June 4th

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, Sidhaye et al. (2023) describe how posttranscriptional factors affect protein abundance and gene expression during human corticogenesis. Ma et al. (2023) used ribosome footprint profiling in conjunction with a multi-omics approach to examine the metabolism of A. truncatum seed oil and its regulatory mechanisms. Lastly, Havkin-Solomon et al. (2023) investigate the role of RPS3 mRNA-binding in mammalian cell-specific mRNA translation and ribosome specialization.

Integrated transcriptome and proteome analysis reveals posttranscriptual regulation of ribosomal genes in human brain organoids

Elfie, 2023
Sidhaye, J., Trepte, P., Sepke, N., Novatchkova, M., Schutzbier, M., Dürnberger, G., Mechtler, K. and Knoblich, J.A.

Excitatory neurons and glial cells are produced by multipotent neural progenitors as the human cerebral cortex develops. Extensive spatiotemporal gene regulatory networks that direct mammalian corticogenesis have been discovered through studies employing mouse model systems, human fetal tissues, and brain organoids. The significance of posttranscriptional gene regulatory mechanisms, such as alternative splicing and translational repression, in regulating progenitor cell fate and neuronal migration, is an emerging theme from investigations on mouse corticogenesis. It remains unclear if comparable pathways contribute to human neurodevelopment and how posttranscriptional factors affect protein abundance and gene expression during human corticogenesis.

The authors investigated this by isolating neural progenitors and neurons from human telencephalic brain organoids developed using a dual reporter cell line, performing cell class and developmental stage-specific transcriptome analysis, and proteome analysis. The two datasets were combined to show gene expression modules during human corticogenesis. Investigation of one of these modules revealed that early progenitor cells have mTOR-mediated translation regulation of the 5’TOP mRNAs encoding some of the translation machinery. They demonstrate that partial suppression of ribosomal gene translation in early progenitors avoids the premature translation of differentiation markers. In summary, the novel posttranscriptional regulatory mechanisms proposed by their multiomics approach are essential for the accuracy of cortical development.

Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum

BMC Biology, 2023

Ma, Q., Wang, Y., Li, S., Wen, J., Zhu, L., Yan, K., Du, Y., Li, S., Yan, L., Xie, Z., Lyu, Y., Shen, F. and Li, Q.

The build-up of fatty acids in plants influences a variety of physiological processes, which in turn affects species adaptations and traits. Acer truncatum, a well-known woody oilseed crop, can be used as a model to comprehend regulation and trait creation in oil-accumulating crops. In this study, the authors combined ribosome profiling with a multi-omics approach to important stages of seed development, and ultimately built a systematic profiling framework from transcription to protein synthesis. Furthermore, they identified numerous translated upstream open reading frames (uORFs) that reduced translation of their main ORFs.

The transcriptional and translational profiles of seeds collected at 85 and 115 days after flowering were compared using Ribo-seq and RNA-seq. LACS, FAD2, FAD3, and KCS, key structural genes associated with biosynthesis, were shown to be translationally regulated. More significantly, it was discovered that the regulators (MYB, ABI, bZIP, and Dof) influence lipid biosynthesis via post-translational controls. In summary, the authors report novel insights into the global mechanisms underpinning developmental regulation of lipid metabolism in plants.

Selective translational control of cellular and viral mRNAs by RPS3 mRNA binding

Nucleic Acids Research, 2023

Havkin-Solomon, T., Itzhaki, E., Joffe, N., Reuven, N., Shaul, Y. and Dikstein, R.

The universal 40S ribosomal subunit core component RPS3 interacts with mRNA at the entry channel. However, the role of RPS3 mRNA-binding in mammalian cell-specific mRNA translation and ribosome specialization remains to be seen. Here, the authors assessed the translational impact of changing the mRNA-contacting residues R116, R146, and K148 of endogenous RP53. R116D impaired cap-proximal initiation and increased leaky scanning, while R146D had the opposite effect. Additionally, the effects of R146D and K148D on start-codon fidelity were different. AUG selection and scanning were likely stabilizing processes, as evidenced by the downregulated genes’ lengthy 5’UTRs and poor AUG context, which were revealed by translatome analysis.

In the sub-genomic 5’UTR of SARS-CoV-2, they also discovered an RPS3-dependent regulatory sequence which consists of a CUG start codon and a downstream element that is also the viral transcription regulatory sequence. Furthermore, SARS-CoV-2 NSP1-mediated suppression of host translation and its ribosomal binding depend on RPS3 mRNA-binding residues. It’s interesting to note that NSP1-induced mRNA decay was similarly diminished in R116D cells, suggesting that mRNA decay occurs in the ribosome context. In order to affect host and viral mRNA translation and stability, SARS-CoV-2 uses RPS3 mRNA-binding residues, which have several translation regulatory activities.

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