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Your search keyword '"Isabelle, Hatin"' showing total 17 results
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17 results on '"Isabelle, Hatin"'

1. Integrated analyses of translatome and proteome identify the rules of translation selectivity in RPS14-deficient cells

Author

Ismael Boussaid, Salomé Le Goff, Célia Floquet, Emilie-Fleur Gautier, Anna Raimbault, Pierre-Julien Viailly, Dina Al Dulaimi, Barbara Burroni, Isabelle Dusanter-Fourt, Isabelle Hatin, Patrick Mayeux, Bertrand Cosson, and Michaela Fontenay

Subjects
Diseases of the blood and blood-forming organs, RC633-647.5
Abstract

In ribosomopathies, the Diamond-Blackfan anemia (DBA) or 5q- syndrome, ribosomal protein (RP) genes are affected by mutation or deletion, resulting in bone marrow erythroid hypoplasia. Unbalanced production of ribosomal subunits leading to a limited ribosome cellular content, regulates translation at the expense of the master erythroid transcription factor GATA1. In RPS14-deficient cells mimicking 5q- syndrome erythroid defects, we show that the transcript length, codon bias of the coding sequence (CDS) and 3'UTR structure are the key determinants of translation. In these cells, short transcripts with a structured 3'UTR and high CAI showed a decreased translation efficiency. Quantitative analysis of the whole proteome confirmed that the post-transcriptional changes depended on the transcript characteristics that governed the translation efficiency in conditions of low ribosome availability. In addition, proteins involved in normal erythroid differentiation share most determinants of translation selectivity. Our findings thus indicate that impaired erythroid maturation due to 5q- syndrome may proceed from a translational selectivity at the expense of the erythroid differentiation program and suggest that an interplay between the CDS and UTRs may regulate mRNA translation.

Published
2020
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2. Global translational impacts of the loss of the tRNA modification t6A in yeast

Author

Patrick C. Thiaville, Rachel Legendre, Diego Rojas-Benítez, Agnès Baudin-Baillieu, Isabelle Hatin, Guilhem Chalancon, Alvaro Glavic, Olivier Namy, and Valérie de Crécy-Lagard

Subjects
t6A, tRNA, ribosome profiling, translation, modified nucleosides, Biology (General), QH301-705.5
Abstract

The universal tRNA modification t6A is found at position 37 of nearly all tRNAs decoding ANN codons. The absence of t6A37 leads to severe growth defects in baker’s yeast, phenotypes similar to those caused by defects in mcm5s2U34 synthesis. Mutants in mcm5s2U34 can be suppressed by overexpression of tRNALysUUU, but we show t6A phenotypes could not be suppressed by expressing any individual ANN decoding tRNA, and t6A and mcm5s2U are not determinants for each other’s formation. Our results suggest that t6A deficiency, like mcm5s2U deficiency, leads to protein folding defects, and show that the absence of t6A led to stress sensitivities (heat, ethanol, salt) and sensitivity to TOR pathway inhibitors. Additionally, L-homoserine suppressed the slow growth phenotype seen in t6A-deficient strains, and proteins aggregates and Advanced Glycation End-products (AGEs) were increased in the mutants. The global consequences on translation caused by t6A absence were examined by ribosome profiling. Interestingly, the absence of t6A did not lead to global translation defects, but did increase translation initiation at upstream non-AUG codons and increased frame-shifting in specific genes. Analysis of codon occupancy rates suggests that one of the major roles of t6A is to homogenize the process of elongation by slowing the elongation rate at codons decoded by high abundance tRNAs and I34:C3 pairs while increasing the elongation rate of rare tRNAs and G34:U3 pairs. This work reveals that the consequences of t6A absence are complex and multilayered and has set the stage to elucidate the molecular basis of the observed phenotypes.

Published
2015
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3. 2-Guanidino-quinazoline promotes the readthrough of nonsense mutations underlying human genetic diseases

Author

Laure Bidou, Olivier Bugaud, Goulven Merer, Matthieu Coupet, Isabelle Hatin, Egor Chirkin, Sabrina Karri, Stéphane Demais, Pauline François, Jean-Christophe Cintrat, and Olivier Namy

Subjects
Muscular Dystrophy, Duchenne, Multidisciplinary, Codon, Nonsense, Genes, Reporter, Codon, Terminator, Drug Evaluation, Preclinical, Genetic Diseases, Inborn, Quinazolines, Humans, Gentamicins, Guanidines, Cell Line, High-Throughput Screening Assays
Abstract

Premature termination codons (PTCs) account for 10 to 20% of genetic diseases in humans. The gene inactivation resulting from PTCs can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a reporter cell line and performed high-throughput screening (HTS) to identify potential readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy (DMD). We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of normal stop codons (TC).

Published
2022

4. p53 activation during ribosome biogenesis regulates normal erythroid differentiation

Author

François Morlé, Stéphane Giraudier, Eric Soler, Naomi Taylor, Charlotte Andrieu-Soler, Olivier Hermine, Patrick Mayeux, Célia Floquet, Rose Ann Padua, Frédérique Verdier, Sarah Ducamp, Michaela Fontenay, Mohammad Salma, Elisabeth M. Cramer-Borde, Ismael Boussaid, Anna Raimbault, Isabelle Hatin, Diane d'Allard, Amandine Houvert, Narla Mohandas, Boris Guyot, Emilie-Fleur Gautier, Sandrina Kinet, Marjorie Leduc, Pierre-Emmanuel Gleizes, Jean-Jacques Diaz, Salomé Le Goff, François Guillonneau, Nathalie Montel-Lehry, Centre de Recherche en Cancérologie de Lyon (UNICANCER/CRCL), Centre Léon Bérard [Lyon]-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Plateforme protéomique 3P5 [Institut Cochin] (3P5), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génomique, Structure et Traduction (GST), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Hématopoïèse normale et pathologique : émergence, environnement et recherche translationnelle [Paris] ((UMR_S1131 / U1131)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut NeuroMyoGène (INMG), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), New York Blood Center, Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Procédés Alimentaires et Microbiologiques (PAM), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Immunology, Ribosome biogenesis, Biology, Biochemistry, Ribosome, Mice, 03 medical and health sciences, 0302 clinical medicine, Erythroid Cells, Downregulation and upregulation, Transcription (biology), Ribosomal protein, hemic and lymphatic diseases, Animals, Humans, Erythropoiesis, Gene, ComputingMilieux_MISCELLANEOUS, Organelle Biogenesis, RNA, Cell Differentiation, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Hematology, Hematopoietic Stem Cells, Cell biology, 030104 developmental biology, 030220 oncology & carcinogenesis, Organelle biogenesis, Tumor Suppressor Protein p53, Ribosomes
Abstract

