Terminate and make a loop: regulation of transcriptional directionality

Abstract

Bidirectional promoters are a common feature of many eukaryotic organisms from yeast to humans. RNA Polymerase II that is recruited to this type of promoter can start transcribing in either direction using alternative DNA strands as the template. Such promiscuous transcription can lead to the synthesis of unwanted transcripts that may have negative effects on gene expression. Recent studies have identified transcription termination and gene looping as critical players in the enforcement of promoter directionality. Interestingly, both mechanisms share key components. Here, we focus on recent findings relating to the transcriptional output of bidirectional promoters.

Keywords: bidirectional promoters; gene loops; transcriptional termination.

Figure 1

Promoter-associated noncoding RNA. (A) Major classes of promoter-associated ncRNA in animals. (B) ncRNA transcribed from divergent promoters in Saccharomyces cerevisiae. NFR acts as a Pol II promoter for both the protein-coding sequence (marked as a red line) and antisense noncoding sequence (black line). The open and unbiased nature of NFR allows for formation of two independent PICs, which share TFs. Such promoter structure allows Pol II to transcribe in both directions. In mammals the upstream regions are transcribed into PROMPTs and longer ncRNA generally referred to as lncRNA. TSSa-RNA, related to Pol II pausing, are synthesized in both directions. S. cerevisiae bidirectional promoters for protein-coding genes are similarly used to initiate transcription of upstream noncoding regions. Transcribed ncRNA are classified as SUTs, CUTs, or XUTs by their susceptibility to different degrading enzymes (Box 1). SRTs are synthesized when interactions between the promoter and the sense open reading frame terminator is disrupted. All ncRNA initiated from Pol II promoters, except for SRTs, may undergo NRD dependent termination and so are classified as NUTs (marked by dotted line). The most common classes of promoter-associated ncRNA are SUTs and CUTs, whereas occurrence of SRTs and XUTs is similar. Due to the lack of Pol II promoter pausing TSSa-RNA are not present in S. cerevisiae. Abbreviations: CUT, cryptic unstable transcript; lncRNA, long noncoding RNA; ncRNA, noncoding RNA; NFR, nucleosome-free region; NRD, NRD complex; NUT, Nrd1-dependent unterminated transcript; PIC, preinitiation complex; Pol II, RNA polymerase II; PROMPT, promoter upstream transcript; SRT, Ssu72-restricted transcript; SUT, stable unannotated transcript; TF, transcription factor; TSSa-RNA, transcription start site-associated RNA; XUT, Xrn1-depednent transcript.

Figure 2

Mechanisms enforcing promoter directionality. (A) In mammalian cells; (B) in Saccharomyces cerevisiae. Transcription of the upstream noncoding region is restricted by over-representation of termination signals (STOP sign, red rectangles), PAS in mammals or NBS in S. cerevisiae. NBS trigger the NRD termination pathway, which depends on both the NRD complex and CPAC. In contrast PAS-dependent termination is mediated by CPAC only. In both cases released ncRNA is degraded by the exosome. PAS and NBS are depleted over the coding regions. Moreover, in mammalian cells, the coding sequence is enriched in 5′ splice-site-related sequences recognized by U1 small nuclear RNA (snRNA), which inhibits PAS-dependent transcription termination (GO sign). A similar mechanism in yeast is yet to be discovered. Transcriptional directionality is also reinforced by chromatin modification. Nucleosomes with transcription-positive histone marks are presented as blue semitransparent circles, whereas nucleosomes with negative marks are shown in red. A pioneer round of transcription of the coding region establishes a gene loop. Termination factors recruited to Pol II transcribing in the vicinity of the terminator region interacts with initiation factors on the promoter and these juxtapose both regions. The formed loop enhances transcriptional reinitiation into the coding sequence (denoted by bent blue arrows). Abbreviations: CPAC, cleavage and polyadenylation complex; NBS, NRD-binding sites; ncRNA, noncoding RNA; NRD, NRD complex; PAS, poly(A) site; Pol II, RNA polymerase II.