Enhancers activate transcription in a distance-, orientation-, and position-independent manner, which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes, especially at the 5' untranslated regions (5'UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40% of identified enhancers carried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks, H3K4me3 and/or H3K27ac, which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes, which overlap poorly with STARR-seq enhancers. In summary, we quantitatively identified enhancers by functional analysis in the genome of rice, an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts.

中文翻译：

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通过STARR-seq对水稻中的增强子进行全球定量定位。

增强子以与距离，方向和位置无关的方式激活转录，这使它们难以被识别。自转录活性调控区测序（STARR-seq）并行测量数百万个DNA片段的增强子活性。在这里，我们使用STARR-seq生成了水稻增强剂的定量全球地图。大多数增强子定位在基因内，尤其是在5'非翻译区（5'UTR）和编码序列中。增强子也经常定位在富含转座因子（TE）区域的沉默和低表达基因附近。分析增强子在其内源性位点的表观遗传特征表明，大多数增强子不与DNase I超敏位点（DHS）共定位，并且缺乏组蛋白修饰H3K4me1的增强子标记。根据增强子的表观遗传标记进行的聚类分析表明，约40％的已鉴定增强子带有一个或多个表观遗传标记。抑制性H3K27me3经常富含阳性标记H3K4me3和/或H3K27ac，它们一起标记增强子。还根据DHS区域相对于基因的位置预测了基因间增强子，与STARR-seq增强子重叠很少。总之，我们通过功能分析水稻的基因组中的重要模型植物定量鉴定了增强子。这项工作为在不同生物学背景下进行进一步的机理研究提供了宝贵的资源。H3K4me3和/或H3K27ac，一起标记增强子。还根据DHS区域相对于基因的位置预测了基因间增强子，与STARR-seq增强子重叠很少。总之，我们通过功能分析水稻的基因组中的重要模型植物定量鉴定了增强子。这项工作为在不同生物学背景下进行进一步的机理研究提供了宝贵的资源。H3K4me3和/或H3K27ac，一起标记增强子。还根据DHS区域相对于基因的位置预测了基因间增强子，与STARR-seq增强子重叠很少。总之，我们通过功能分析水稻的基因组中的重要模型植物定量鉴定了增强子。这项工作为在不同生物学背景下进行进一步的机理研究提供了宝贵的资源。