Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription.
Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription.
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DOI：
10.1186/s12870-017-1108-1
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发表时间：
2017-10-12
影响因子：
5.3
通讯作者：
Varotto S
中科院分区：
文献类型：
--
作者：
Forestan C;Farinati S;Aiese Cigliano R;Lunardon A;Sanseverino W;Varotto S
RNA 指导的 DNA 甲基化 (RdDM) 是一种植物特异性表观遗传过程，依赖于 RNA 聚合酶 IV (Pol IV) 产生 24 核苷酸小干扰 RNA (siRNA)，指导胞嘧啶甲基化以及基因和转座子的沉默。玉米 RPD1/RMR6 基因编码 Pol IV 的最大亚基，是正常植物发育、副突变、某些转座元件 (TE) 的转录抑制和特定等位基因的转录调控所必需的。在本研究中，我们应用总 RNA 测序方法来比较 B73 和 rpd1/rmr6 叶转录组。尽管之前的研究表明，RdDM 突变体中 siRNA 产生的丧失会导致拟南芥和玉米中 CHH DNA 甲基化的严重丧失，但不会引起大量基因或 TE 转录激活，但我们对 rpd1/rmr6 转录组的总 RNA-Seq 分析表明，Pol IV 活性的丧失导致玉米基因组转录部分的整体增加。我们的结果表明，具有附近 TE 插入的基因受 Pol IV 介导的基因沉默影响最强烈。附近基因表达的 TE 调节与基因侧翼区域的替代甲基化谱相关，并且这些谱严格依赖于插入的 TE 成员的具体特征。尽管 Pol IV 对于 siRNA 的生物发生至关重要，但具有相关 siRNA 位点的基因受 pol IV 突变的影响较小。对基因表达、TEs 分布、小 RNA 靶向和 DNA 甲基化水平的深入综合分析揭示了 Pol IV 活性的丧失在全球范围内影响基因组调控，指出 TEs 作为附近基因表达的调节剂，并表明存在多级表观遗传沉默机制。我们的结果还表明，Pol IV 介导的 RdDM 途径在玉米基因组优势调控以及亚基因组稳定性和进化中发挥着主导作用。本文的在线版本 (10.1186/s12870-017-1108-1) 包含补充材料，可供授权用户使用。
RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles. In this study we applied a total RNA-Seq approach to compare the B73 and rpd1/rmr6 leaf transcriptomes. Although previous studies indicated that loss of siRNAs production in RdDM mutants provokes a strong loss of CHH DNA methylation but not massive gene or TEs transcriptional activation in both Arabidopsis and maize, our total RNA-Seq analysis of rpd1/rmr6 transcriptome reveals that loss of Pol IV activity causes a global increase in the transcribed fraction of the maize genome. Our results point to the genes with nearby TE insertions as being the most strongly affected by Pol IV-mediated gene silencing. TEs modulation of nearby gene expression is linked to alternative methylation profiles on gene flanking regions, and these profiles are strictly dependent on specific characteristics of the TE member inserted. Although Pol IV is essential for the biogenesis of siRNAs, the genes with associated siRNA loci are less affected by the pol IV mutation. This deep and integrated analysis of gene expression, TEs distribution, smallRNA targeting and DNA methylation levels, reveals that loss of Pol IV activity globally affects genome regulation, pointing at TEs as modulator of nearby gene expression and indicating the existence of multiple level epigenetic silencing mechanisms. Our results also suggest a predominant role of the Pol IV-mediated RdDM pathway in genome dominance regulation, and subgenome stability and evolution in maize. The online version of this article (10.1186/s12870-017-1108-1) contains supplementary material, which is available to authorized users.
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DOI：
10.1073/pnas.1201043109
发表时间：
2012-02-28
影响因子：
11.1
作者：
Greaves, Ian K.;Groszmann, Michael;Dennis, Elizabeth S.
通讯作者：
Dennis, Elizabeth S.
影响因子：
4.6
作者：
Forestan C;Aiese Cigliano R;Farinati S;Lunardon A;Sanseverino W;Varotto S
通讯作者：
Varotto S
DOI：
10.1093/bioinformatics/btv562
发表时间：
2016-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gel B;Díez-Villanueva A;Serra E;Buschbeck M;Peinado MA;Malinverni R
通讯作者：
Malinverni R
影响因子：
7
作者：
Gent JI;Ellis NA;Guo L;Harkess AE;Yao Y;Zhang X;Dawe RK
通讯作者：
Dawe RK
影响因子：
64.5
作者：
Calarco JP;Borges F;Donoghue MT;Van Ex F;Jullien PE;Lopes T;Gardner R;Berger F;Feijó JA;Becker JD;Martienssen RA
通讯作者：
Martienssen RA