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.

中文翻译：

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使用总RNA鉴定和动态定量调控元件。

转录起始的时空调节对于控制基因表达至关重要。在这里，我们介绍带帽小RNA-seq（csRNA-seq），它使用总RNA作为起始材料，以单核苷酸分辨率检测稳定和不稳定RNA的转录起始位点（TSS）。csRNA-seq对转录的急性变化高度敏感，并且比RNA-seq识别出更多受调控的转录本。遍及真核生物物种的组织的询问发现，在跨越16亿年进化的多细胞动物，植物和真菌中，不稳定的转录本类似于增强子RNA，pri-miRNA，反义转录本和启动子上游转录本。这些生物的表观基因组数据的整合显示，组蛋白H3三甲基化（H3K4me3）很大程度上局限于稳定转录本的TSS，而H3K27ac则标记了所有活性TSS下游的核小体，表明翻译后组蛋白修饰在转录中的古老作用。我们的研究结果表明，总RNA足以识别转录的调控元件，并捕获真核生物中单核苷酸分辨率的稳定和不稳定转录本的动力学。