Identification and dynamic quantification of regulatory elements using total RNA
Identification and dynamic quantification of regulatory elements using total RNA
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DOI：
10.1101/gr.253492.119
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发表时间：
2019-11-01
期刊：
影响因子：
7
通讯作者：
Benner, Christopher
中科院分区：
文献类型：
--
作者：
Duttke, Sascha H.;Chang, Max W.;Benner, Christopher
转录启动的时空调控是调控基因表达的关键。在这里，我们介绍了csRNA-seq(csRNA-seq)，它以总RNA为起始材料，在单核苷酸分辨率下检测稳定和不稳定RNA的转录起始位点(TSS)。CsRNA-seq对转录的急剧变化高度敏感，并识别出比RNA-seq更受调控的转录本一个数量级。通过对真核物种组织的询问，在跨越16亿年的进化过程中，在多细胞动物、植物和真菌中发现了类似增强子RNAs、pri-miRNAs、反义转录物和启动子上游转录物的不稳定转录产物。整合来自这些生物的表观基因组数据表明，组蛋白H3三甲基化(H3K4me3)主要限于稳定转录本的TSS，而H3K27ac标记了所有活性TSS下游的核小体，表明组蛋白翻译后修饰在转录中具有古老的作用。我们的发现表明，总RNA足以识别转录的调控元件，并捕获启动的稳定和不稳定的转录本在单核苷酸分辨率真核生物的动态。
The spatial and temporal regulation of transcription initiation is pivotal for controlling gene expression. Here, we introduce capped-small RNA-seq (csRNA-seq), which uses total RNA as starting material to detect transcription start sites (TSSs) of both stable and unstable RNAs at single-nucleotide resolution. csRNA-seq is highly sensitive to acute changes in transcription and identifies an order of magnitude more regulated transcripts than does RNA-seq. Interrogating tissues from species across the eukaryotic kingdoms identified unstable transcripts resembling enhancer RNAs, pri-miRNAs, antisense transcripts, and promoter upstream transcripts in multicellular animals, plants, and fungi spanning 1.6 billion years of evolution. Integration of epigenomic data from these organisms revealed that histone H3 trimethylation (H3K4me3) was largely confined to TSSs of stable transcripts, whereas H3K27ac marked nucleosomes downstream from all active TSSs, suggesting an ancient role for posttranslational histone modifications in transcription. Our findings show that total RNA is sufficient to identify transcribed regulatory elements and capture the dynamics of initiated stable and unstable transcripts at single-nucleotide resolution in eukaryotes.