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Series GSE83108 Query DataSets for GSE83108
Status Public on Oct 06, 2016
Title Nascent RNA sequencing reveals distinct features in Plant transcription
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Transcriptional regulation of gene expression is a major mechanism utilized by plants to confer phenotypic plasticity, yet compared to archaebacteria, eubacteria, and other eukaryotes, very little is known about the design principles of plant transcription. We generated an extensive catalog of nascent and steady state transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5'GRO-seq and RNA-seq and reanalyzed published maize data to capture the general characteristics of plant transcription. De novo annotation of nascent transcripts enabled accurate start site annotations and revealed novel unstable transcripts. Coding and non-coding transcripts exhibit comparable promoter chromatin configurations. Motif analysis revealed new regulatory DNA elements including a conserved 'TGT core promoter motif' and unreported transcription factor (TF) binding sites. Mapping of engaged RNA polymerases revealed a lack of enhancer RNAs, promoter proximal pausing, and divergent transcription in Arabidopsis and maize, which are commonly present in humans and yeast. In contrast, Arabidopsis and maize genes accumulate RNA polymerases adjacent to the polyadenylation site immediately downstream of genes, a trend that correlated with increasing gene length and coincided with hypomethylation of CpG residues. Lack of promoter proximal pausing and a higher correlation of nascent and steady state transcripts indicates Arabidopsis regulates transcription predominantly at the level of initiation. Together, these findings provide insight into plant transcriptional mechanisms, but also eukaryotic transcription in general.
 
Overall design Transcriptional profiling by 5'GRO-seq, GRO-seq, and RNA-seq
 
Contributor(s) Hetzel J, Duttke SH, Benner C, Chory J
Citation(s) 27729530
Submission date Jun 08, 2016
Last update date May 15, 2019
Contact name Christopher Benner
E-mail(s) cbenner@ucsd.edu
Organization name University of California, San Diego (UCSD)
Department Medicine
Street address 9500 Gilman Dr. MC 0640
City La Jolla
State/province California
ZIP/Postal code 92093-0640
Country USA
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (5)
GSM2193123 5'GRO-seq
GSM2193124 GRO-seq rep1
GSM2193125 GRO-seq rep2
Relations
BioProject PRJNA324774
SRA SRP076266

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83108_transcripts.txt.gz 653.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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