High-resolution HIV-1 m6A epitranscriptome reveals isoform-dependent methylation clusters and unique 2-LTR transcript modifications Delphine Naquin, Sandra Blanchet, Erwin van Dijk, Lisa Bertrand, Sylvie Grégoire, Bertha Cecilia Ramirez, Rania Ouazahrou, Yan Jaszczyszyn, Arnaud Moris, Claude Thermes, Céline Hernandez, Olivier Namy Nar Genomics and Bioinformatics, 2025 The N6-methyladenosine (m6A) modification of HIV-1 has been widely studied but the number and precise positions of the m6A sites remain unclear due to the lack of precision of detection methods. Using the latest Nanopore chemistry and direct m6A base-calling, we identified 18 m6A: 14 at the 3′ end and 4 in central regions of the genome. Our data reveal differential methylation of these positions between splicing isoforms. Eleven of these sites are clustered in two short segments with peak-shaped methylation profiles. Single-molecule analysis revealed that a very small number of transcripts were unmethylated in both clusters. We also identified a ∼732 nt RNA species resulting from the transcription of non-integrated viral DNA circles closed by two long terminal repeats. These transcripts started in the first LTR, terminated at the polyA site of the second LTR, and harbored six m6A sites. Five of these sites were present in other transcripts and, remarkably, had the highest methylation rates. The sixth site was methylated only in this transcript, suggesting a role for this RNA in HIV-1 infection. These findings reveal a new landscape of HIV m6A transcriptome modifications and pave the way for studies deciphering their role in the viral life cycle.
Non-AUG HIV-1 uORF translation elicits specific T cell immune response and regulates viral transcript expression Emmanuel Labaronne, Didier Décimo, Lisa Bertrand, Laura Guiguettaz, Thibault J. M. Sohier, David Cluet, Valérie Vivet-Boudou, Ana Luiza Chaves Valadão, Clara Dahoui, Pauline François, Isabelle Hatin, Olivier Lambotte, Assia Samri, Brigitte Autran, Lucie Etienne, Caroline Goujon, Jean-Christophe Paillart, Olivier Namy, Bertha Cecilia Ramirez, Théophile Ohlmann, Arnaud Moris, Emiliano P. Ricci Nature Communications, 2025 Human immunodeficiency virus type-1 (HIV-1) is a complex retrovirus that relies on alternative splicing, translational, and post-translational mechanisms to produce over 15 functional proteins from its single ~10 kb transcriptional unit. Using ribosome profiling, nascent protein labeling, RNA sequencing, and whole-proteomics of infected CD4 + T lymphocytes, we characterized the transcriptional, translational, and post-translational landscape during infection. While viral infection exerts a significant impact on host transcript abundance, global translation rates are only modestly affected. Proteomics data reveal extensive transcriptional and post-translational regulation, with many genes showing opposing trends between transcript/ribosome profiling and protein abundance. These findings highlight a complex regulatory network orchestrating gene expression at multiple levels. Viral ribosome profiling further uncovered extensive non-AUG translation of small peptides from upstream open reading frames (uORFs) within the 5’ long terminal repeat, which elicit specific T cell responses in people living with HIV. Conservation of uORF translation among retroviruses, along with TAR sequences, shapes DDX3 dependency for efficient translation of the main viral open reading frames. Here, integrating ribosome profiling, RNA-seq and proteomics to reveal transcriptional and post-translational regulation in HIV-infected T cells, the authors show that non-AUG translation of viral upstream ORFs elicits distinct immune responses and regulates viral gene expression in a DDX3-dependent manner.
Correction to: Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling (Nature Communications, (2025), 16, 1, (1707), 10.1038/s41467-025-56773-2) Lisa Bertrand, Annika Nelde, Bertha Cecilia Ramirez, Isabelle Hatin, Hugo Arbes, Pauline François, Stéphane Demais, Emmanuel Labaronne, Didier Decimo, Laura Guiguettaz, Sylvie Grégoire, Anne Bet, Guillaume Beauclair, Antoine Gross, Maja C. Ziegler, Mathias Pereira, Raphaël Jeger-Madiot, Yann Verdier, Joelle Vinh, Sylvain Cardinaud, Stéphanie Graff-Dubois, Audrey Esclatine, Cécile Gouttefangeas, Marcus Altfeld, Laurent Hocqueloux, Assia Samri, Brigitte Autran, Olivier Lambotte, Hans-Georg Rammensee, Emiliano P. Ricci, Juliane Walz, Olivier Namy, Arnaud Moris Nature Communications, 2025 In the version of the article initially published, in Fig. 1, the white circle and “98” were missing from panel c and the colour scale bars were missing from panel d. Fig. 1 has now been corrected in the HTML and PDF versions of the article.
