Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis

Abstract

RNA polymerase II (RNAPII) transcription converts the DNA sequence of a single gene into multiple transcript isoforms that may carry alternative functions. Gene isoforms result from variable transcription start sites (TSSs) at the beginning and polyadenylation sites (PASs) at the end of transcripts. How alternative TSSs relate to variable PASs is poorly understood. Here, we identify both ends of RNA molecules in Arabidopsis thaliana by transcription isoform sequencing (TIF-seq) and report four transcript isoforms per expressed gene. While intragenic initiation represents a large source of regulated isoform diversity, we observe that~14% of expressed genes generate relatively unstable short promoter-proximal RNAs (sppRNAs) from nascent transcript cleavage and polyadenylation shortly after initiation. The location of sppRNAs correlates with the position of promoter-proximal RNAPII stalling, indicating that large pools of promoter-stalled RNAPII may engage in transcriptional termination. We propose that promoter-proximal RNAPII stalling-linked to premature transcriptional termination may represent a checkpoint that governs plant gene expression.

Chromatin-associated SUMOylation controls the transcriptional switch between plant development and heat stress responses

“…Interestingly, further analysis indicated that these SUMO binding sites were predominantly located around TSSs, including promoter-proximal regions and potential 5′ UTR regions ( Figure 1 C, Supplemental Figure 3 A). Because previous work indicated that these regions are critical for TF binding and transcription regulation ( Ohler and Wassarman, 2010 ; Shao and Zeitlinger, 2017 ; Thomas et al., 2020 ), our results suggest that SUMOylation may play a role in the modulation of gene transcription. By contrast, SUMO signals were weak in intergenic, transposon, and heterochromatin regions ( Supplemental Figure 4 ).…”

“…Our ChIP-seq data indicated that SUMO-associated chromatin peaks are predominantly located on promoter-TSS gene regions, which harbor active epigenetic markers ( Figure 1 D and 1F) ( He et al., 2011 ), suggesting that SUMOylation plays a role in transcriptional activation. Interestingly, these SUMO-enriched sites are preferentially localized around the TSS ( Figure 1 C), similar to the distribution of TFs ( Ohler and Wassarman, 2010 ; Shao and Zeitlinger, 2017 ; Thomas et al., 2020 ), such as HSFA1a ( Supplemental Figure 12 A). Consistently, predicted motifs in the HS SUMO peaks are also highly enriched in these regions ( Supplemental Figure 12 B).…”

TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes

“…2E). Transcription of Arabidopsis genes frequently produces short promoter-proximal RNAs (sppRNA) which are sensitive to the HEN2 exonuclease and terminate about 100 nt downstream from the TSS [31]. We found that 5’ borders of genes called by TranscriptomeReconstructoR are in a better agreement with the sppRNA termination sites than 5’ borders of their annotated mates in both TAIR10 and Araport11 (Fig.…”

“…A representative example of such gene on Fig. S4 (see Additional File 2) demonstrates that its split nature can be further supported by independent TIF-seq dataset which detects both ends of mature RNA transcripts [31].…”

Terminus-Associated Non-coding RNAs: Trash or Treasure?

“…On the other hand, evidence of transcriptional stalling via RNAPII backtracking triggering nucleolytic degradation of the nascent RNA indicates that TTSa-RNAs may be implied in the termination of mRNA transcription ( Valen et al, 2011 ). For instance, a recent study in A. thaliana indicated that promoter-proximal RNAPII stalling can regulate plant gene transcription ( Thomas et al, 2020 ). Thus, it is reasonable to infer that mammalian TTSa-RNAs might participate in the regulation of gene transcription through the modulation of transcriptional termination ( Figure 3 ).…”