1
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Bhattacharjee R, Jolly LA, Corbett MA, Wee IC, Rao SR, Gardner AE, Ritchie T, van Hugte EJH, Ciptasari U, Piltz S, Noll JE, Nazri N, van Eyk CL, White M, Fornarino D, Poulton C, Baynam G, Collins-Praino LE, Snel MF, Nadif Kasri N, Hemsley KM, Thomas PQ, Kumar R, Gecz J. Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment. Nat Commun 2024; 15:1210. [PMID: 38331934 PMCID: PMC10853216 DOI: 10.1038/s41467-024-45121-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
We implicated the X-chromosome THOC2 gene, which encodes the largest subunit of the highly-conserved TREX (Transcription-Export) complex, in a clinically complex neurodevelopmental disorder with intellectual disability as the core phenotype. To study the molecular pathology of this essential eukaryotic gene, we generated a mouse model based on a hypomorphic Thoc2 exon 37-38 deletion variant of a patient with ID, speech delay, hypotonia, and microcephaly. The Thoc2 exon 37-38 deletion male (Thoc2Δ/Y) mice recapitulate the core phenotypes of THOC2 syndrome including smaller size and weight, and significant deficits in spatial learning, working memory and sensorimotor functions. The Thoc2Δ/Y mouse brain development is significantly impacted by compromised THOC2/TREX function resulting in R-loop accumulation, DNA damage and consequent cell death. Overall, we suggest that perturbed R-loop homeostasis, in stem cells and/or differentiated cells in mice and the patient, and DNA damage-associated functional alterations are at the root of THOC2 syndrome.
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Affiliation(s)
- Rudrarup Bhattacharjee
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lachlan A Jolly
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Mark A Corbett
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ing Chee Wee
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sushma R Rao
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alison E Gardner
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tarin Ritchie
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Eline J H van Hugte
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Ummi Ciptasari
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Sandra Piltz
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Jacqueline E Noll
- School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide and Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Nazzmer Nazri
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Clare L van Eyk
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Melissa White
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Dani Fornarino
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Rare Care Centre, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Lyndsey E Collins-Praino
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Marten F Snel
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Kim M Hemsley
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Paul Q Thomas
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Raman Kumar
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jozef Gecz
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia.
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2
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Nassar R, Thompson L, Fouquerel E. Molecular mechanisms protecting centromeres from self-sabotage and implications for cancer therapy. NAR Cancer 2023; 5:zcad019. [PMID: 37180029 PMCID: PMC10167631 DOI: 10.1093/narcan/zcad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/27/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Centromeres play a crucial role in DNA segregation by mediating the cohesion and separation of sister chromatids during cell division. Centromere dysfunction, breakage or compromised centromeric integrity can generate aneuploidies and chromosomal instability, which are cellular features associated with cancer initiation and progression. Maintaining centromere integrity is thus essential for genome stability. However, the centromere itself is prone to DNA breaks, likely due to its intrinsically fragile nature. Centromeres are complex genomic loci that are composed of highly repetitive DNA sequences and secondary structures and require the recruitment and homeostasis of a centromere-associated protein network. The molecular mechanisms engaged to preserve centromere inherent structure and respond to centromeric damage are not fully understood and remain a subject of ongoing research. In this article, we provide a review of the currently known factors that contribute to centromeric dysfunction and the molecular mechanisms that mitigate the impact of centromere damage on genome stability. Finally, we discuss the potential therapeutic strategies that could arise from a deeper understanding of the mechanisms preserving centromere integrity.
