Paired-End Analysis of Transcription Start Sites in Arabidopsis Reveals Plant-Specific Promoter Signatures  

Abstract

Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here, we present a publicly available, large-scale transcription start site (TSS) data set in plants using a high-resolution method for analysis of 59 ends of mRNA transcripts. Our data set is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole root samples. Using this data set, we grouped TSS reads into "TSS tag clusters" and categorized clusters into three spatial initiation patterns: narrow peak, broad with peak, and weak peak. We then designed a machine learning model that predicts the presence of TSS tag clusters with outstanding sensitivity and specificity for all three initiation patterns. We used this model to analyze the transcription factor binding site content of promoters exhibiting these initiation patterns. In contrast to the canonical notions of TATA-containing and more broad "TATA-less" promoters, the model shows that, in plants, the vast majority of transcription start sites are TATA free and are defined by a large compendium of known DNA sequence binding elements. We present results on the usage of these elements and provide our Plant PEAT Peaks (3PEAT) model that predicts the presence of TSSs directly from sequence.

Small Genetic Circuits and MicroRNAs: Big Players in Polymerase II Transcriptional Control in Plants

“…The scans used the positional weight matrix (PWM) representing each CPE used by Morton et al (2014), along with additional PWMs from the JASPAR database (Bryne et al, 2008) in order to include TFs analyzed by Kumari and Ware (2013). We found that for any given CPE, very liberal cutoff settings resulted in "identifying" that CPE in 54 to 85% of sequences (Table 1), with only 1% percent of genes having no "identified" CPE.…”

“…TSS-Seq data provide a new window into associations between TSS distribution along the genome, the location of TF binding sites (TFBSs), chromatin state surrounding the TSS regions, and gene function. Studies in both plants and animals conclude that TSSs fall into several general "shape" categories according to the distribution of TSSs along the genome (Carninci et al, 2006;Ni et al, 2010;Morton et al, 2014) (Figure 2). In all of these studies, TSS peak shapes tend to associate with gene functional categories in the following way: Narrow peaks tend to associate with time or tissue-specifically expressed genes, broad/ weak peaks with housekeeping and other constitutively and/or ubiquitously expressed genes, and broad with peaks with circadian and other genes that have a mixture of these qualities over space and time.…”

Carotenogenesis Is Regulated by 5′UTR-Mediated Translation of Phytoene Synthase Splice Variants

“…They differ in the length and in the exon/intron retention of their 59UTR. Recent transcript start site analyses suggest that both splice variants emerge from different premRNAs through alternative transcription initiation (Morton et al, 2014; a scheme on the formation of both ASVs is shown in Fig. 1A; a sequence alignment is shown in Supplemental Fig.…”

Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis

“…It is well known that transcription initiation at a transcription start site is not always initiated with single nucleotide accuracy (Schlüter et al 2010;Sharma et al 2010;Cortes et al 2013;Morton et al 2014). To take this into account, when locations distant by 4 bp or less from each other have mapped reads with TSStags and at least one of them is classified as a TSS candidate, the multiple tag signals are grouped in a single region that encompasses all those locations (Supplemental Tables SA, SB).…”