Unveiling conserved HIV-1 open reading frames encoding T cell antigens using ribosome profiling Lisa Bertrand, Annika Nelde, Bertha Cecilia Ramirez, Isabelle Hatin, Hugo Arbes, Pauline François, Stéphane Demais, Emmanuel Labaronne, Didier Decimo, Laura Guiguettaz, Sylvie Grégoire, Anne Bet, Guillaume Beauclair, Antoine Gross, Maja C. Ziegler, Mathias Pereira, Raphaël Jeger-Madiot, Yann Verdier, Joelle Vinh, Sylvain Cardinaud, Stéphanie Graff-Dubois, Audrey Esclatine, Cécile Gouttefangeas, Marcus Altfeld, Laurent Hocqueloux, Assia Samri, Brigitte Autran, Olivier Lambotte, Hans-Georg Rammensee, Emiliano P. Ricci, Juliane Walz, Olivier Namy, Arnaud Moris Nature Communications, 2025 The development of ribosomal profiling (Riboseq) revealed the immense coding capacity of human and viral genomes. Here, we used Riboseq to delineate the translatome of HIV-1 in infected CD4+ T cells. In addition to canonical viral protein coding sequences (CDSs), we identify 98 alternative open reading frames (ARFs), corresponding to small Open Reading Frames (sORFs) that are distributed across the HIV genome including the UTR regions. Using a database of HIV genomes, we observe that most ARF amino-acid sequences are likely conserved among clade B and C of HIV-1, with 8 ARF-encoded amino-acid sequences being more conserved than the overlapping CDSs. Using T cell-based assays and mass spectrometry-based immunopeptidomics, we demonstrate that ARFs encode viral polypeptides. In the blood of people living with HIV, ARF-derived peptides elicit potent poly-functional T cell responses mediated by both CD4+ and CD8+ T cells. Our discovery expands the list of conserved viral polypeptides that are targets for vaccination strategies and might reveal the existence of viral microproteins or pseudogenes. Here, using ribosomal profiling, the authors characterize the translatome of HIV-1 revealing tens of alternative open reading frames (ARF) that encode conserved viral antigens and show that ARF-derived peptides elicit potent HIV-specific poly-functional immune responses mediated by both CD4+ and CD8+ T cells.
Translon: a single term for translated regions Michał I. Świrski, Jack A. S. Tierney, M. Mar Albà, Dmitry E. Andreev, Julie L. Aspden, John F. Atkins, Michal Bassani-Sternberg, Marla J. Berry, Stefano Biffo, Kathleen Boris-Lawrie, Mark Borodovsky, Ian Brierley, Matthew Brook, Marie A. Brunet, Janusz M. Bujnicki, Neva Caliskan, Lorenzo Calviello, Anne-Ruxandra Carvunis, Jamie H. D. Cate, Can Cenik, Kung Yao Chang, Yiwen Chen, Sonia Chothani, Jyoti S. Choudhary, Patricia L. Clark, Jim Clauwaert, Lynn Cooley, Erik Dassi, Kellie Dean, Jean-Jacques Diaz, Christoph Dieterich, Rivka Dikstein, Jonathan D. Dinman, Sergey E. Dmitriev, Olga A. Dontsova, Christine M. Dunham, Sandeep M. Eswarappa, Philip J. Farabaugh, Pouya Faridi, Ivo Fierro-Monti, Andrew E. Firth, David Gatfield, Fátima Gebauer, Mikhail S. Gelfand, Nicola K. Gray, Rachel Green, Chris H. Hill, Ya-Ming Hou, Norbert Hübner, Zoya Ignatova, Pavel Ivanov, Shintaro Iwasaki, Rory Johnson, Ahmad Jomaa, Marko Jovanovic, Irwin Jungreis, Manolis Kellis, Jeffrey S. Kieft, Alex V. Kochetov, Eugene V. Koonin, Andrei A. Korostelev, Joanna Kufel, Ivan V. Kulakovskiy, Leo Kurian, Denis L. J. Lafontaine, Ola Larsson, Gary Loughran, Julius Lukeš, Marco Mariotti, Elena S. Martens-Uzunova, Thomas F. Martinez, Akinobu Matsumoto, Joel McManus, Jan Medenbach, Sergey V. Melnikov, Gerben Menschaert, Catharina Merchante, Martin Mikl, W. Allen Miller, Oliver Mühlemann, Olivier Namy, Danny D. Nedialkova, Jozef