April 28th, 2024
Recent Publications Harnessing the Power of Translatomics.
Every week we provide a digest of a small number of recent interesting papers in the field of translatomics.
In this week’s Sunday papers, Hansel Fröse, A.F. et al. look into dynamic alternative polyadenylation start sites which might alter the availability of miRNA target sites in 3′ UTR throughout cardiomyogenic differentiation, while Gao, L. et al. delve into mechanisms of maintenance of human tRNA anticodon pools during differentiation and finally, Eliseeva, I.A. et al. uncovers the dual role of Y-box-binding proteins in cellular translation.
Alternative polyadenylation and dynamic 3'UTR length is associated with polysome recruitment throughout cardiomyogenic differentiation of hESCs
Frontiers in Molecular Biosciences, 2024
Hansel Fröse, A.F., Allmer, J., Friedrichs, M., dos Santos, H.G., Dallagiovanna, B., Spangenberg, L.
Given that cardiovascular disease remains the primary cause of death worldwide, there is a clear imperative for increased research into cardiomyogenic differentiation to enhance potential therapeutic interventions. The process of cardiomyogenic differentiation is significantly regulated at post-transcriptional level. Alternative polyadenylation (APA) is one of the ways in which a cell can achieve transcript diversity via generation of isoforms with varying 3’ UTRs. It is known that 3’ UTRs have various regulatory elements including microRNA and RNA-binding protein target sites which can influence gene expression. APA site usage can be dynamic and can vary during cell differentiation.
In this study, Hansel Fröse, A.F et al. through the use of polysome-seq discovered that transcripts with shorter 3’UTRs are preferentially expressed in differentiated cardiomyocytes in comparison to the pluripotent stage. Five differentiation stages were monitored: the pluripotency stage (Day 0), aggregation of embryoid bodies (Day 1), cardiac mesodermal stage (Day 4), cardiac progenitor (Day 9), and cardiomyocytes (Day 15). The authors observed that transcripts with shorter 3’ UTRs were preferably expressed on Day 1 and Day 15, while a preference for longer 3’ UTRs was detected on Day 4 and Day 9, with the most significant difference seen on Day 4.
The authors also searched for miRNA that would target the alternative 3’ UTR region of the differentially expressed transcripts during differentiation stages and constructed a regulatory network of targeted genes. By using this network, they identified a set of suppressed cell cycle genes on Day 15 which is the differentiated state of cardiomyocytes and it corresponds well with the fact that differentiated cells and cardiomyocytes show low proliferation capability due to their inability to re-enter the cell cycle.
Selective gene expression maintains human tRNA anticodon pools during differentiation
Nature Cell Biology, 2024
Gao, L., Behrens, A., Rodschinka, G., Forcelloni, S., Wani, S., Strasser, K., Nedialkova, D.D.
The relative abundance of tRNAs matching a given codon can influence the rate and fidelity of mRNA translation. The human genome encodes hundreds of predicted tRNAs, many of them in multiple copies. The mechanisms of regulation of tRNA expression that selectively shapes the tRNA repertoire in different cells remain largely unknown due to the tRNA gene’s multicopy nature. A simplistic transcription regulation model of tRNA genes cannot fully explain the differences in tRNA levels.
In this study, Gao L. and colleagues measured tRNA expression of human induced pluripotent stem cells (hiPSC) and their differentiated states of neuronal and cardiac cells by utilising modification-induced misincorporation tRNA sequencing (mim-tRNAseq), ribosome profiling and Pol III chromatin immunoprecipitation–sequencing (ChIP–Seq).
They discovered that differential RNA polymerase III (Pol III) occupancy at tRNA loci explains nearly all of the variation in mature tRNA abundance in hiPSC as well as during their differentiation. It is driven by sequence features in the tRNA gene body and 5′ flanking regions. A significantly higher density of both the A- and B-box promoter consensus sequences were found in housekeeping tRNAs relative to repressed and inactive tRNAs. Additionally, housekeeping tRNAs tend to have GC-rich sequences and poly-A stretches in 5’ flanking regions.
Overall, while Pol III transcribes a wide variety of tRNA transcripts in stem cells, during differentiation, only a subset of tRNAs, defined as ‘housekeeping,’ are produced. This shift can be explained by the decrease of mTORC1 signalling which activates the RNA polymerase III repressor MAF1. MAF1 works as a restrictor of Pol III to a ‘housekeeping’ set of tRNA genes – those that are stably expressed and constitute the most abundant isodecoders in each anticodon family.
Y-Box-Binding Proteins Have a Dual Impact on Cellular Translation
International Journal of Molecular Sciences, 2024
Y-box-binding proteins (YB proteins) are implicated in translation, transcription, and regulation of mRNA stability and their roles in the development of cancer have been thoroughly explored. YB proteins have highly homological cold shock domains and similar arginine-rich motifs, which suggests that they might function similarly in the cell. There are two YB proteins in somatic cells – YB-1 and YB-3. In a previous study it was demonstrated that knockout of YB-1 induces overexpression of YB-3 which interacts with a similar subset of mRNAs as YB-1 suggesting that YB-1 and YB-3 might functionally substitute one another in regulation of translation.
In this study, Eliseeva I.A. et al. through the use of RNA-seq, Ribo-seq, PAR-CLIP and eCLIP data in HEK293T cells demonstrated that YB-1 and YB-3 proteins have a dual effect on translation. It was shown that overexpression of the YB proteins decreased global translation, however expression of either partially restores global translation compared to the cells where no YB protein was produced. To investigate this increase on global translation the authors looked at Ribo-seq and RNA-seq and calculated the translation efficiency of each gene. Looking at the genes with the largest changes, they found 3 genes known to be involved in global translation regulation, EIF4EBP1, EIF4EBP2, and SESN2. The translation efficiency of EIF4EBP1 and SESN2 in particular decreased by 40% in YB-expressing cells, which the authors propose is in turn responsible for the overall increase in translation levels.