The role of ribosome biogenesis in erythroid development is supported by the recognition of erythroid defects in ribosomopathies in both Diamond-Blackfan anemia and 5q− syndrome. Whether ribosome biogenesis exerts a regulatory function on normal erythroid development is still unknown. In the present study, a detailed characterization of ribosome biogenesis dynamics during human and murine erythropoiesis showed that ribosome biogenesis is abruptly interrupted by the decline in ribosomal DNA transcription and the collapse of ribosomal protein neosynthesis. Its premature arrest by the RNA Pol I inhibitor CX-5461 targeted the proliferation of immature erythroblasts. p53 was activated spontaneously or in response to CX-5461, concomitant to ribosome biogenesis arrest, and drove a transcriptional program in which genes involved in cell cycle–arrested, negative regulation of apoptosis, and DNA damage response were upregulated. RNA Pol I transcriptional stress resulted in nucleolar disruption and activation of the ATR-CHK1-p53 pathway. Our results imply that the timing of ribosome biogenesis extinction and p53 activation is crucial for erythroid development. In ribosomopathies in which ribosome availability is altered by unbalanced production of ribosomal proteins, the threshold downregulation of ribosome biogenesis could be prematurely reached and, together with pathological p53 activation, prevents a normal expansion of erythroid progenitors.

Published
2021

5. Translation is a key determinant controlling the fate of cytoplasmic long non-coding RNAs

Author

Sara Andjus, Ugo Szachnowski, Nicolas Vogt, Isabelle Hatin, Chris Papadopoulos, Anne Lopes, Olivier Namy, Maxime Wery, and Antonin Morillon

Abstract

SummaryDespite predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes, resulting in some cases into the production of functional peptides. However, the biological and mechanistic relevance of this pervasive lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are translated, which impacts their abundance. We show that XUTs globally accumulate upon translation elongation inhibition, but not when initial ribosome loading is impaired. Translation also affects XUTs independently of NMD, by interfering with their decapping. Ribo-Seq confirmed ribosomes binding to XUTs and identified actively translated small ORFs in their 5’-proximal region. Mechanistic analyses revealed that their NMD-sensitivity depends on the 3’-untranslated region length. Finally, we detected the peptide derived from the translation of an NMD-sensitive XUT reporter in NMD-competent cells. Our work highlights the role of translation in the metabolism of XUTs, which could contribute to expose genetic novelty to the natural selection, while NMD restricts their expression.

Published
2022

6. Extensive uORF translation from HIV-1 transcripts conditions DDX3 dependency for expression of main ORFs and elicits specific T cell immune responses in infected individuals

Author

Emmanuel Labaronne, Didier Décimo, Lisa Bertrand, Laura Guiguettaz, Thibault J.M. Sohier, David Cluet, Valérie Vivet-Boubou, Clara Dahoui, Pauline François, Isabelle Hatin, Olivier Lambotte, Assia Samri, Brigitte Autran, Lucie Etienne, Caroline Goujon, Jean-Christophe Paillart, Olivier Namy, Berta Cecilia Ramirez, Théophile Ohlmann, Arnaud Moris, Emiliano P. Ricci, Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV]Life Sciences [q-bio], [SDV.IMM]Life Sciences [q-bio]/Immunology
Abstract

Human immunodeficiency virus type-1 (HIV-1) is a complex retrovirus which relies on alternative splicing, translational and post-translational mechanisms to produce more than 15 functional proteins from its single ∼10kb transcriptional unit. Here, we have applied ribosome profiling and nascent protein labeling at different time points during infection of CD4+ T lymphocytes to characterize the translational landscape of cellular and viral transcripts during the course of infection. Our results indicate a strong impact of viral infection on host cellular transcript levels but a modest impact on global translation rates. Analysis of ribosome profiling reads from viral transcripts reveals extensive and productive non-AUG translation of small peptides from multiple upstream open reading-frames (uORFs) located in the 5’ long terminal repeat. Remarkably, these uORFs derived peptides elicit specific T cell responses in HIV-infected individuals. uORFs are conserved among other retroviruses and, together with the TAR sequence, condition the dependency on DDX3 for efficient translation of the main viral open-reading frames.

Published
2022

7. Integrated analyses of translatome and proteome identify the rules of translation selectivity in RPS14-deficient cells

Author

Michaela Fontenay, Pierre-Julien Viailly, Bertrand Cosson, Patrick Mayeux, Anna Raimbault, Dina Al Dulaimi, Emilie-Fleur Gautier, Barbara Burroni, Isabelle Dusanter-Fourt, Ismael Boussaid, Salomé Le Goff, Célia Floquet, Isabelle Hatin, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génomique, Structure et Traduction (GST), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
Ribosomal Proteins, 5q- syndrome, Proteome, [SDV]Life Sciences [q-bio], Red Cells, Biology, Ribosomopathies, medicine.disease_cause, Ribosome, Article, 03 medical and health sciences, 0302 clinical medicine, Ribosomal protein, hemic and lymphatic diseases, medicine, Coding region, Humans, Diamond-Blackman, Anemia, Macrocytic, Gene, 030304 developmental biology, Anemia, Diamond-Blackfan, 0303 health sciences, Mutation, Translation (biology), GATA1, Hematology, Cell biology, 030220 oncology & carcinogenesis, Codon usage bias, Myelodysplastic Syndromes, Ribosomes
Abstract

In ribosomopathies, the Diamond-Blackfan anemia (DBA) or 5q- syndrome, ribosomal protein (RP) genes are affected by mutation or deletion, resulting in bone marrow erythroid hypoplasia. Unbalanced production of ribosomal subunits leading to a limited ribosome cellular content regulates translation at the expense of the master erythroid transcription factor GATA1. In RPS14-deficient cells mimicking 5q- syndrome erythroid defects, we show that the transcript length, codon bias of the coding sequence (CDS) and 3’UTR (untranslated region) structure are the key determinants of translation. In these cells, short transcripts with a structured 3’UTR and high codon adaptation index (CAI) showed a decreased translation efficiency. Quantitative analysis of the whole proteome confirmed that the post-transcriptional changes depended on the transcript characteristics that governed the translation efficiency in conditions of low ribosome availability. In addition, proteins involved in normal erythroid differentiation share most determinants of translation selectivity. Our findings thus indicate that impaired erythroid maturation due to 5q- syndrome may proceed from a translational selectivity at the expense of the erythroid differentiation program, and suggest that an interplay between the CDS and UTR may regulate mRNA translation.