Nosek, Sandra Orchard, Petar Ozretić, Mihaela Pertea, Dmitri D. Pervouchine, Luísa Romão, David Ron, Xavier Roucou, Maria P. Rubtsova, Jorge Ruiz-Orera, Alan Saghatelian, Steven L. Salzberg, Lucia A. Seale, Cathal Seoighe, Petr V. Sergiev, Premal Shah, Nikolay Shirokikh, Sarah A. Slavoff, Nahum Sonenberg, Timothy J. Stasevich, Roman J. Szczesny, Tiina Tamm, Marek Tchórzewski, Ivan Topisirovic, Michel L. Tremblay, Tamir Tuller, Igor Ulitsky, Leoš Shivaya Valášek, Petra Van Damme, Gabriella Viero, Juan Antonio Vizcaino, Christine Vogel, Edward W. J. Wallace, Jonathan S. Weissman, Eric Westhof, Nicola Whiffin, Daniel N. Wilson, Zhi Xie, Jonathan W. Yewdell, Martina M. Yordanova, Chien-Hung Yu, Vyacheslav Yurchenko, Bojan Zagrovic, , Maria Inês Almeida, Nese Atabey, Nikolaos Balatsos, Pavel Baranov, Anca Simona Bojan, Theodora Choli-Papadopoulou, Pierre Close, Victoria Cowling, Erik Dassi, Alexandre David, Kellie Dean, Jean-Jacques Diaz, Aleksandar Eftimov, Fátima Gebauer, Mark Helm, Cristina-Adela Iuga, Dana Jurkovičová, Arvydas Kanopka, Denis Lafontaine, Elena Martens-Uzunova, Lucia Messingerová, Henrik Nielsen, Petar Ozretić, Mehmet Ozturk, Vicent Pelechano, Marianna Penzo, Paulina Podszywalow-Bartnicka, Lejla Pojskić, John Le Quesne, Luísa Romão, Barak Rotblat, Ariel Stanhill, Georg Stoecklin, Tiina Tamm, Marek Tchorzewski, Vladimir Trajković, Leos Shivaya Valasek, Eivind Valen, Sinisa Volarevic, Ljubica Vucicevic, Kathleen Watt, Anne Willis, Masa Zdralevic, Taja Železnik Ramuta, Eivind Valen, Pavel V. Baranov Nature Methods, 2025
Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR) Gary Loughran, Dmitry E. Andreev, Ilya M. Terenin, Olivier Namy, Martin Mikl, Martina M. Yordanova, C. Joel McManus, Andrew E. Firth, John F. Atkins, Christopher S. Fraser, Zoya Ignatova, Shintaro Iwasaki, Joanna Kufel, Ola Larsson, Sebastian A. Leidel, Alexander S. Mankin, Marco Mariotti, Marvin E. Tanenbaum, Ivan Topisirovic, Nora Vázquez-Laslop, Gabriela Viero, Neva Caliskan, Yiwen Chen, Patricia L. Clark, Jonathan D. Dinman, Philip J. Farabaugh, Wendy V. Gilbert, Pavel Ivanov, Jeffrey S. Kieft, Oliver Mühlemann, Matthew S. Sachs, Ivan N. Shatsky, Nahum Sonenberg, Anna-Lena Steckelberg, Anne E. Willis, Michael T. Woodside, Leos Shivaya Valasek, Sergey E. Dmitriev, Pavel V. Baranov Nature Structural and Molecular Biology, 2025
Intricate ribosome composition and translational reprogramming in epithelial-mesenchymal transition Chloé Morin, Agnès Baudin-Baillieu, Flora Nguyen Van Long, Caroline Isaac, Laure Bidou, Hugo Arbes, Pauline François, Roxane M. Pommier, Annie Adrait, Akari Saku, Stephanie Gran-Ruaz, Camélia Machkouri, Christophe Vanbelle, Romain Morichon, Mathieu Boissan, Frédéric Catez, Anthony Ferrari, Anne-Pierre Morel, Yohann Couté, Sophie Chat, Emmanuel Giudice, Reynald Gillet, Alain Puisieux, Caroline Moyret-Lalle, Jean-Jacques Diaz, Olivier Namy, Virginie Marcel Proceedings of the National Academy of Sciences of the United States of America, 2024 Epithelial–mesenchymal transition (EMT) involves profound changes in cell morphology, driven by transcriptional and epigenetic reprogramming. However, evidence suggests that translation and ribosome composition also play key roles in establishing pathophysiological phenotypes. Using genome-wide analyses, we reported significant rearrangement of the translational landscape and machinery during EMT. Specifically, a cell line overexpressing the EMT transcription factor ZEB1 displayed alterations in translational reprogramming and fidelity. Furthermore, using riboproteomics, we unveiled an increased level of the ribosomal protein RPL36A in mesenchymal ribosomes, indicating precise tuning of ribosome composition. Remarkably, RPL36A overexpression alone was sufficient to trigger the acquisition of mesenchymal features, including a switch in the molecular pattern, cell morphology, and behavior, demonstrating its pivotal role in EMT. These findings underline the importance of translational reprogramming and fine-tuning of ribosome composition in EMT.
