RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants.
RNA polymerase mapping in plants identifies intergenic regulatory elements enriched in causal variants.
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植物中的RNA聚合酶图谱鉴定了富含因果变异的基因间调节元件。
DOI：
10.1093/g3journal/jkab273
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发表时间：
2021-10-19
期刊：
影响因子：
--
通讯作者：
Jannink JL
中科院分区：
文献类型：
--
作者：
Lozano R;Booth GT;Omar BY;Li B;Buckler ES;Lis JT;Del Carpio DP;Jannink JL
基因表达的控制在细胞功能的各个层面都是至关重要的。启动子近端暂停和启动子和增强子处的趋异转录是动物中的突出特征，仅在少数植物研究实验中进行了研究。木薯（Manihot esculenta）中的PRO-Seq分析在基因的5′端和3′端鉴定了转录参与的RNA聚合酶的峰，与暂停或缓慢移动的聚合酶一致。此外，我们确定了不同的转录在基因间位点。使用哺乳动物中开发的增强子检测算法（dREG）进行双向转录的全基因组搜索鉴定了许多基因间调节元件（IRE）候选物。基于基因组进化速率分析（GERP），这些位点显示出不同的甲基化和核苷酸保守模式。在这些IRE候选人的SNPs解释显着更多的变化，健身和根组成比随机确定从相同的基因间分布的染色体片段中的SNPs，强烈表明这些网站的功能的重要性。玉米GRO-Seq数据显示，IRE处的RNA聚合酶占据与木薯中的模式一致。此外，玉米中的这些IRE与先前基于开放染色质、组蛋白标记和甲基化鉴定的位点显著重叠，并且富集了报道的eQTL。我们的研究结果表明，双向转录可以识别在转录调控中起重要作用的植物基因组间区域，其识别具有帮助作物改良的潜力。
Control of gene expression is fundamental at every level of cell function. Promoter-proximal pausing and divergent transcription at promoters and enhancers, which are prominent features in animals, have only been studied in a handful of research experiments in plants. PRO-Seq analysis in cassava (Manihot esculenta) identified peaks of transcriptionally engaged RNA polymerase at both the 5′ and 3′ end of genes, consistent with paused or slowly moving Polymerase. In addition, we identified divergent transcription at intergenic sites. A full genome search for bi-directional transcription using an algorithm for enhancer detection developed in mammals (dREG) identified many intergenic regulatory element (IRE) candidates. These sites showed distinct patterns of methylation and nucleotide conservation based on genomic evolutionary rate profiling (GERP). SNPs within these IRE candidates explained significantly more variation in fitness and root composition than SNPs in chromosomal segments randomly ascertained from the same intergenic distribution, strongly suggesting a functional importance of these sites. Maize GRO-Seq data showed RNA polymerase occupancy at IREs consistent with patterns in cassava. Furthermore, these IREs in maize significantly overlapped with sites previously identified on the basis of open chromatin, histone marks, and methylation, and were enriched for reported eQTL. Our results suggest that bidirectional transcription can identify intergenic genomic regions in plants that play an important role in transcription regulation and whose identification has the potential to aid crop improvement.
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