The development of ribosome profiling (Ribo-seq) by Ingolia et al. introduced a powerful new method for monitoring translation genome-wide. Application of Ribo-seq across multiple organisms has since revealed thousands of unannotated translated small open reading frames (ORFs) and enhanced efforts to study their encoded proteins, called microproteins.
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The translational landscape of HIV-1 infected cells reveals key gene regulatory principles.
Nat Struct Mol Biol
January 2025
Helmholtz Institute for RNA-based Infection Research, Helmholtz Centre for Infection Research (HIRI-HZI), Würzburg, Germany.
Human immunodeficiency virus-1 (HIV-1) uses a number of strategies to modulate viral and host gene expression during its life cycle. To characterize the transcriptional and translational landscape of HIV-1 infected cells, we used a combination of ribosome profiling, disome sequencing and RNA sequencing. We show that HIV-1 messenger RNAs are efficiently translated at all stages of infection, despite evidence for a substantial decrease in the translational efficiency of host genes that are implicated in host cell translation.
View Article and Find Full Text PDFRibosome profiling reveals hidden world of small proteins.
Trends Genet
January 2025
Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92617, USA. Electronic address:
The development of ribosome profiling (Ribo-seq) by Ingolia et al. introduced a powerful new method for monitoring translation genome-wide. Application of Ribo-seq across multiple organisms has since revealed thousands of unannotated translated small open reading frames (ORFs) and enhanced efforts to study their encoded proteins, called microproteins.
View Article and Find Full Text PDFRibosome profiling shows variable sensitivity to detect open reading frames for conventional and different types of cryptic T cell antigens.
Mol Ther Methods Clin Dev
March 2025
Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands.
T cell-based immunotherapies targeting antigens on tumor cells have shown efficacy as anti-cancer treatments. While neoantigens are created by somatic mutations acquired during tumorigenesis, allogeneic stem cell transplantation as treatment for hematological malignancies exploits minor histocompatibility antigens encoded by genetic differences between patients and donors. Screening methods to predict neoantigens and minor histocompatibility antigens typically consider only conventional antigens created by nonsynonymous mutations or polymorphisms coding for amino acid changes in canonical open reading frames (ORFs).
View Article and Find Full Text PDFRoles of NOC3L and DDX17 in acquired immunodeficiency complicated with viral myocarditis and osteoporosis.
Medicine (Baltimore)
November 2024
Department of Orthopaedics, Beijing Ditan Hospital Affiliated to Capital Medical University, Chaoyang District, Beijing, China.
Acquired immunodeficiency syndrome is a systemic infectious disease caused by human immunodeficiency virus infection, which could attack the bones and heart. However, the relationship between Nuclear Complex Associated 3 Homolog (NOC3L) and DEAD box helicase 17 (DDX17) and acquired immunodeficiency complicated with viral myocarditis and osteoporosis is unclear. The acquired immune deficiency dataset GSE140713, GSE147162 and the osteoporosis dataset (GSE230665), and viral myocarditis dataset (GSE150392) configuration files were generated from gene expression omnibus.
View Article and Find Full Text PDFGenome-wide changes of protein translation levels for cell and organelle proliferation in a simple unicellular alga.
Proc Jpn Acad Ser B Phys Biol Sci
January 2025
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Cell proliferation is a fundamental characteristic of organisms, driven by the holistic functions of multiple proteins encoded in the genome. However, the individual contributions of thousands of genes and the millions of protein molecules they express to cell proliferation are still not fully understood, even in simple eukaryotes. Here, we present a genome-wide translation map of cells during proliferation in the unicellular alga Cyanidioschyzon merolae, based on the sequencing of ribosome-protected messenger RNA fragments.
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