GSE184099
Landscape of Transcription Termination in Arabidopsis Revealed by Single-molecule Nascent RNA Sequencing [BS-seq]
The dynamic process of transcription termination produces transient RNA intermediates, such as the full-length readthrough, 5' and 3' cleavage products, and polyadenylated nascent RNAs, which are difficult to distinguish from each other via short-read sequencing methods. Here, we used single-molecule nascent RNA sequencing to characterize these various forms of transient RNAs during termination at genome-wide scale in Arabidopsis. Our data revealed a wide range of termination windows (defined as the median readthrough distance) among genes, ranging from ~50 nt to over 1000 nt. The ends of termination windows precisely match the peak of Pol II occupancy and co-localize with termination factors. We also discovered a termination mechanism shaped by the downstream tRNA genes, suggesting that elongating Pol II can be expelled by Pol III activity. Mutation of the exonuclease AtXRN3 leads to a drastic accumulation of 3' cleaved readthrough RNAs. Moreover, 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. Our results revealed the diverse termination patterns in Arabidopsis, and our method is applicable to study the global termination landscape in a broad range of species. Overall design: Nanopore nascent RNA sequencing to study the termination landscape BS_seq profiling of WT and xrn3 mutant seedlings