Published
2020

8. 2-Guanidino-quinazoline promotes the readthrough of nonsense mutations underlying human genetic diseases

Author

Olivier Bugaud, Laure Bidou, Egor Chirkin, Pauline François, Isabelle Hatin, Olivier Namy, Matthieu Coupet, Jean-Christophe Cintrat, and Goulven Merer

Subjects
Genetics, Drug, viruses, Duchenne muscular dystrophy, media_common.quotation_subject, fungi, Nonsense mutation, Biology, medicine.disease, Stop codon, chemistry.chemical_compound, chemistry, Cell culture, medicine, Quinazoline, Inducer, Gene, media_common
Abstract

Premature termination codons (PTCs) account for 10% to 20% of genetic diseases in humans. The gene inactivation resulting from PTC can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a new reporter cell line and performed high-throughput screening (HTS) to identify potential new readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy. We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of natural stop codons.

Published
2021

9. Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

Author

Olivier Namy, Anne Lopes, Isabelle Callebaut, Olivier Lespinet, Isabelle Hatin, Maxime Renard, Jean-Christophe Gelly, and Chris Papadopoulos

Subjects
Open reading frame, Intergenic region, Protein structure, Proteome, Ribosome profiling, Computational biology, Biology, ORFS, Gene, Genome
Abstract

The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences’ properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic ORFs (Open Reading Frames) of S. cerevisiae with the aim of (i) exploring whether the large structural diversity observed in proteomes is already present in noncoding sequences, and (ii) estimating the potential of the noncoding genome to produce novel protein bricks that can either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural diversity of canonical proteins with strikingly the majority predicted as foldable. Then, we investigated the early stages of de novo gene birth by identifying intergenic ORFs with a strong translation signal in ribosome profiling experiments and by reconstructing the ancestral sequences of 70 yeast de novo genes. This enabled us to highlight sequence and structural factors determining de novo gene emergence. Finally, we showed a strong correlation between the fold potential of de novo proteins and the one of their ancestral amino acid sequences, reflecting the relationship between the noncoding genome and the protein structure universe.

Published
2021

10. Divergent effects of translation termination factor eRF3A and nonsense-mediated mRNA decay factor UPF1 on the expression of uORF carrying mRNAs and ribosome protein genes

Author

Affaf Aliouat, Pauline François, Vérène Stierlé, Olivier Jean-Jean, Pierre Bertin, Samia Salhi, Isabelle Hatin, Olivier Namy, Adaptation Biologique et Vieillissement = Biological Adaptation and Ageing (B2A), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Département de Mathématiques et Applications - ENS Paris (DMA), Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Centre recherche en CardioVasculaire et Nutrition (C2VN), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génomique, Structure et Traduction (GST), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ANR-17-CE12-0024,Rescue_ribosome,Voies de sauvetage pour les ribosomes non recyclés(2017), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and SERRE, Marie-Claude

Subjects
Ribosomal Proteins, eRF3, [SDV]Life Sciences [q-bio], Nonsense-mediated decay, MRNA Decay, nonsense-mediated mRNA decay, Biology, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Ribosome, Open Reading Frames, 03 medical and health sciences, 0302 clinical medicine, RNA, Messenger, Molecular Biology, Gene, Translation termination, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, ribosome protein genes, GSPT1, RNA, translation termination, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Cell Biology, Nonsense Mediated mRNA Decay, Cell biology, [SDV] Life Sciences [q-bio], Gene Expression Regulation, 030220 oncology & carcinogenesis, UPF1, Trans-Activators, RNA Helicases, Peptide Termination Factors, Research Paper, uORF
Abstract

International audience; In addition to its role in translation termination, eRF3A has been implicated in the nonsense-mediated mRNA decay (NMD) pathway through its interaction with UPF1. NMD is a RNA quality control mechanism, which detects and degrades aberrant mRNAs as well as some normal transcripts including those that harbour upstream open reading frames in their 5' leader sequence. In this study, we used RNA-sequencing and ribosome profiling to perform a genome wide analysis of the effect of either eRF3A or UPF1 depletion in human cells. Our bioinformatics analyses allow to delineate the features of the transcripts controlled by eRF3A and UPF1 and to compare the effect of each of these factors on gene expression. We find that eRF3A and UPF1 have very different impacts on the human transcriptome, less than 250 transcripts being targeted by both factors. We show that eRF3A depletion globally derepresses the expression of mRNAs containing translated uORFs while UPF1 knockdown derepresses only the mRNAs harbouring uORFs with an AUG codon in an optimal context for translation initiation. Finally, we also find that eRF3A and UPF1 have opposite effects on ribosome protein gene expression. Together, our results provide important elements for understanding the impact of translation termination and NMD on the human transcriptome and reveal novel determinants of ribosome biogenesis regulation.

Published
2019

11. Turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Author

Isabelle Gagnon-Arsenault, Christian R. Landry, Isabelle Hatin, Johan Hallin, Alexandre K. Dubé, Lou Nielly-Thibault, Eléonore Durand, Olivier Namy, Département de Biologie [Québec], Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS)-Université Laval [Québec] (ULaval), Département de Biochimie, Microbiologie et Bioinformatique [Québec, Canada], Université Laval [Québec] (ULaval)-Pavillon Charles-Eugène-Marchand [Québec, Canada] (CHM), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génomique, Structure et Traduction (GST), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was supported by a Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery grant and a Fonds de recherche Nature et Technologies Quebec (FRQNT) Team Grant (2015-PR-181807) to C.R.L. C.R.L. holds the Canada Research Chair in Evolutionary Cell and Systems Biology., Pavillon Charles-Eugène-Marchand [Québec, Canada] (CHM)-Université Laval [Québec] (ULaval), and Namy, Olivier

Subjects
Transcription, Genetic, Biology, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Ribosome, Open Reading Frames, 03 medical and health sciences, 0302 clinical medicine, Intergenic region, Gene Expression Regulation, Fungal, Yeasts, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetics, Protein biosynthesis, Saccharomyces paradoxus, ORFS, Gene, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Reporter gene, Research, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, Biological Evolution, Open reading frame, Protein Biosynthesis, [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Ribosomes, 030217 neurology & neurosurgery
Abstract

