Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression

Abstract

Summary Long undecoded transcript isoforms (LUTIs) represent a class of non-canonical mRNAs that downregulate gene expression through the combined act of transcriptional and translational repression. While single gene studies revealed important aspects of LUTI-based repression, how these features affect gene regulation on a global scale is unknown. Using transcript leader and direct RNA sequencing, here, we identify 74 LUTI candidates that are specifically induced in meiotic prophase. Translational repression of these candidates appears to be ubiquitous and is dependent on upstream open reading frames. However, LUTI-based transcriptional repression is variable. In only 50% of the cases, LUTI transcription causes downregulation of the protein-coding transcript isoform. Higher LUTI expression, enrichment of histone 3 lysine 36 trimethylation, and changes in nucleosome position are the strongest predictors of LUTI-based transcriptional repression. We conclude that LUTIs downregulate gene expression in a manner that integrates translational repression, chromatin state changes, and the magnitude of LUTI expression.

Monitoring the 5’UTR landscape reveals 5’terminal oligopyrimidine (TOP) motif switches to drive translational efficiencies

“…Nevertheless, given the relatively small cohort of 5`UTR isoform switches, our observations also suggest that the network of translational regulators is genome-wide still the main factor determining protein synthesis rates. 5`UTR isoform switches have emerged as an elegant non-canonical mode of gene expression regulation (Chen et al, 2017;Cheng et al, 2018;Chia et al, 2017;Tresenrider et al, 2021). Our findings add yet another simple mechanism to the 5`UTR landscape and suggest that exposing or masking TOP motifs from the 5`UTR can markedly alter the translational efficiency of the mRNA coding sequence.…”

“…5’UTR isoform switches have emerged as an elegant non-canonical mode of gene expression regulation (Chen et al, 2017; Cheng et al, 2018; Chia et al, 2017; Tresenrider et al, 2021). Our findings add yet another simple mechanism to the 5’UTR landscape and suggest that exposing or masking TOP motifs from the 5’UTR can markedly alter the translational efficiency of the mRNA coding sequence.…”

“…Transcriptional and translational control are key steps in the gene expression pathway; however, to what extent these two processes can be collectively coordinated is still poorly understood. Recently, several studies have suggested a non-canonical mode of regulation, by which a large cohort of yeast genes switch between short and long 5’ untranslated regions (UTRs) while keeping the coding sequences (CDSes) identical (Chen et al, 2017; Cheng et al, 2018; Hollerer et al, 2019; Tresenrider et al, 2021). Since 5’UTRs are critical for ribosome recruitment and ultimately initiation of translation (Hinnebusch et al, 2016), switching between these 5’UTR isoforms resulted in differential translational efficiencies of these mRNAs.…”

“…Our findings suggest that switching between TOP and non-TOP motif-containing 5’UTR isoforms is a previously unappreciated, elegantly simple way to effectively alter translational efficiencies of a cohort of genes in squamous cell carcinomas. More generally, since alternative transcription start sites (Pelechano et al, 2013) and alternative splicing events are widespread (Kahles et al, 2018), the set of post-transcriptional regulatory elements such as RNA-binding protein (RBP) binding sites, uORFs (Cheng et al, 2018; Tresenrider et al, 2021), or TOP motifs could be widely used in different biological contexts to link transcription and translation and direct the translational potential of an mRNA by the precise 5’ transcript sequence.…”

Post-transcriptionally regulated genes are essential for pluripotent stem cell survival

“…Furthermore, exogenous cytosolic SRRT mRNA was translated in HDFs (Figure 5G), suggesting the cytoplasmic mRNA level is key for proper protein expression. Another possible mechanism for translation inhibition in differentiated cells is ribosome pausing, in which the mRNA binds to ribosomes that are not active or select non-canonical start codons (Chandrasekaran et al, 2019; Darnell et al, 2018; Tresenrider et al, 2021). A third possibility is that aberrant proteins were degraded immediately after the production by a quality control pathway of the mRNA and ribosome (D’Orazio and Green, 2021).…”