512 / 2019-03-01 11:43:43

Immediate transcriptional responses to heat shock revealed by nascent RNA sequencing

nascent RNA,GRO-seq,pNET-seq,heat stress,Arabidopsis,polymerase II

全体主题 > RNA Biology

As sessile organisms, plants have to deal with fluctuated environment at transcriptional level promptly. RNA polymerase II (Pol II) is the key protein responsible for the transcription of protein-coding genes and some of the non-coding genes. Pol II activity can be monitored by detecting its product, nascent RNA. To directly measure Pol II's response to heat shock (HS), we have developed two nascent RNA profiling methods, plant native elongating transcript sequencing (pNET-seq) and global run-on sequencing (GRO-seq). pNET-seq and GRO-seq revealed RNA Pol II activity features: 1) 5' pausing at proximal promoter; 2) the Pol II with an unphosphorylated carboxyl terminal domain (CTD) mainly accumulates at 5' end, while the Ser5P CTD Pol II associates with spliceosome; 3) the Ser2P CTD Pol II presents a sharp peak at the polyadenylation site; 4) active genes can be classified into three clusters with different transcription modes and chromatin states. Furthermore, we investigated the transcription engaged Pol II distribution upon 5-min heat shock using GRO-seq. We found that plants' HS response is transcriptionally very quick. GRO-seq is more sensitive and robust than RNA-seq to dectect quick response to HS. Heat stress memory takes place at multiple steps of transcription cycles such as Pol II recruitment, 5' pausing, elongation, and termination.