Little is known about the rate of emergence of de novo genes, what their initial properties are, and how they spread in populations. We examined wild yeast populations (Saccharomyces paradoxus) to characterize the diversity and turnover of intergenic ORFs over short evolutionary timescales. We find that hundreds of intergenic ORFs show translation signatures similar to canonical genes, and we experimentally confirmed the translation of many of these ORFs in laboratory conditions using a reporter assay. Compared with canonical genes, intergenic ORFs have lower translation efficiency, which could imply a lack of optimization for translation or a mechanism to reduce their production cost. Translated intergenic ORFs also tend to have sequence properties that are generally close to those of random intergenic sequences. However, some of the very recent translated intergenic ORFs, which appeared

Published
2019

12. The high turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations

Author

Éléonore Durand, Isabelle Gagnon-Arsenault, Johan Hallin, Isabelle Hatin, Alexandre K Dubé, Lou Nielly-Thibaut, Olivier Namy, and Christian R Landry

Subjects
Genetics, 0303 health sciences, Mutation rate, Biology, biology.organism_classification, Genome, 03 medical and health sciences, 0302 clinical medicine, Intergenic region, Mutation (genetic algorithm), Gene duplication, Saccharomyces paradoxus, ORFS, Gene, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Little is known about the rate of emergence of genes de novo, how they spread in populations and what their initial properties are. We examined wild Saccharomyces paradoxus populations to characterize the diversity and turnover of intergenic ORFs over short evolutionary time-scales. We identified ~34,000 intergenic ORFs per individual genome for a total of ~64,000 orthogroups, which resulted from an estimated turnover rate relatively smaller than the rate of gene duplication in yeast. Hundreds of intergenic ORFs show translation signatures, similar to canonical genes, but lower translation efficiency, which could reduce their potential production cost or simply reflect a lack of optimization. Translated intergenic ORFs tend to display low expression levels with sequence properties that are on average closer to expectations based on intergenic sequences. However, some predicted de novo polypeptides with gene-like properties emerged from ancient as well as recent birth events, illustrating that the raw material for functional innovations may appear even over short evolutionary time-scales. Our results suggest that variation in the mutation rate along the genome impacts the turnover of random polypeptides, which may in turn influence their early evolutionary trajectory. Whereas low mutation rate regions allow more time for random intergenic ORFs to evolve and become functional before being lost, mutation hotspots allow for the rapid exploration of the molecular landscape, thereby increasing the probability to acquire a polypeptide with immediate gene-like properties and thus functional potential.

Published
2018
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13. Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli

