Promoter architecture determines cotranslational regulation of mRNA

Abstract

Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of cotranslational regulation on mRNA levels is determined by promoter architecture. By using a novel computational genetic screen of 6402 RNA-seq experiments, we identify the RNA helicase Dbp2 as the mechanism by which cotranslational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus, the ORF sequence is a major regulator of gene expression, and a nonlinear interaction between promoters and ORFs determines mRNA levels.

Poor codon optimality as a signal to degrade transcripts with frameshifts

“…In yeast, NMD is thought to act on long 3'UTRs [15,16], so that transcripts bearing 3'UTRs longer than 250 nucleotides are targeted by NMD (Figure 1). Recent work from our group has shown that this is mostly true and, importantly, the strength of NMD depends linearly on 3'UTR length [11] ( Figure 3B). However, native 3'UTR lengths are highly variable, ranging from 0 to 1461 nucleotides [17].…”

“…We found that almost all frameshifts produce a large decrease in tAI after the mutation ( Figure 3D). The change in tAI range due to frameshifts decreases mRNA levels [11] ( Figure 3A). In contrast, ~50% of errors produce 3'UTRs in the range of native 3'UTR lengths ( Figure 3D), likely unaffected by NMD [11] ( Figure 3B).…”

“…Recent work from our group [11] provides an unexpected clue towards understanding mRNA quality control. We found that two mechanisms of co-translational regulation, NMD and codon bias-dependent mRNA expression [18,19] (Figure 2A) are genetically linked; both pathways are regulated by the DEAD-box RNA helicase Dbp2 and by promoter architecture.…”

“…This follows from the observation that frameshifts generate premature termination codons (PTCs), recognition of which targets the transcript for NMD. However, the quantitative effects of NMD, when measured, are often small [11,12]. In addition, a large fraction native transcripts (between 5%-30% depending on the genome) are targeted by NMD [13].…”

Gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

“…mRNA transcription is controlled via the gene regulatory structure, comprised of coding and cis -regulatory regions that include promoters, untranslated regions (UTRs), and terminators each encoding a significant amount of information related to mRNA levels 9 . For instance, in Saccharomyces cerevisiae , properties of individual cis -regulatory regions can explain up to half of the variation in mRNA levels [10][11][12][13][14][15] . Considering that each part of the gene structure controls a specific process related to mRNA synthesis and decay 9,16,17 , as well as the overall transcription efficiency 18 , all gene parts must be concerted in perfectly timed execution in order to regulate expression.…”