Small RNAs, DNA methylation and transposable elements in wheat.
Small RNAs, DNA methylation and transposable elements in wheat.
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DOI：
10.1186/1471-2164-11-408
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发表时间：
2010-06-29
期刊：
影响因子：
4.4
通讯作者：
Dubcovsky J
中科院分区：
文献类型：
--
作者：
Cantu D;Vanzetti LS;Sumner A;Dubcovsky M;Matvienko M;Distelfeld A;Michelmore RW;Dubcovsky J
小麦基因组的80%以上是由转座因子（TEs）组成的。由于活性TE可以移动到不同的位置并可能施加显著的突变负荷，因此它们的表达通过小的非编码RNA（sRNA）在基因组中被抑制。sRNA在转录水平（主要是24-nt sRNA）和转录后水平（主要是21-nt sRNA）指导TE的沉默。在这项研究中，我们报告了这两种类型的sRNA在不同类别的小麦TE中的分布，TE中的靶向区域，以及它们对靶向区域甲基化模式的影响。我们从六倍体小麦中构建了一个sRNA文库，并开发了一个数据库，其中包括我们的文库和其他三个公开的小麦sRNA文库。对于五个完全测序的小麦BAC重叠群，最完美匹配的sRNA代表TE序列，表明大部分小麦sRNA来源于TE。对存在于小麦重复序列数据库中的所有小麦TE的分析表明，sRNA丰度与每个类别内的TE的估计数量相关。与微型反向重复转座元件（miniature inverted repeat transposable elements，MITEs）完全匹配的sRNAs大多属于21-nt类，主要定位于末端反向重复序列（terminal inverted repeats，TIR）。相反，大多数匹配I类和II类TE的sRNA属于24-nt类，并且主要靶向I类TE中的长末端重复序列（LTR）和CACTA转座子中的末端重复序列。在潜在的甲基化位点的突变频率的分析显示，相对于内含子和非翻译基因区域的TE突变频率增加了三倍。这种增加与小麦TE优先甲基化一致，可能是通过sRNA靶向。我们的研究检查了小麦表观基因组与已知TE的关系。在小麦基因组中，转录沉默和转录后沉默在TEs的短期抑制中起重要作用，而DNA甲基化和突变率的增加可能是TEs抑制的长期机制。
More than 80% of the wheat genome is composed of transposable elements (TEs). Since active TEs can move to different locations and potentially impose a significant mutational load, their expression is suppressed in the genome via small non-coding RNAs (sRNAs). sRNAs guide silencing of TEs at the transcriptional (mainly 24-nt sRNAs) and post-transcriptional (mainly 21-nt sRNAs) levels. In this study, we report the distribution of these two types of sRNAs among the different classes of wheat TEs, the regions targeted within the TEs, and their impact on the methylation patterns of the targeted regions. We constructed an sRNA library from hexaploid wheat and developed a database that included our library and three other publicly available sRNA libraries from wheat. For five completely-sequenced wheat BAC contigs, most perfectly matching sRNAs represented TE sequences, suggesting that a large fraction of the wheat sRNAs originated from TEs. An analysis of all wheat TEs present in the Triticeae Repeat Sequence database showed that sRNA abundance was correlated with the estimated number of TEs within each class. Most of the sRNAs perfectly matching miniature inverted repeat transposable elements (MITEs) belonged to the 21-nt class and were mainly targeted to the terminal inverted repeats (TIRs). In contrast, most of the sRNAs matching class I and class II TEs belonged to the 24-nt class and were mainly targeted to the long terminal repeats (LTRs) in the class I TEs and to the terminal repeats in CACTA transposons. An analysis of the mutation frequency in potentially methylated sites revealed a three-fold increase in TE mutation frequency relative to intron and untranslated genic regions. This increase is consistent with wheat TEs being preferentially methylated, likely by sRNA targeting. Our study examines the wheat epigenome in relation to known TEs. sRNA-directed transcriptional and post-transcriptional silencing plays important roles in the short-term suppression of TEs in the wheat genome, whereas DNA methylation and increased mutation rates may provide a long-term mechanism to inactivate TEs.
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影响因子：
3.7
作者：
Fahlgren N;Howell MD;Kasschau KD;Chapman EJ;Sullivan CM;Cumbie JS;Givan SA;Law TF;Grant SR;Dangl JL;Carrington JC
通讯作者：
Carrington JC
影响因子：
5.1
作者：
Cloutier, Sylvie;McCallum, Brent D.;Jordan, Mark C.
通讯作者：
Jordan, Mark C.
影响因子：
5.4
作者：
Echenique, V;Stamova, B;Dubcovsky, J
通讯作者：
Dubcovsky, J
影响因子：
64.8
作者：
GRANDBASTIEN, MA;SPIELMANN, A;CABOCHE, M
通讯作者：
CABOCHE, M
DOI：
10.1073/pnas.96.26.15330
发表时间：
1999-12-21
影响因子：
11.1
作者：
Chopra, S;Brendel, V;Peterson, T
通讯作者：
Peterson, T