September 15th, 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, Pinello et al. investigate changes in m6A and 5 hmC RNA methylation during macrophage differentiation. Aviner et al. investigates how expansions of CAG in the Huntington gene contribute to neurodegeneration. Fu et al. explores the role of the METTL1 enzyme in cellular senescence and aging.
Dynamic changes in RNA m⁶A and 5 hmC influence gene expression programs during macrophage differentiation and polarisation
Cellular and Molecular Life Sciences, 2024
Pinello N., Song R., Lee Q., Calonne E., Duan K.L., Wong E., Tieng J., Mehravar M., Rong B., Lan F., Roediger B., Ma C.J., Yuan B.F., Rasko J.E.J., Larance M., Ye D., Fuks F. and Wong J.J.
This paper explores the roles of N6-methyladenosine (m6A) and 5-hydroxymethylcytosine (5hmC) in macrophage biology. These modifications are important for gene expression regulation in immune cells but have not been well studied in monocyte-to-macrophage differentiation.
m6A-seq and 5hmC-seq were used to map the distribution of these RNA modifications across the transcriptome of THP-1 monocytic cells, and THP-1-derived macrophages at rest and in pro- and anti-inflammatory states. The study found that the levels of m6A and 5hmC generally decrease during the differentiation from monocytes to macrophages. However, specific transcripts essential for macrophage functions were enriched for these modifications. Polysome fractions were isolated using polysome profiling, and RNA-seq was performed. There was a strong correlation between the transcripts that showed increased m6A modifications upon macrophage differentiation and those that had increased translation.
Interestingly, the study also discovered that m6A and 5hmC can co-occur on the same transcripts, potentially influencing their stability, splicing, and translation in a coordinated manner. Moreover, 5hmC was found to have a distinct role in controlling mRNA decay independently of m6A, highlighting its unique contribution to gene regulation in macrophages.
Overall, this work provides valuable insights into the complex epitranscriptomic regulation of macrophages, which are key players in the innate immune response, and offers a resource for further exploration of RNA modifications in immune cells.
Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington’s disease
Nature Cell Biology, 2024
Aviner R., Lee T.T., Masto V.B., Li K.H., Andino R. and Frydman J.
This paper investigates how expansions of CAG trinucleotide repeats in the Huntingtin (HTT) gene, encoding a polyglutamine (polyQ) tract, contribute to the neurodegeneration seen in Huntington’s disease (HD) by promoting abortive termination by ribosomes. These aggregation-prone truncated protein fragments sequester eIF5A, promoting widespread ribosome pausing.
Ribo-seq data revealed that polyglutamine (polyQ) expansions in mutants of HTT with expanded CAG repeats (mHTT) lead to ribosome pausing and collisions during translation, which leads to abortive termination. This study also looks at an inhibitory upstream open reading frame (uORF) of HTT that was detected from ribo-seq data. Polysome profiling was used to collect actively translating ribosomes in samples with and without ER-stress. As expected, stress greatly reduced the polysome fraction. However, more HTT was found in the heavy polysome fraction under stress, as expected for uORF-repressed transcripts.
The aggregation-prone truncated mHTT protein fragments were found to sequester eIF5A. eIF5A facilitates translation elongation across ribosomal stall sites. Ribo-seq data showed that in cells expressing mHTT, there was a global increase in ribosome pausing and collisions, leading to ribo- and proteotoxicity.
This work provides new insights into the molecular mechanisms by which polyQ expansions contribute to HD pathology and highlights the critical role of ribosome-associated processes in the disease.
Perturbation of METTL1-mediated tRNA N⁷-methylguanosine modification induces senescence and aging
Nature Communications, 2024
Fu Y., Jiang F., Zhang X., Pan Y., Xu R., Liang X., Wu X., Li X., Lin K., Shi R., Zhang X., Ferrandon D., Liu J., Pei D., Wang J. and Wang T.
This paper explores the role of the METTL1 enzyme, which catalyzes the N⁷-methylguanosine (m7G) modification on tRNAs, in cellular senescence and aging.
METTL1 protein and mRNA levels are downregulated during cell senescence and aging. tRNA-seq revealed a marked reduction in tRNAs with m7G modifications in METTL1 deficient cells. Ribo-seq results demonstrated that METTL1 deficiency leads to significant ribosome stalling at specific codons, particularly those that require m7G-modified tRNAs for efficient translation, including mRNA that is essential in pathways such as Wnt signalling and ribosome biogenesis. This stalling triggers ribotoxic stress, contributing to the cellular senescence process. Polysome profiling showed a decrease in the number of actively translating ribosomes in METTL1-deficient cells, highlighting a global reduction in translation efficiency. This impairment in translation is linked to the onset of senescence due to the inability to maintain proteostasis.
Overall, the study elucidates how disruptions in tRNA modifications by METTL1 can lead to translational defects, contributing to cellular aging and the development of senescence-associated phenotypes. This research underscores the importance of tRNA modifications in maintaining cellular homeostasis and preventing premature aging.