Author

Jacob, Beal, Trac Haddock Angellii, Markus, Gershater, Kim de Mora, Meagan, Lizarazo, Jim, Hollenhorst, Randy, Rettberg, Philipp, Demling, Rene, Hanke, Michae, Osthegel, Anna, Schechtel, Suresh, Sudarsan, Arne, Zimmermann, Bartosz, Gabryelczyk, Martina, Ikonen, Minnamari, Salmela, Muradıye, Acar, Muhammed Fatih Aktas, Furkan, Bestepe, Furkan Sacit Ceylan, Sadık, Cigdem, Mikail, Dohan, Mustafa, Elitok, Mehmet, Gunduz, Esra, Gunduz, Omer Faruk Hatipoglu, Turan, Kaya, Orhan, Sayin, Safa, Tapan, Osman Faruk Tereci, Abdullah, Uçar, Mustafa, Yilmaz, Jeffrey, Barrick, Alex, Gutierrez, Dennis, Mishler, Jordan, Monk, Kate, Mortensen, Nathan, Shin, Ella, Watkins, Yintong, Chen, Yuji, Jin, Yuanjie, Shi, Haoqian Myelin Zhang, Bruno, Ono, Ieda Maria Martinez Paino, Lais, Ribovski, Ivan, Silva, Danilo Keiji Zampronio, Nils, Birkholz, Rudiger Frederik Busche, Oliver, Konzock, Steffen, Lippold, Carsten, Ludwig, Melanie, Philippi, Lukas, Platz, Christian, Sigismund, Susanne, Weber, Maren, Wehrs, Niels, Werchau, Anna, Wronska, Zen Zen Yen, Yash, Agarwal, Evan, Appleton, Douglas, Densmore, Ariela, Esmurria, Kathleen, Lewis, Alan, Pacheco, Marcel, Bruchez, Danielle, Peters, Cheryl, Telmer, Lena, Wang, Silvia Canas Duarte, Daniel Giraldo Perez, Camilo Gomez Garzon, Jorge Madrid Wolff, Nathaly Marin Medina, Valentina, Mazzanti, Laura Rodriguez Forero, Eitan, Scher, Robin, Dowell, Samantha, O’Hara, Cloe Simone Pogoda, Kendra, Shattuck, Ali, Altintas, Anne Pihl Bali, Rasmus, Bech, Anne, Egholm, Anne Sofie Laerke Hansen, Kristian, Jensen, Kristian Barreth Karlsen, Caroline, Mosbech, Sophia, Belkhelfa, Noemie, Berenger, Romain, Bodinier, Cecile, Jacry, Laura Matabishi Bibi, Pierre, Parutto, Julie, Zaworski, Andries de Vries, Freek de Wijs, Rick, Elbert, Lisa, Hielkema, Chandhuru, Jagadeesan, Bayu, Jayawardhana, Oscar, Kuipers, Anna, Lauxen, Thomas, Meijer, Sandra, Mous, Renske van Raaphorst, Aakanksha, Saraf, Otto, Schepers, Oscar, Smits, Jan Willem Veening, Ruud Detert Oude Weme, Lianne, Wieske, Catherine, Ainsworth, Xenia Spencer Milnes, Alejandro, Gómezávila, Eddie Cano Gamez, Ana Laura Torres Huerta, Carlos Alejandro Meza Ramirez, Philipp, Popp, Jara, Radeck, Anna, Sommer, Xiangkai, Li, Qi, Wu, Hongxia, Zhao, Ruixue, Zhao, Irem, Bastuzel, Yasemin, Ceyhan, Mayda, Gursel, Burak, Kizil, Ilkem, Kumru, Yasemin, Kuvvet, Helin, Tercan, Seniz, Yuksel, Luiza, Niyazmetova, Timothy, Ang, Lucas, Black, Ciaran, Kelly, George, Wadhams, Clovis, Basier, Urszula, Czerwinska, Cindy Suci Ananda, Muhammad Al Azhar, Adelia, Elviantari, Maya, Fitriana, Arief Budi Witarto, Yuliant, Jia Fangxing, Qingfeng, Hou, Wan, Pei, Chen, Rifei, Wang, Rong, Huang, Wei, Zhang, Yushan, Jianguo, He, Dengwen, Lai, Pai, Li, Jianheng, Liu, Chunyang, Ni, Qianbin, Zhang, Cinthya, Cadenas, Zardain Canabal, Eduardo J., Claudia Nallely Alonso Cantu, Mercedes Alejandra Vazquez Cantu, Eduardo Cepeda Canedo, Cesar Miguel Valdez Cordova, Jose Alberto de la Paz Espinosa, Carlos Enrique Alavez Garcia, Ana Laura Navarro Heredia, Adriana, Hernandez, Sebastian Valdivieso Jauregui, Eduardo Ramirez Montiel, Eduardo Serna Morales, Yamile Minerva Castellanos Morales, Omar Alonso Cantu Pena, Ramirez Rodríguez, Eduardo A., Elizabeth Vallejo Trejo, Jesus Gilberto Rodriguez Ceja, Jesus Eduardo Martinez Hernandez, Mario Alberto Pena Hernandez, Enrique Amaya Perez, Rebeca Paola Torres Ramirez, Cla, J., Martin, Hanzel, Sarah Mohand Said, Shihab, Sawar, Dylan, Siriwardena, Alex, Tzahristos, Nils, Anlind, Martin, Friberg, Erik, Gullberg, Stephanie, Herman, Dallin, Christensen, Sara, Gertsch, Cody, Maxfield, Charles, Miller, Ryan, Putman, Christine, Bauerl, Estelles Lopez, Lucia T., Estefania Huet Trujillo, Marta Vazquez Vilar, Marlène Sophie Birk, Nico, Claassens, Walter de Koster, Rik van Rosmalen, Wen Ying Wu, Sian, Davies, Dan, Goss, William, Rostain, Chelsey, Tye, Waqar, Yousaf, Natalie, Farny, Chloe, Lajeunesse, Alex, Turland, Chen, An, Jielin, Chen, Yahong, Chen, Zehua, Che, Baishan, Fang, Xiaotong, Fu, Xifeng, Guo, Yue, Jiang, Yiying, Lei, Jianqiao, Li, Zhe, Li, Chang, Liu, Weibing, Liu, Yang, Li, Yizhu, Lv, Qingyu, Ruan, Yue, Su, Chun, Tang, Yushen, Wang, Fan, Wu, Xiaoshan, Yan, Ruihua, Zhang, Tangduo, Zhang, Farren, Isaacs, Ariel Leyva Hernandez, Natalie, Ma, Stephanie, Mao, Yamini, Naidu, Tuukka, Miinalainen, Marion Aruann, Daniel Calendini, Yoann Chabert, Gael Chambonnier, Myriam, Choukour, Ella de Gaulejac, Camille, Houy, Axel, Levier, Loreen, Logger, Sebastien, Nin, Valerie, Prima, Sturgis, James N., Beibei, Fang, Sadik, Cigdem, Abdullah, Ucar, Alejandro, Gutierrez, Revanth, Poondla, Sanjana, Reddy, Tyler, Rocha, Natalie, Schulte, Devin, Wehle, Marta Eva Jackowski, Sean Ross Craig, Ariana Mirzarafie Ahi, Elliott, Parris, Luba, Prout, Barbara, Steijl, Rachel, Wellman, Zhao, Fan, Zhang, Jing, Yang, Wei, Yang, Yuanzhan, Wen, Zhaosen, Evan, Appletion, Jeffrey, Chen, Abha, Patil, Shaheer, Priracha, Kate, Ryan, Nick, Salvador, John, Viola, Boralli, Camila Maria S., Camila Barbosa Bramorski, Juliana Cancino Bernardi, Ana Laura de Lima, Paula Maria Pincela Lins, Cristiane Casonato Melo, Deborah Cezar Mendonca, Thiago, Mosqueiro, Everton, Silva, Graziele, Vasconcelos, Ruchi, Asthana, Donna, Lee, Michelle, Yu, Peter, Choi, Effie, Lau, Kenneth, Lau, Oscar, Ying, Brandon, Malone, Paul, Young, Aidan, Ceney, Dakota, Hawthorne, Sharon, Lian, Sam, Mellentine, Dylan, Miller, Barbara Castro Moreira, Christie, Peebles, Olivia, Smith, Kevin, Walsh, Allison, Zimont, Michael, Brasino, Michael, Donovan, Hannah, Young, Jan, Bejvl, Daniel, Georgiev, Hynek, Kasl, Katerina Pechotova, Vaclav Pelisek, Anna, Sosnova, Pavel, Zach, Anthony, Ciesla, Benjamin, Hoover, Elliott, Chapman, Jon Marles Wright, Vicky, Moynihan, Liusaidh, Owen, Brooke Rothschild Mancinelli, Emilie, Cuillery, Joseph, Heng, Vincent, Jacquot, Paola, Malsot, Rocco, Meli, Cyril, Pulver, Ari, Sarfatis, Loic, Steiner, Victor, Steininger, Nina van Tiel, Gregoire, Thouvenin, Axel, Uran, Lisa, Baumgartner, Anna, Fomitcheva, Daniel, Gerngross, Verena, Jagger, Michael, Meier, Anja, Michel, Jasmine, Bird, Bradley, Brown, Todd, Burlington, Daniel, Herring, Joseph, Slack, Georgina, Westwood, Emilia, Wojcik, Julian, Bender, Julia, Donauer, Ramona, Emig, Rabea, Jesser, Julika, Neumann, Lara, Stuhn, Takema, Hasegawa, Tomoya, Kozakai, Haruka, Maruyama, Sean, Colloms, Charlotte, Flynn, Vilija, Lomeikaite, James, Provan, Kang, Ning, Shuyan, Tang, Guozhao, Wu, Yunjun, Yang, Zhi, Zeng, Zhan, Yi, Pan, Chu, Jun, Li, Keji, Yan, Athale, Chaitanya A., Swapnil, Bodkhe, Manasi, Gangan, Harsh, Gakhare, Yash, Jawale, Snehal, Kadam, Prachiti, Moghe, Gayatri, Mundhe, Neha, Khetan, Ira, Phadke, Prashant, Uniyal, Siddhesh, Zadey, Ines, Cottignie, Eline, Deprez, Astrid, Deryckere, Jasper, Janssens, Frederik, Jonnaert, Katarzyna, Malczewska, Thomas, Pak, Johan, Robben, Ovia Margaret Thirukkumaran, Vincent Van Deuren, Laurens, Vandebroek, Laura Van Hese, Laetitia Van Wonterghem, Leen, Verschooten, Moritz, Wolter, Joss, Auty, Richard, Badge, Liam, Crawford, Raymond, Dalgleish, Amy, Evans, Cameron, Grundy, Charlie, Kruczko, Payal, Karia, Graeme, Glaister, Rhys, Hakstol, Seme, Mate, Karin, Otero, Dustin, Smith, Jeff, Tingley, Hans Joachim Wieden, Haotian, Wang, Ningning, Yao, Matthias, Franz, Anna, Knoerlein, Nicolas, Koutsoubelis, Loechner, Anne C., Max, Mundt, Alexandra, Richter, Oliver, Schauer, Marjorie, Buss, Sivateja, Tangirala, Brian, Teague, Tianyi, Huang, Xinhao, Song, Yibing, Wei, Zhaoran, Zhang, Longzhi, Cao, Cheng Li, Kang Yang, Zhiqin, Chen, Yuxing, Fang, Libo, Sun, Weiyi, Wang, Yang, Yang, David, Adams, Joshua, Colls, Joshua, Timmons, David, Urick, Julia Anna Adrian, Madina, Akan, Youssef, Chahibi, Rahmi, Lale, Typhaine Le Doujet, Marit Vaagen Roee, Altynay, Abdirakhmanova, Askarbek, Orakov, Azhar, Zhailauova, Jinyang, Liang, Yu, Ma, Qikai, Qin, Yetian, Su, Ju Yeon Han, Raphaella, Hull, Wei Chung Kong, Li Chieh Lu, Duke, Quinton, Pauline, Aubert, Johan, Bourdarias, Olivier, Bugaud, Coralie Demon Chaine, Isabelle, Hatin, Ibtissam Kaid Slimane, Seong Koo Kang, Audrey, Moatti, Cheikh Fall Ndiaye, Mathilde, Ananos, Alexander, Arkhipenko, Valentin, Bailly, Jules, Caput, Javier, Castillo, Alma Chapet Batlle, Floriane, Cherrier, Claudia Demarta Gatsi, Deshmukh, Gopaul, Muriel, Gugger, Caroline, Lambert, Lucas, Krauss, Amelie, Vandendaele, Xiaojing, Li, Lin, Xiaomei, Luo Xunxun, Anders C. h. r. Hansen, Tina, Kronborg, Pettersen, Jens S., Charles, Calvet, Tyler Dae Devlin, Kosuke, Fujishima, Danny, Greenberg, Tina, Ju, Ryan, Kent, Daniel, Kunin, Erica, Lieberman, Griffin, Mccutcheon, Thai, Nguyen, Lynn, Rothschild, Shih, Joseph D., Jack, Takahashi, Kirsten, Thompson, Forrest, Tran, Daniel, Xiang, Felix, Richter, Yang, Xiaoran, Xiangyue, Hu, Changyuan, Deng, Shuyu, Hua, Yumeng, Li, Xinyu, Meng, Boxiang, Wang, Yingqi, Wang, Xuan, Wang, Zixuan, Xu, Jieyu, Yan, Ming, Yan, Yineng, Zhou, Edgar Alberto Alcalá Orozco, José Alberto Cristerna Bermúdez, Daniela Flores Gómez, José Ernesto Hernández Castañeda, Diana Clarisse Montaño Navarro, Juana Yessica PérezÁvila, María Fernanda Salazar Figueroa, María Fernanda Sánchez Arroyo, Oliva Angélica Sánchez Montesinos, Ángel Farid Rojas Cruz, Carlos Ramos Gutiérrez, Alonso Pérez Lona, Carlos Alejandro Meza Ramírez, Fernanda Sotomayor Olivares, Jorge Sebastián Rodríguez Iniesta, Juan Carlos Rueda Silva, Shotaro, Ayukawa, Takahiro, Kashiwagi, Daisuke, Kiga, Misa, Minegishi, Riku, Shinohara, Hiraku, Tokuma, Yuta, Yamazaki, Shuhei, Yasunishi, Erinn Sim Zixuan, Remsha, Afzal, Matthew, Carrigan, Barry, Moran, Marlena, Mucha, Arnas, Petrauskas, Stefan, Marsden, Michelle, Post, Anne, Rodenburg, Hector, Sanguesa, Marit van der Does, Erwin van Rijn, Max van’t Hof, Yeshi de Bruin, Hans de Ferrante, Elles, Elschot, Laura, Jacobs, Jan Willem Muller, Sjoerd, Nooijens, Femke, Vaassen, Cas van der Putten, Esther van Leeuwen, Laura van Smeden, Kwan Kwan Zhu, Kevin, Sabath, Katharina, Sporbeck, Nicolai von Kügelgen, Lisa, Wellinger, Stefanie, Braun, Jack, Ho, Yash, Mishra, Mariola, Sebastian, Lucas von Chamier, Ahsan, Fasih M., Satyadi, Megan A., Vivienne, Gunadhi, Phillip, Kyriakakis, Jenny, Lee, Walter, Thavarajah, Kimia, Abtahi, Robert, Hand, Chun Mun Loke, Adam, Wahab, Iowis, Zhu, Del Bianco, Cristina, Chizzolini, Fabio, Elisa, Godino, Lentini, Roberta, Mansy, Sheref Samir, Yeh Martin, Noel, Claudio Oss Pegorar, Alexander, Cook, Timothy, Kerns, Chad, Nielsen, Michael, Paskett, Alexander, Torgesen, Stephen, Lee, Ophir, Ospovat, Sikandar, Raza, Daniel, Shaykevich, Jarrod, Shilts, Barbora, Bajorinaite, Mykolas, Bendorius, Ieva, Rauluseviciute, Ieva, Savickyte, Sarunas, Tumas, William, Buchser, Elli, Cryan, Caroline, Golino, Andrew, Halleran, Taylor, Jacobs, Michael, Lefew, Joe, Maniaci, John, Marken, Margaret, Saha, Panya, Vij, Kayla, Desanty, Julie, Mazza, Raytheon BBN Technologies, iGEM Foundation, Synthace, Agilent Technology [Santa Clara], Raytheon BBN Technologies, Synthace, and Agilent provided support in the form of salaries for authors JB, MG, and JH, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the author contributions section, The authors wish to thank Sarah Munro and Marc Salit of NIST for help in designing this study. Consortium authors include all persons self-identified by contributing teams as deserving co-authorship credit. Contributors are listed alphabetically within team, and teams alphabetically and by year. Note that some persons may be credited as contributing in both years. Team names are given as identified in iGEM records: full details of each team’s institution and additional members may be found online in the iGEM Foundation archives at:http://year.igem.org/Team:name e.g.: full information on the 2015 ETH_Zurich team may be found at: http://2015.igem.org/Team:ETH_Zurich, BBN Technologies, IGEM Foundation, Synthace Ltd., Agilent Technologies, Department of Biotechnology and Chemical Technology, Helsinki Institute for Information Technology HIIT, ATOMS Turkiye, Boston University, Carnegie Mellon University, Technical University of Denmark, Ludwig Maximilian University of Munich, Middle East Technical University, Sumbawa University of Technology, Southern University of Science and Technology, Sun Yat-Sen University, Tecnológico de Monterrey, Universidad Autonoma de Nuevo Leon, University of Ottawa, Universitat Politècnica de València, Wageningen University and Research Centre, Worcester Polytechnic Institute, Xiamen University, University of Texas at Austin, Bielefeld University, Birkbeck University of London, USP-Brazil, City University of Hong Kong, Colorado State University, CU Boulder, Swiss Federal Institute of Technology Lausanne, Swiss Federal Institute of Technology Zurich, University of Exeter, Indian Institute of Science Education and Research, KU Leuven, Massachusetts Institute of Technology, Northeast Agricultural University, Nanjing Agricultural University, Norwegian University of Science and Technology, Ocean University of China, University of Southern Denmark, Shenzhen Middle School - SZMS 15, Tokyo Institute of Technology, Trinity College Dublin, Delft University of Technology, Eindhoven University of Technology, Tuebingen, University of California Los Angeles, University of California San Diego, University of Maryland, University of Trento, Vanderbilt University, College of William and Mary, Department of Bioproducts and Biosystems, Aalto-yliopisto, Aalto University, Jones, D Dafydd, Discrete Technology and Production Automation, and ​Robotics and image-guided minimally-invasive surgery (ROBOTICS)

