TT-seq maps the human transient transcriptome
TT-seq maps the human transient transcriptome
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DOI：
10.1126/science.aad9841
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发表时间：
2016-06-03
期刊：
影响因子：
56.9
通讯作者：
Cramer, Patrick
中科院分区：
文献类型：
--
作者：
Schwalb, Bjorn;Michel, Margaux;Cramer, Patrick
基因组的普遍转录产生稳定的和瞬时的RNA。我们开发了瞬时转录组测序 (TT-seq)，这是一种统一绘制整个 RNA 生成单位范围并估计 RNA 合成和降解速率的方案。将 TT-seq 应用于人 K562 细胞可恢复稳定的信使 RNA 和长基因间非编码 RNA，并另外绘制瞬时增强子、反义和启动子相关 RNA 的图谱。 TT-seq 分析表明增强子 RNA 寿命较短且缺乏 U1 基序和二级结构。 TT-seq 还绘制了多聚腺苷酸化位点下游的瞬时 RNA 并揭示了转录终止位点；我们发现，平均有四个转录终止位点，分布在中位宽度约为 3300 个碱基对的窗口中。终止位点与 DNA 基序一致，该基序与 RNA 聚合酶从基因组释放之前的暂停相关。
Pervasive transcription of the genome produces both stable and transient RNAs. We developed transient transcriptome sequencing (TT-seq), a protocol that uniformly maps the entire range of RNA-producing units and estimates rates of RNA synthesis and degradation. Application of TT-seq to human K562 cells recovers stable messenger RNAs and long intergenic noncoding RNAs and additionally maps transient enhancer, antisense, and promoter-associated RNAs. TT-seq analysis shows that enhancer RNAs are short-lived and lack U1 motifs and secondary structure. TT-seq also maps transient RNA downstream of polyadenylation sites and uncovers sites of transcription termination; we found, on average, four transcription termination sites, distributed in a window with a median width of similar to 3300 base pairs. Termination sites coincide with a DNA motif associated with pausing of RNA polymerase before its release from the genome.