June 23rd, 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, Barlit et al. present a comprehensive genome-wide analysis of protein synthesis in yeast under iron scarcity using ribosome profiling (Ribo-Seq). Wei et al. use single-cell RNA-Seq of Drosophila to investigate the evolution and trajectory of germline sex chromosome regulation. Lastly, Horvath et al. use eTCP-Seq and AI to examine rapid changes in mRNA translation in yeast experiencing glucose depletion.

Ribosome profiling reveals the role of yeast RNA-binding proteins Cth1 and Cth2 in translational regulation

iScience, 2024

Barlit, H., Romero, A.M., Gülhan, A., Patnaik, P.K., Tyshkovskiy, A., Martínez-Pastor, M.T., Gladyshev, V.N., Puig, S. and Labunskyy V.M.

Iron is a vital trace element that functions as a cofactor for enzymes critical to various cellular processes, including protein synthesis. Previous studies have demonstrated that iron deficiency leads to a global reduction in protein synthesis, which is influenced by the TORC1 and Gcn2/eIF2α pathways. Additionally, iron acts as a cofactor for several enzymes involved in various stages of protein synthesis, including modifications of factors that affect translation elongation, post-transcriptional transfer RNA (tRNA) modifications, translational termination, and ribosome recycling. Cth2 has also been found to suppress the translation of specific transcripts in response to iron deficiency. Despite this, the broader effects of iron deficiency on protein synthesis at the genome-wide level and the detailed mechanisms of translational regulation by iron have not been thoroughly explored.

In this study, the authors present a comprehensive genome-wide analysis of protein synthesis in yeast under iron scarcity using ribosome profiling (Ribo-Seq). Their findings reveal that iron depletion significantly impacts overall protein synthesis, leading to the translational repression of numerous genes associated with iron-dependent processes. They also identify the RNA-binding proteins Cth1 and Cth2 as key regulators in this context, that hinder mitochondrial translation and heme biosynthesis. They also suppress the activity of the iron-dependent Rli1 ribosome recycling factor which results in an increased ribosome density in the 3’UTR region. Moreover, the results indicate that iron deficiency reduces the translation of MRS3 mRNA, a gene encoding a mitochondrial iron transporter, through increased levels of antisense long non-coding RNA. Collectively, this study uncovers intricate changes in gene expression and protein synthesis in response to low iron, highlighting the multifaceted role of this essential metal in regulating translation.

Single-cell RNA-seq of Drosophila miranda testis reveals the evolution and trajectory of germline sex chromosome regulation

PLoS Biology2024

Wei, K.H., Chatla, K. and Bachtrog, D.

Despite evolving from autosomes, sex chromosomes often exhibit unique regulatory mechanisms that are specific to sex and cell type, such as dosage compensation (DC) and meiotic sex chromosome inactivation (MSCI). These distinctive transcriptional programs are crucial for genome evolution, yet their molecular underpinnings and evolutionary pressures, particularly concerning MSCI in Drosophila, remain a topic of ongoing debate. In this study, the authors utilize the younger sex chromosomes in Drosophila miranda (XR and the neo-X) to investigate how former autosomes develop sex-chromosome-specific regulatory programs. Using single-cell and bulk RNA sequencing as well as ribosome profiling (Ribo-Seq) within a comparative evolutionary framework, they demonstrate that, unlike in mammals and worms, the X chromosome down-regulation throughout germline progression aligns more closely with the cessation of DC rather than MSCI. This results in halved gene dosage for all three X chromosomes by the end of meiosis.

Furthermore, genes on the neo-X chromosome that are lowly expressed in the germline and during meiosis were already lowly expressed in their ancestral state, rather than being suppressed due to their association with sex linkage. On the young neo-X chromosome, DC remains incomplete across various tissues and cell types, and this dosage imbalance is offset by Y-linked gametologs that generate transcripts to balance both gene and protein dosage. The study found that neo-Y genes with truncated coding sequences still showed significant ribosome occupancy, suggesting they are actively translated. This finding underscores the role of the neo-Y chromosome in compensating for dosage imbalances, particularly in the testis where expression from both neo-X and neo-Y is critical. They observe a surplus of formerly autosomal genes in the testes becoming Y-specific, suggesting that the neo-Y chromosome and its masculinization play a role in resolving sexual antagonism. Neo-sex genes with multiple copies are primarily active during the meiotic phases of spermatogenesis, indicating that their amplification may be driven by the need to interfere with Mendelian segregation.

Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress

Nucleic Acids Research, 2024

Horvath, A., Janapala, Y., Woodward, K., Mahmud, S., Cleynen, A., Gardiner, E.E., Hannan, R.D., Eyras, E., Preiss, T. and Shirokikh, N.E.


Translational control plays a crucial role in all forms of life, yet accurately measuring it remains challenging. During the process of translation, ribosomes bind sequentially to messenger RNA (mRNA), forming polyribosomes which often co-localize on the mRNA strand. In this study, the authors employ computational modelling to explore new types of co-localized ribosomal complexes on mRNA. Their enhanced approach to translation complex profile sequencing (eTCP-Seq), which is facilitated by rapid in vivo crosslinking, allows for the identification of new types of co-localized ribosomal complexes on mRNA. Their findings reveal the presence of long disome footprints beyond areas of non-random elongation stalls, which they link to the rates of translation initiation and protein biosynthesis.

They employ artificial intelligence (AI) to analyse the footprints of disomes and other translation complexes, creating a new metric for translation called stochastic translation efficiency (STE). Utilizing STE, they examine rapid changes in mRNA translation in yeast experiencing glucose depletion. Notably, their analysis reveals that alongside merely marking elongation stalls, the footprints of co-localized ribosomes offer valuable insights into translational mechanisms, polysome dynamics, and topology. This includes not only the traditionally recognized stalling-induced disomes but also stochastic disomes resulting from the spatial proximity of ribosomes which represent a new type of signal to explore. By providing a detailed understanding of translation efficiency and control, the AI-driven STE metric can inform the development of more efficient and targeted mRNA therapies and synthetic biology applications, potentially leading to better therapeutic outcomes and innovative biological designs.

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