Subjects
0106 biological sciences, 0301 basic medicine, green fluorescent protein, Laboratory Proficiency Testing, Transcription, Genetic, International Genetically Engineered Machine, [SDV]Life Sciences [q-bio], lcsh:Medicine, Protein Engineering, 01 natural sciences, Infographics, Synthetic biology, genetics, lcsh:Science, Promoter Regions, Genetic, Macromolecular Engineering, transcription initiation, Measurement, Multidisciplinary, Chemistry, Strain (biology), gene expression regulation, good laboratory practice, Research Assessment, Fluorescence, Reproducibility, 3. Good health, Bioassays and Physiological Analysis, Engineering and Technology, Educational Status, Synthetic Biology, Genetic Engineering, Transcription, Graphs, Research Article, Biotechnology, Transcriptional Activation, Computer and Information Sciences, General Science & Technology, Green Fluorescent Proteins, Bioengineering, Computational biology, iGEM Interlab Study Contributors, Research and Analysis Methods, Promoter Regions, 03 medical and health sciences, promoter region, Genetic, 010608 biotechnology, Escherichia coli, ta215, business.industry, Data Visualization, lcsh:R, Fluorescence Competition, genetic transcription, DNA structure, Reproducibility of Results, Biology and Life Sciences, protein engineering, 030104 developmental biology, Good Health and Well Being, 7 INGENIERÍA Y TECNOLOGÍA, Synthetic Bioengineering, People and Places, lcsh:Q, Population Groupings, biosynthesis, business, metabolism, Undergraduates
Abstract