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Affiliation(s)
- Rim Nassar
- UPMC Hillman Cancer Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
| | - Lily Thompson
- UPMC Hillman Cancer Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232, USA
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3
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Silva Dos Santos F, Neves RAF, Bernay B, Krepsky N, Teixeira VL, Artigaud S. The first use of LC-MS/MS proteomic approach in the brown mussel Perna perna after bacterial challenge: Searching for key proteins on immune response. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108622. [PMID: 36803779 DOI: 10.1016/j.fsi.2023.108622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
The brown mussel Perna perna is a valuable fishing resource, primarily in tropical and subtropical coastal regions. Because of their filter-feeding habits, mussels are directly exposed to bacteria in the water column. Escherichia coli (EC) and Salmonella enterica (SE) inhabit human guts and reach the marine environment through anthropogenic sources, such as sewage. Vibrio parahaemolyticus (VP) is indigenous to coastal ecosystems but can be harmful to shellfish. In this study, we aimed to assess the protein profile of the hepatopancreas of P. perna mussel challenged by introduced - E. coli and S. enterica - and indigenous marine bacteria - V. parahaemolyticus. Bacterial-challenge groups were compared with non-injected (NC) and injected control (IC) - that consisted in mussels not challenged and mussels injected with sterile PBS-NaCl, respectively. Through LC-MS/MS proteomic analysis, 3805 proteins were found in the hepatopancreas of P. perna. From the total, 597 were significantly different among conditions. Mussels injected with VP presented 343 proteins downregulated compared with all the other conditions, suggesting that VP suppresses their immune response. Particularly, 31 altered proteins - upregulated or downregulated - for one or more challenge groups (EC, SE, and VP) compared with controls (NC and IC) are discussed in detail in the paper. For the three tested bacteria, significantly different proteins were found to perform critical roles in immune response at all levels, namely: recognition and signal transduction; transcription; RNA processing; translation and protein processing; secretion; and humoral effectors. This is the first shotgun proteomic study in P. perna mussel, therefore providing an overview of the protein profile of the mussel hepatopancreas, focused on the immune response against bacteria. Hence, it is possible to understand the immune-bacteria relationship at molecular levels better. This knowledge can support the development of strategies and tools to be applied to coastal marine resource management and contribute to the sustainability of coastal systems.
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Affiliation(s)
- Fernanda Silva Dos Santos
- Graduate Program in Sciences and Biotechnology, Institute of Biology, Fluminense Federal University (UFF), R. Mario Santos Braga, S/n. Centro, Niterói, RJ, CEP 24.020-141, Brazil; Research Group of Experimental and Aquatic Ecology, Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458-307, Urca, Rio de Janeiro, RJ, CEP: 22.290-240, Brazil.
| | - Raquel A F Neves
- Graduate Program in Neotropical Biodiversity (PPGBIO), Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458, Urca, Rio de Janeiro, RJ, CEP: 22.290-255, Brazil; Research Group of Experimental and Aquatic Ecology, Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458-307, Urca, Rio de Janeiro, RJ, CEP: 22.290-240, Brazil.
| | - Benoît Bernay
- Plateforme Proteogen, SFR ICORE 4206, Université de Caen Basse-Normandie, Esplanade de la paix, 14032, Caen cedex, France.
| | - Natascha Krepsky
- Graduate Program in Neotropical Biodiversity (PPGBIO), Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458, Urca, Rio de Janeiro, RJ, CEP: 22.290-255, Brazil.
| | - Valéria Laneuville Teixeira
- Graduate Program in Sciences and Biotechnology, Institute of Biology, Fluminense Federal University (UFF), R. Mario Santos Braga, S/n. Centro, Niterói, RJ, CEP 24.020-141, Brazil; Graduate Program in Neotropical Biodiversity (PPGBIO), Institute of Biosciences (IBIO), Federal University of the State of Rio de Janeiro (UNIRIO), Av. Pasteur, 458, Urca, Rio de Janeiro, RJ, CEP: 22.290-255, Brazil.
| | - Sébastien Artigaud
- Université de Brest, CNRS, IRD, Ifremer, UMR 6539 LEMAR, F-29280, Plouzané, France.
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4
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Mechanisms of germ cell survival and plasticity in Caenorhabditis elegans. Biochem Soc Trans 2022; 50:1517-1526. [PMID: 36196981 PMCID: PMC9704514 DOI: 10.1042/bst20220878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
Animals constantly encounter environmental and physiological stressors that threaten survival and fertility. Somatic stress responses and germ cell arrest/repair mechanisms are employed to withstand such challenges. The Caenorhabditis elegans germline combats stress by initiating mitotic germ cell quiescence to preserve genome integrity, and by removing meiotic germ cells to prevent inheritance of damaged DNA or to tolerate lack of germline nutrient supply. Here, we review examples of germline recovery from distinct stressors - acute starvation and defective splicing - where quiescent mitotic germ cells resume proliferation to repopulate a germ line following apoptotic removal of meiotic germ cells. These protective mechanisms reveal the plastic nature of germline stem cells.
