Noise reduction by upstream open reading frames

Abstract

Gene expression is prone to burst production, making it a highly noisy process that requires additional controls. Upstream open reading frames (uORFs) are widely present in the 5′ leader sequences of 30–50% of eukaryotic messenger RNAs1–3. The translation of uORFs can repress the translation efficiency of the downstream main coding sequences. Whether the low translation efficiency leads to a different variation, or noise, in gene expression has not been investigated, nor has the direct biological impact of uORF-repressed translation. Here we show that uORFs achieve low but precise protein production in plant cells, possibly by reducing the protein production rate. We also demonstrate that, by buffering a stable TIMING OF CAB EXPRESSION 1 (TOC1) protein production level, uORFs contribute to the robust operation of the plant circadian clock. Our results provide both an action model and the biological impact of uORFs in translational control to mitigate transcriptional noise for precise protein production.

A natural uORF variant confers phosphorus acquisition diversity in soybean

“…Even though the variant in 5’UTR might affect the binding of a transcription factor 41 , the contribution of transcriptional regulation could be minor in our study because the causal SNP changes the length of a uORF, which often functions at the post-transcriptional and translational levels 42 . uORF is known to play instrumental roles in translation control of the downstream main ORF in a broad spectrum of eukaryotes 43 . Furthermore, when a uORF is translated, a long 3’UTR downstream of the uORF may activate nonsense-mediated decay to affect mRNA stability and thus steady-state mRNA levels 26 .…”

Circadian ribosome profiling reveals a role for thePeriod2upstream open reading frame in sleep

“…Approximately 50% of mouse and human mRNAs contain uORFs, and uORFs are associated with widespread translational repression (Johnstone et al, 2016). Thus, uORF translation suppression may constitutively lower the abundance of circadian proteins or provide a post-transcriptional foothold to adjust protein abundance by altering the activities of ribosome reinitiation factors (Bohlen et al, 2020; Morris and Geballe, 2000; Schleich et al, 2014), and mutagenesis of uORFs have been shown to alter rhythmicity in other circadian systems (Diernfellner et al, 2005; Wu et al, 2022)…”

“…Thus, uORF-mediated translation suppression may constitutively suppress the abundance of circadian proteins or provide a post-transcriptional foothold to adjust protein abundance by altering the activities of ribosome reinitiation factors (37)(38)(39). Moreover, mutagenesis of uORFs have been shown to alter rhythmicity in other circadian systems (40,41). Not all ribosome binding in 5'UTRs was associated with uORFs, and we observed extensive ribosome binding in areas without an apparent uORF for Cry1, Nr1d1, Clock, Dbp, and Per3 (Fig.…”

“…Approximately 50% of mouse and human mRNAs contain uORFs, and uORFs are associated with widespread translational repression (Johnstone et al, 2016). Thus, uORF translation suppression may constitutively lower the abundance of circadian proteins or provide a post-transcriptional foothold to adjust protein abundance by altering the activities of ribosome reinitiation factors (Bohlen et al, 2020;Morris and Geballe, 2000;Schleich et al, 2014), and mutagenesis of uORFs have been shown to alter rhythmicity in other circadian systems (Diernfellner et al, 2005;Wu et al, 2022) The uORF in the Per2 5'UTR is an attractive target to understand the role of uORFs in circadian biology, not only because cis-elements within the Per2 promoter are wellunderstood (Doi et al, 2019;Gekakis et al, 1998;Hao et al, 1997;Ueda et al, 2005), but also because the Per2 uORF is too short to encode a peptide. PER2 production is posttranscriptionally controlled by miRNAs (Park et al, 2020;Yoo et al, 2017), antisense transcription (Mosig et al, 2021), and hnRNP1-mediated mRNA degradation (Woo et al, 2009), which suggests that Per2 post-transcriptional control is important for producing the correct amount of PER2 protein.…”

The Emerging Role of uORF-Encoded uPeptides and HLA uLigands in Cellular and Tumor Biology

“…Main protein expression in uORF-bearing transcripts requires leaky scanning across the uORF start site(s) or reinitiation of ribosomes after translating the uORF followed by reloading with essential co-factors [ 71 , 72 ]. Upstream ORFs play critical roles in diverse cellular programs including the integrated stress response (ISR) [ 71 , 73 ], circadian timekeeping [ 74 , 75 ], and microtubule organization [ 76 ]. Translational regulation allows for immediate responses to changing environmental conditions, bypassing the need for time-consuming transcription of new mRNAs.…”