We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices. Copyright: © 2016 Beal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Published
2016

14. Global translational impacts of the loss of the tRNA modification t

Author

Patrick C, Thiaville, Rachel, Legendre, Diego, Rojas-Benítez, Agnès, Baudin-Baillieu, Isabelle, Hatin, Guilhem, Chalancon, Alvaro, Glavic, Olivier, Namy, and Valérie, de Crécy-Lagard

Subjects
ribosome profiling, t6A, Applied Microbiology, Genetics, translation, modified nucleosides, Microbiology, Molecular Biology, tRNA
Abstract

The universal tRNA modification t6A is found at position 37 of nearly all tRNAs decoding ANN codons. The absence of t6A37 leads to severe growth defects in baker’s yeast, phenotypes similar to those caused by defects in mcm5s2U34 synthesis. Mutants in mcm5s2U34 can be suppressed by overexpression of tRNALysUUU, but we show t6A phenotypes could not be suppressed by expressing any individual ANN decoding tRNA, and t6A and mcm5s2U are not determinants for each other’s formation. Our results suggest that t6A deficiency, like mcm5s2U deficiency, leads to protein folding defects, and show that the absence of t6A led to stress sensitivities (heat, ethanol, salt) and sensitivity to TOR pathway inhibitors. Additionally, L-homoserine suppressed the slow growth phenotype seen in t6A-deficient strains, and proteins aggregates and Advanced Glycation End-products (AGEs) were increased in the mutants. The global consequences on translation caused by t6A absence were examined by ribosome profiling. Interestingly, the absence of t6A did not lead to global translation defects, but did increase translation initiation at upstream non-AUG codons and increased frame-shifting in specific genes. Analysis of codon occupancy rates suggests that one of the major roles of t6A is to homogenize the process of elongation by slowing the elongation rate at codons decoded by high abundance tRNAs and I34:C3 pairs while increasing the elongation rate of rare tRNAs and G34:U3 pairs. This work reveals that the consequences of t6A absence are complex and multilayered and has set the stage to elucidate the molecular basis of the observed phenotypes.

