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Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12316-12321. Epub 2016 Oct 11.

Nascent RNA sequencing reveals distinct features in plant transcription.

Author information

1
Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093; Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037.
2
School of Medicine, University of California, San Diego, La Jolla, CA 92093 cbenner@ucsd.edu chory@salk.edu.
3
Plant Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093; Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, CA 92037; cbenner@ucsd.edu chory@salk.edu.

Abstract

Transcriptional regulation of gene expression is a major mechanism used by plants to confer phenotypic plasticity, and yet compared with other eukaryotes or bacteria, little is known about the design principles. 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 characteristics of plant transcription. De novo annotation of nascent transcripts accurately mapped start sites and unstable transcripts. Examining the promoters of coding and noncoding transcripts identified comparable chromatin signatures, a conserved "TGT" core promoter motif and unreported transcription factor-binding sites. Mapping of engaged RNA polymerases showed a lack of enhancer RNAs, promoter-proximal pausing, and divergent transcription in Arabidopsis seedlings and maize, which are commonly present in yeast and humans. In contrast, Arabidopsis and maize genes accumulate RNA polymerases in proximity of the polyadenylation site, a trend that coincided with longer genes and CpG hypomethylation. Lack of promoter-proximal pausing and a higher correlation of nascent and steady-state transcripts indicate Arabidopsis may regulate transcription predominantly at the level of initiation. Our findings provide insight into plant transcription and eukaryotic gene expression as a whole.

KEYWORDS:

5′GRO-seq; GRO-seq; RNA polymerase pausing; nascent transcripts; plant transcription

PMID:
27729530
PMCID:
PMC5087027
DOI:
10.1073/pnas.1603217113
[Indexed for MEDLINE]
Free PMC Article

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