DNA Methylation Signatures of the Plant Chromomethyltransferases.
DNA Methylation Signatures of the Plant Chromomethyltransferases.
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植物铬甲基转移酶的DNA甲基化特征。
DOI：
10.1371/journal.pgen.1006526
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发表时间：
2016-12
期刊：
影响因子：
4.5
通讯作者：
Baulcombe DC
中科院分区：
文献类型：
--
作者：
Gouil Q;Baulcombe DC
植物中的DNA甲基化传统上被分为CG、CHG和CHH三种环境(其中H是除G之外的任何核苷酸)。通过研究四种被子植物三核苷酸环境中的DNA甲基化模式，我们发现这种表达隐藏了不同甲基化途径的空间和功能划分，并且是不完整的。CG甲基化(MCG)在很大程度上是上下文无关的，而在CHG基序中，mCCG在拟南芥和番茄的着丝点周围区域以及玉米和水稻的整个染色体中都表达不足。在拟南星天牛中，mCCG在异染色质中的偏向表达与H3K9甲基转移酶SuvH家族成员的特异性有关。在CHH基序中，存在mCHH不同变体的过度表达，类似于mCCG的低甲基化，被分割到两个双子叶的着丝粒周围区域，但分散在单子叶染色体中。在拟南芥中过度表达的mCHH基序与特定类型的转座子有关，包括I类和II类元件。在mCHH中，上下文偏见是由于各种色甲基转移酶的参与，而在拟南芥和番茄中，与上下文无关的CHH甲基化是由RNA指导的DNA甲基化过程介导的，该过程在富含基因的常染色质中最活跃。因此，这一分析揭示了植物基因组甲基组的序列背景是关于与维持甲基化和上覆染色质结构相关的机制的信息。真核生物中致密的胞嘧啶DNA甲基化(MC)与封闭染色质和基因沉默有关。在植物中，众所周知MC(MCG、MCHG或mCHH)的序列上下文提供了涉及几种机制中的哪一种的线索，但现在，基于对四个植物物种野生型和突变体的DNA甲基组的详细分析，我们揭示了MC序列上下文中还有额外的信息。在拟南芥和番茄中，mCCG的低表达和MCAA、MCTA或MCAT的过度表达使着丝粒附近的染色体区域发生了分化，在着丝粒附近的区域，甲基化由染色体臂上的铬甲基转移酶主导，其中mCHH是上下文无关的，主要是RNA控制的。水稻和玉米具有相似的序列上下文相关的DNA甲基化，但相应的染色体结构域不像双子叶植物那样在空间上分离。根据序列背景发现植物甲基组的亚组分，将使过去和未来对植物甲基组的分析有更大的分辨率。
DNA methylation in plants is traditionally partitioned into CG, CHG and CHH contexts (with H any nucleotide but G). By investigating DNA methylation patterns in trinucleotide contexts in four angiosperm species, we show that such a representation hides spatial and functional partitioning of different methylation pathways and is incomplete. CG methylation (mCG) is largely context-independent whereas, at CHG motifs, there is under-representation of mCCG in pericentric regions of A. thaliana and tomato and throughout the chromosomes of maize and rice. In A. thaliana the biased representation of mCCG in heterochromatin is related to specificities of H3K9 methyltransferase SUVH family members. At CHH motifs there is an over-representation of different variant forms of mCHH that, similarly to mCCG hypomethylation, is partitioned into the pericentric regions of the two dicots but dispersed in the monocot chromosomes. The over-represented mCHH motifs in A. thaliana associate with specific types of transposon including both class I and II elements. At mCHH the contextual bias is due to the involvement of various chromomethyltransferases whereas the context-independent CHH methylation in A. thaliana and tomato is mediated by the RNA-directed DNA methylation process that is most active in the gene-rich euchromatin. This analysis therefore reveals that the sequence context of the methylome of plant genomes is informative about the mechanisms associated with maintenance of methylation and the overlying chromatin structure. Dense cytosine DNA methylation (mC) in eukaryotes is associated with closed chromatin and gene silencing. In plants it is well known that the sequence context of the mC (either mCG, mCHG or mCHH) provides a clue as to which of several mechanisms is involved but now, based on detailed analyses of the DNA methylome in wild type and mutants of four plant species, we reveal that there is additional information in the mC sequence context. Low mCCG and over-representation of mCAA and mCTA or mCAT in A. thaliana and tomato differentiates regions of the chromosomes near the centromere where methylation is dominated by chromomethyltransferases from the chromosome arms in which mCHH is context-independent and predominantly RNA-directed. Rice and maize have similar sequence context-dependent DNA methylation but the corresponding chromosome domains are not spatially separate as in the dicots. The discovery of the subcomponents of plant methylomes based on sequence context will allow greater resolution in past and future analyses of plant methylomes.