Published
2016

15. Translation Analysis at the Genome Scale by Ribosome Profiling

Author

Olivier Namy, Rachel Legendre, Agnès Baudin-Baillieu, Isabelle Hatin, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule ( I2BC ), and Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 )

Subjects
0301 basic medicine, MESH : Protein Biosynthesis, MESH : RNA, Messenger, [SDV]Life Sciences [q-bio], 5.8S ribosomal RNA, Computational biology, Biology, Ribosome profiling, Deep sequencing, 03 medical and health sciences, Ribo-seq, Translational regulation, MESH: Genome, MESH: High-Throughput Nucleotide Sequencing, MESH: RNA, Messenger, MESH : Ribosomes, Genetics, [ SDV ] Life Sciences [q-bio], Recoding, Shine-Dalgarno sequence, Translation (biology), Ribosomal binding site, 030104 developmental biology, Translation regulation, MESH: Protein Biosynthesis, MESH : Polyribosomes, MESH : Genome, Eukaryotic Ribosome, MESH: Polyribosomes, MESH: Ribosomes, MESH : High-Throughput Nucleotide Sequencing
Abstract

International audience; Ribosome profiling is an emerging approach using deep sequencing of the mRNA part protected by the ribosome to study protein synthesis at the genome scale. This approach provides new insights into gene regulation at the translational level. In this review we describe the protocol to prepare polysomes and extract ribosome protected fragments before to deep sequence them.

Published
2016

16. Ribosome Biogenesis Controls Erythroid Differentiation Via a p53-Dependent Transcriptional Checkpoint and Its Limitation By RPS14 Haploinsufficiency Results in Selective Defects in Translation

Author

Michaela Fontenay, Patrick Mayeux, Mohandas Narla, Olivier Kosmider, Isabelle Hatin, Ismael Boussaid, Celia Floquet, Charlotte Andrieu-Soler, Eric Soler, Emilie-fleur Gautier, Anna Raimbault, and Salome Le Goff

Subjects
Cell cycle checkpoint, Three prime untranslated region, Immunology, Ribosome biogenesis, Translation (biology), Cell Biology, Hematology, Biology, Biochemistry, Cell biology, Ribosome Subunits, hemic and lymphatic diseases, Polysome, Transcriptional regulation, Haploinsufficiency
Abstract

Haploinsufficiency in genes encoding ribosomal proteins (RP) or ribosome-associated proteins either by mutation or deletion leads to a predominant erythroid phenotype. In acquired 5q- myelodysplasic syndrome (MDS), the macrocytic anemia has been linked to the monoallelic deletion of RPS14 gene which results in altered ribosome biogenesis. Because of the defective maturation of the small 40S ribosome subunit, the RPL5/RPL11/5SrARN complex, normally involved in the assembly of the large 60S subunit assembly, accumulates and inhibits E3-ligase-HDM2 leading to the stabilization and activation of p53 resultig in cell cycle arrest, increased apoptosis and defective differentiation of maturing erythroblasts. In the present work, we hypothesized that p53 could play a key role in the control of normal erythroid differentiation by ribosome biogenesis and we further investigated the involvement of the decreased pool of ribosome on erythroid defects in the 5q- syndrome. To investigate the first hypothesis, we studied the kinetics of ribosome biogenesis in human primary erythroblasts by mass spectrometry after pulse-SILAC. We noted that ribosome renewal collapses begining at the polychromatophilic erythroblast stage. We subsequently used the pharmacological agent CX-5461 to inhibit RNA polymerase I. When ribosome biogenesis in proerythroblasts is blocked by CX-5461, p53 is activated and proerythroblasts enter the terminal differentiation by expressing GATA1-erythroid target genes without apoptosis. By ChIP-seq in primary erythroblasts, we demonstrated that p53 binds to 1289 genes including 263 genes specifically activated by CX-5461, 6 of them being upregulated during CX-5461-induced erythroid differentiation and 3 of them being known GATA1 targets. We further used an shRNA strategy to demonstrate that one of these genes is required to permit entry into terminal erythroid differentiation when ribosome biogenesis is abrogated. We thus showed that normal erythroid differentiation is controlled by ribosome biogenesis through a p53-dependent checkpoint. In 5q- syndrome, ribosome biogenesis is continuously decreased along all stages of erythropoiesis and in contrast to the normal conditions, erythroid differentiation is defective with an excess of apoptosis affecting mature erythroblasts. We previously reported that GATA1 is targeted by a caspase-dependent cleavage since GATA1 is not protected by its chaperone HSP70 in the nucleus of MDS erythroblasts. We confirmed that GATA1 protein is decreased in 5q- primary erythroblasts and in RPS14 shRNA-expressing normal erythroblasts. To obtain further insights into the defective erythroid maturation of RPS14-deleted erythroblasts, we developed an inducible shRNA to RPS14 in the UT7/Epo cell line. Polysome profiling confirmed the decrease of 40S subunit and absolute quantification of RP by deep proteomics demonstrated a 50% decrease of RPS in conjunction with 50% reduction of ribosome content in these cells. GATA1 expression was decreased and was only partially rescued by treatment with either caspase inhibitor qVD or proteasome inhibitor, bortezomib. We then tested the hypothesis of a decrease in GATA1 translation, as previously shown in a shRNA RPS19 Diamond-Blackfan model, by analyzing and comparing the global transcriptome and the translatome corresponding to transcripts present in high molecular weight polysomes using Affymetrix HTA 2.0 microarrays. We observed a decoupling between transcriptome and translatome suggesting a selectivity of translational defects. Thermodynamic characteristics i.e. the fold energy, energy per base and length of the 3'UTR and the energy per base of the 5'UTR (Vienna RNA Package, UCSC genome browser) were the determinants of transcript selection on the polysome. The shortest transcripts with a highly structured 3'UTR including GATA1 were the transcripts which were less effectively translated. Consistently, the diminution of GATA1 protein was associated with a decrease of its target genes. Our results suggest that GATA1 is a potentially interesting therapeutic target. In summary, our results show that ribosome biogenesis controls erythroid differentiation via a p53-dependent transcriptional regulation and that a reduction of the ribosome pool leads to a selective translation at the expense of erythroid master gene GATA1. Disclosures Fontenay: Celgene: Research Funding.

Published
2017

17. Translation Analysis at the Genome Scale by Ribosome Profiling

Author

Agnès, Baudin-Baillieu, Isabelle, Hatin, Rachel, Legendre, and Olivier, Namy

Subjects
Genome, Polyribosomes, Protein Biosynthesis, High-Throughput Nucleotide Sequencing, RNA, Messenger, Ribosomes
Abstract

Ribosome profiling is an emerging approach using deep sequencing of the mRNA part protected by the ribosome to study protein synthesis at the genome scale. This approach provides new insights into gene regulation at the translational level. In this review we describe the protocol to prepare polysomes and extract ribosome protected fragments before to deep sequence them.

Published
2015

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