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5
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Hicks T, Koury E, McCabe C, Williams C, Crahan C, Smolikove S. R-loop-induced irreparable DNA damage evades checkpoint detection in the C. elegans germline. Nucleic Acids Res 2022; 50:8041-8059. [PMID: 35871299 PMCID: PMC9371901 DOI: 10.1093/nar/gkac621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/28/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022] Open
Abstract
Accumulation of DNA–RNA hybrids in the form of R-loops can result in replication–transcription conflict that leads to the formation of DNA double strand breaks (DSBs). Using null mutants for the two Caenorhabditis elegans genes encoding for RNaseH1 and RNaseH2, we identify novel effects of R-loop accumulation in the germline. R-loop accumulation leads, as expected, to replication stress, followed by the formation of DSBs. A subset of these DSBs are irreparable. However, unlike irreparable DSBs generated in other systems, which trigger permanent cell cycle arrest, germline irreparable DSBs are propagated to oocytes. Despite DNA damage checkpoint activation in the stem cell niche, the signaling cannot be sustained and nuclei with irreparable DNA damage progress into meiosis. Moreover, unlike other forms of DNA damage that increase germline apoptosis, R-loop-generated DSBs remain undetected by the apoptotic checkpoint. This coincides with attenuation of ATM/ATR signaling in mid-to-late meiotic prophase I. These data altogether indicate that in the germline, DSBs that are generated by R-loops can lead to irreparable DSBs that evade cellular machineries designed for damage recognition. These studies implicate germline R-loops as an especially dangerous driver of germline mutagenesis.
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Affiliation(s)
- Tara Hicks
- Department of Biology, The University of Iowa , IA City, IA 52242, USA
| | - Emily Koury
- Department of Biology, The University of Iowa , IA City, IA 52242, USA
| | - Caleb McCabe
- Department of Biology, The University of Iowa , IA City, IA 52242, USA
| | - Cameron Williams
- Department of Biology, The University of Iowa , IA City, IA 52242, USA
| | - Caroline Crahan
- Department of Biology, The University of Iowa , IA City, IA 52242, USA
| | - Sarit Smolikove
- Department of Biology, The University of Iowa , IA City, IA 52242, USA
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6
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Kamp JA, Lemmens BBLG, Romeijn RJ, González-Prieto R, Olsen J, Vertegaal ACO, van Schendel R, Tijsterman M. THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1. Nucleic Acids Res 2022; 50:6235-6250. [PMID: 35670662 PMCID: PMC9226523 DOI: 10.1093/nar/gkac472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/11/2022] [Accepted: 06/02/2022] [Indexed: 12/25/2022] Open
Abstract
The integrity and proper expression of genomes are safeguarded by DNA and RNA surveillance pathways. While many RNA surveillance factors have additional functions in the nucleus, little is known about the incidence and physiological impact of converging RNA and DNA signals. Here, using genetic screens and genome-wide analyses, we identified unforeseen SMG-1-dependent crosstalk between RNA surveillance and DNA repair in living animals. Defects in RNA processing, due to viable THO complex or PNN-1 mutations, induce a shift in DNA repair in dividing and non-dividing tissues. Loss of SMG-1, an ATM/ATR-like kinase central to RNA surveillance by nonsense-mediated decay (NMD), restores DNA repair and radio-resistance in THO-deficient animals. Mechanistically, we find SMG-1 and its downstream target SMG-2/UPF1, but not NMD per se, to suppress DNA repair by non-homologous end-joining in favour of single strand annealing. We postulate that moonlighting proteins create short-circuits in vivo, allowing aberrant RNA to redirect DNA repair.
