遏主要来自A. thaliana基因组和A. arenosa homeplasmid基因座受甲基化缺陷的影响较小。高水平的A。拟南芥着丝粒小RNA积累与A.拟南芥着丝粒降低DNA甲基化对转座子和着丝粒重复序列的影响更大。thaliana比A. arenosa中的许多基因的抑制是一致的，这些基因在A. thaliana比A. arenosa在重新合成的异源四倍体中。此外，A.拟南芥At 2g 23810保留在重新合成的异源四倍体中，并且甲基化在天然拟南芥的启动子区域内扩散。suecica，导致At 2g 23810沉默。At 2g 23810在met 1-RNAi A中被去甲基化并重新激活。苏西卡线。我们认为，许多A。thaliana基因在再合成的异源四倍体中受到转录抑制，A.在天然异源多倍体中，包括转座子和着丝粒重复序列的拟南芥基因座高度甲基化，并经历同源异型染色体基因组特异性RNA介导的DNA甲基化。
Changes in genome structure and gene expression have been documented in both resynthesized and natural allopolyploids that contain two or more divergent genomes. The underlying mechanisms for rapid and stochastic changes in gene expression are unknown. Arabidopsis suecica is a natural allotetraploid derived from the extant A. thaliana and A. arenosa genomes that are homeologous in the allotetraploid. Here we report that RNAi of met1 reduced DNA methylation and altered the expression of similar to 200 genes, many of which encode transposons, predicted proteins, and centromeric and heterochromatic RNAs. Reduced DNA methylation occurred frequently in promoter regions of the upregulated genes, and an En/Spm-like transposon was reactivated in met1-RNAi A. suecica lines. Derepression of transposons, heterochromatic repeats, and centromeric small RNAs was primarily derived from the A. thaliana genome, and A. arenosa homeologous loci were less affected by methylation defects. A high level of A. thaliana centromeric small RNA accumulation was correlated with hypermethylation of A. thaliana centromeres. The greater effects of reduced DNA methylation on transposons and centromeric repeats in A. thaliana than in A. arenosa are consistent with the repression of many genes that are expressed at higher levels in A. thaliana than in A. arenosa in the resynthesized allotetraploids. Moreover, non-CG (CC) methylation in the promoter region of A. thaliana At2g23810 remained in the resynthesized allotetraploids, and the methylation spread within the promoter region in natural A. suecica, leading to silencing of At2g23810. At2g23810 was demethylated and reactivated in met1-RNAi A. suecica lines. We suggest that many A. thaliana genes are transcription ally repressed in resynthesized allotetraploids, and a subset of A. thaliana loci including transposons and centromeric repeats are heavily methylated and subjected to homeologous genome-specific RNA-mediated DNA methylation in natural allopolyploids.