A pre-initiation complex at the 3′-end of genes drives antisense transcription independent of divergent sense transcription

Abstract

The precise nature of antisense transcripts in eukaryotes such as Saccharomyces cerevisiae remains elusive. Here we show that the 3′ regions of genes possess a promoter architecture, including a pre-initiation complex (PIC), which mirrors that at the 5′ region and which is much more pronounced at genes with a defined antisense transcript. Remarkably, for genes with an antisense transcript, average levels of PIC components at the 3′ region are ∼60% of those at the 5′ region. Moreover, at these genes, average levels of nascent antisense transcription are ∼45% of sense transcription. We find that this 3′ promoter architecture persists for highly transcribed antisense transcripts where there are only low levels of transcription in the divergent sense direction, suggesting that the 3′ regions of genes can drive antisense transcription independent of divergent sense transcription. To validate this, we insert short 3′ regions into the middle of other genes and find that they are capable of both initiating antisense transcripts and terminating sense transcripts. Our results suggest that antisense transcription can be regulated independently of divergent sense transcription in a PIC-dependent manner and we propose that regulated production of antisense transcripts represents a fundamental and widespread component of gene regulation.

Using both strands: The fundamental nature of antisense transcription

“…A study in human cells by Conley & Jordan 30 identified many thousands of antisense promoters using CAGE analysis, which characterizes the 5 0 ends of transcripts, and found that such promoters were generally present toward the 3 0 ends of genes. Antisense transcription from these promoters was abundant, though not as high as from sense promoters, in agreement with our findings in yeast, 4 varied between different cell types, and showed evidence of activatory histone marks at their promoters that correlated with the level of RNAPII occupancy. Perhaps most importantly, they found that the activity of sense promoters did not correlate with the levels of activity of their associated antisense promoter.…”

“…9 Based on this, and the abundant nature of antisense transcription genome-wide, 4 we propose that antisense transcription should be considered a canonical feature of genes, as opposed to an idiosyncrasy particular to just a subset of genes. Future work should seek to understand the function of the dynamic chromatin established by antisense transcription.…”

“…1A). 4,5 This leads to transcription along the antisense strand of the gene, giving rise to non-coding, antisense transcripts, the function of which is poorly understood.…”

“…Shown are the average levels of TBP and TFIIB, 2 factors that play a critical role in transcription initiation, as well as nucleosome occupancy, relative to the start site and end site of the sense transcript. 4 This reveals the presence of 2 promoter architectures at both ends of the gene, one directing sense transcription and the other antisense transcription, referred to here as the sense and antisense promoters respectively. (B) Transcription occurs extensively on both the sense and antisense strands of genes across the yeast genome.…”

“…2 Using NET-seq measurements in S. cerevisiae, we previously demonstrated that the level of antisense transcription across a gene is, on average, onetenth of the level of protein-coding sense transcription, 4 increased to one-fifth when considering those genes with a previously defined antisense transcript (approximately a third of genes). 7,8 Considering that coding transcription plays a fundamental role in protein biosynthesis, while antisense transcription does not, this is a staggering ratio, posing the immediate question: if so much energy is being invested in producing transcripts that are themselves being extensively degraded, then why is this transcription happening in the first place?…”