title: Nascent RNA sequencing reveals distinct features in plant transcription.
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.
authors.affiliation: 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.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Hetzel
authors.affiliation: 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.
authors.forename: Sascha H
authors.initials: SH
authors.lastname: Duttke
authors.affiliation: School of Medicine, University of California, San Diego, La Jolla, CA 92093 cbenner@ucsd.edu chory@salk.edu.
authors.forename: Christopher
authors.initials: C
authors.lastname: Benner
authors.affiliation: 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.
authors.forename: Joanne
authors.initials: J
authors.lastname: Chory
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D002843:Chromatin / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D011401:Promoter Regions, Genetic; D012313:RNA / Q000235:genetics; D036226:Seedlings / Q000235:genetics* / Q000254:growth & development; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D012313:RNA
keywords: 5′GRO-seq; GRO-seq; RNA polymerase pausing; nascent transcripts; plant transcription