The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation Chris Papadopoulos, Hugo Arbes, David Cornu, Nicolas Chevrollier, Sandra Blanchet, Paul Roginski, Camille Rabier, Safiya Atia, Olivier Lespinet, Olivier Namy, Anne Lopes Genome Biology, 2024 BACKGROUND: Pervasive translation is a widespread phenomenon that plays a critical role in the emergence of novel microproteins, but the diversity of translation patterns contributing to their generation remains unclear. Based on 54 ribosome profiling (Ribo-Seq) datasets, we investigated the yeast Ribo-Seq landscape using a representation framework that allows the comprehensive inventory and classification of the entire diversity of Ribo-Seq signals, including non-canonical ones. RESULTS: We show that if coding regions occupy specific areas of the Ribo-Seq landscape, noncoding regions encompass a wide diversity of Ribo-Seq signals and, conversely, populate the entire landscape. Our results show that pervasive translation can, nevertheless, be associated with high specificity, with 1055 noncoding ORFs exhibiting canonical Ribo-Seq signals. Using mass spectrometry under standard conditions or proteasome inhibition with an in-house analysis protocol, we report 239 microproteins originating from noncoding ORFs that display canonical but also non-canonical Ribo-Seq signals. Each condition yields dozens of additional microprotein candidates with comparable translation properties, suggesting a larger population of volatile microproteins that are challenging to detect. Our findings suggest that non-canonical translation signals may harbor valuable information and underscore the significance of considering them in proteogenomic studies. Finally, we show that the translation outcome of a noncoding ORF is primarily determined by the initiating codon and the codon distribution in its two alternative frames, rather than features indicative of functionality. CONCLUSION: Our results enable us to propose a topology of a species' Ribo-Seq landscape, opening the way to comparative analyses of this translation landscape under different conditions.
Factors influencing readthrough therapy for frequent cystic fibrosis premature termination codons Iwona Pranke, Laure Bidou, Natacha Martin, Sandra Blanchet, Aurélie Hatton, Sabrina Karri, David Cornu, Bruno Costes, Benoit Chevalier, Danielle Tondelier, Emmanuelle Girodon, Matthieu Coupet, Aleksander Edelman, Pascale Fanen, Olivier Namy, Isabelle Sermet-Gaudelus, Alexandre Hinzpeter Erj Open Research, 2018
Evidence for rRNA 2′-O-methylation plasticity: Control of intrinsic translational capabilities of human ribosomes Jenny Erales, Virginie Marchand, Baptiste Panthu, Sandra Gillot, Stéphane Belin, Sandra E. Ghayad, Maxime Garcia, Florian Laforêts, Virginie Marcel, Agnès Baudin-Baillieu, Pierre Bertin, Yohann Couté, Annie Adrait, Mélanie Meyer, Gabriel Therizols, Marat Yusupov, Olivier Namy, Théophile Ohlmann, Yuri Motorin, Frédéric Catez, Jean-Jacques Diaz Proceedings of the National Academy of Sciences of the United States of America, 2017
