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Series GSE109974 Query DataSets for GSE109974
Status Public on Sep 30, 2018
Title RNA polymerase II activity revealed by GRO-seq and pNET-seq in Arabidopsis
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary RNA polymerase II (Pol II) play an essential role in gene expression. Here, we adapted mammalian Native Elongation Transcript sequencing and Global Run On sequencing to profile nascent RNA genome wide in Arabidopsis. We found Pol II tends to accumulate downstream of transcription start site and pausing at proximal promoter is an important regulatory step for Pol II transcription although loosely controlled. Furthermore, the Pol II with unphosphorylated carboxyl-terminal domain (CTD) mainly accumulates downstream the TSS, while the Ser5P CTD Pol II associates with spliceosome, and the Ser2P CTD Pol II presents a sharp peak 250 base pair downstream of polyadenylation site indicating a stringent control of termination for protein coding genes; whilst the termination of noncoding genes is not. Active expressed genes can be classified into three clusters according to the distribution patterns of different Pol II isoforms. In summary, we demonstrated the modified plant GRO-seq and mNET-seq are suitable to study RNA Pol II dynamics in planta. Although transcription is conserved among high eukaryotes, Pol II has its feature in Arabidopsis.
Overall design Transcriptional profiling by GRO-seq and mNET-seq
Contributor(s) Zhu J, Liu M, Liu X, Dong Z
Citation(s) 30374093
Submission date Feb 01, 2018
Last update date Jan 23, 2019
Contact name Zhicheng Dong
Organization name Guangzhou University
Department School of Life Sciences
Street address 230 Wai Huan Xi Road,Guangzhou Higher Education Mega Center
City Guangzhou
State/province Guangdong
ZIP/Postal code 510006
Country China
Platforms (3)
GPL13222 Illumina HiSeq 2000 (Arabidopsis thaliana)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (12)
GSM2974947 GRO-seq_rep1
GSM2974948 GRO-seq_rep2
GSM2974949 mNET_total_rep1
BioProject PRJNA432502
SRA SRP131952

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Supplementary file Size Download File type/resource
GSE109974_RAW.tar 133.2 Mb (http)(custom) TAR (of BEDGRAPH, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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