Nascent RNA sequencing reveals distinct features in Plant transcription

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