通过单分子新生 RNA 测序揭示拟南芥转录终止的全景。

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing.

机构信息

Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.

Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, 518055, China.

出版信息

Genome Biol. 2021 Nov 25;22(1):322. doi: 10.1186/s13059-021-02543-4.

BACKGROUND

The dynamic process of transcription termination produces transient RNA intermediates that are difficult to distinguish from each other via short-read sequencing methods.

RESULTS

Here, we use single-molecule nascent RNA sequencing to characterize the various forms of transient RNAs during termination at genome-wide scale in wildtype Arabidopsis and in atxrn3, fpa, and met1 mutants. Our data reveal a wide range of termination windows among genes, ranging from ~ 50 nt to over 1000 nt. We also observe efficient termination before downstream tRNA genes, suggesting that chromatin structure around the promoter region of tRNA genes may block pol II elongation. 5' Cleaved readthrough transcription in atxrn3 with delayed termination can run into downstream genes to produce normally spliced and polyadenylated mRNAs in the absence of their own transcription initiation. Consistent with previous reports, we also observe long chimeric transcripts with cryptic splicing in fpa mutant; but loss of CG DNA methylation has no obvious impact on termination in the met1 mutant.

CONCLUSIONS

Our method is applicable to establish a comprehensive termination landscape in a broad range of species.

背景

转录终止的动态过程会产生瞬时 RNA 中间体，通过短读测序方法很难将它们彼此区分开来。

结果

在这里，我们使用单分子新生 RNA 测序技术，在野生型拟南芥和 atxrn3、fpa 和 met1 突变体中，在全基因组范围内对终止过程中的各种瞬时 RNA 进行了表征。我们的数据显示，基因之间存在广泛的终止窗口，范围从~50nt 到超过 1000nt。我们还观察到在下游 tRNA 基因之前存在有效的终止，这表明 tRNA 基因启动子区域周围的染色质结构可能会阻止 pol II 的延伸。atxrn3 中的 5' 切割通读转录会延迟终止，可以进入下游基因，在没有自身转录起始的情况下产生正常剪接和多聚腺苷酸化的 mRNA。与之前的报道一致，我们还观察到 fpa 突变体中存在带有隐匿性剪接的长嵌合转录本；但是 CG DNA 甲基化的缺失对 met1 突变体中的终止没有明显影响。