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Affiliation(s)
| | | | - Ron J Romeijn
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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7
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Sewell AK, Poss ZC, Ebmeier CC, Jacobsen JR, Old WM, Han M. The TORC1 phosphoproteome in C. elegans reveals roles in transcription and autophagy. iScience 2022; 25:104186. [PMID: 35479415 PMCID: PMC9036118 DOI: 10.1016/j.isci.2022.104186] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/14/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The protein kinase complex target of rapamycin complex 1 (TORC1) is a critical mediator of nutrient sensing that has been widely studied in cultured cells and yeast, yet our understanding of the regulatory activities of TORC1 in the context of a whole, multi-cellular organism is still very limited. Using Caenorhabditis elegans, we analyzed the DAF-15/Raptor-dependent phosphoproteome by quantitative mass spectrometry and characterized direct kinase targets by in vitro kinase assays. Here, we show new targets of TORC1 that indicate previously unknown regulation of transcription and autophagy. Our results further show that DAF-15/Raptor is differentially expressed during postembryonic development, suggesting a dynamic role for TORC1 signaling throughout the life span. This study provides a comprehensive view of the TORC1 phosphoproteome, reveals more than 100 DAF-15/Raptor-dependent phosphosites that reflect the complex function of TORC1 in a whole, multi-cellular organism, and serves as a rich resource to the field. Detailed, unbiased analysis of the Caenorhabditis elegans TORC1 phosphoproteome Characterization of DAF-15 expression and localization TORC1 direct targets with roles in transcription machinery and autophagy Unique technical approach and datasets provide rich resource to the field
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8
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Kow RL, Black AH, Saxton AD, Liachko NF, Kraemer BC. Loss of aly/ALYREF suppresses toxicity in both tau and TDP-43 models of neurodegeneration. GeroScience 2022; 44:747-761. [PMID: 35122183 PMCID: PMC9135935 DOI: 10.1007/s11357-022-00526-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/27/2022] [Indexed: 11/04/2022] Open
Abstract
Neurodegenerative diseases with tau pathology, or tauopathies, include Alzheimer's disease and related dementia disorders. Previous work has shown that loss of the poly(A) RNA-binding protein gene sut-2/MSUT2 strongly suppressed tauopathy in Caenorhabditis elegans, human cell culture, and mouse models of tauopathy. However, the mechanism of suppression is still unclear. Recent work has shown that MSUT2 protein interacts with the THO complex and ALYREF, which are components of the mRNA nuclear export complex. Additionally, previous work showed ALYREF homolog Ref1 modulates TDP-43 and G4C2 toxicity in Drosophila melanogaster models. We used transgenic C. elegans models of tau or TDP-43 toxicity to investigate the effects of loss of ALYREF function on tau and TDP-43 toxicity. In C. elegans, three genes are homologous to human ALYREF: aly-1, aly-2, and aly-3. We found that loss of C. elegans aly gene function, especially loss of both aly-2 and aly-3, suppressed tau-induced toxic phenotypes. Loss of aly-2 and aly-3 was also able to suppress TDP-43-induced locomotor behavior deficits. However, loss of aly-2 and aly-3 had divergent effects on mRNA and protein levels as total tau protein levels were reduced while mRNA levels were increased, but no significant effects were seen on total TDP-43 protein or mRNA levels. Our results suggest that although aly genes modulate both tau and TDP-43-induced toxicity phenotypes, the molecular mechanisms of suppression are different and separated from impacts on mRNA and protein levels. Altogether, this study highlights the importance of elucidating RNA-related mechanisms in both tau and TDP-43-induced toxicity.
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Affiliation(s)
- Rebecca L Kow
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA.
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, 98104, USA.
| | - Aristide H Black
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA
| | - Aleen D Saxton
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA
| | - Nicole F Liachko
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, 98104, USA
| | - Brian C Kraemer
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, S182, 1660 South Columbian Way, Seattle, WA, 98108, USA.
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, 98104, USA.
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
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9
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Zheleva A, Camino LP, Fernández-Fernández N, García-Rubio M, Askjaer P, García-Muse T, Aguilera A. THSC/TREX-2 deficiency causes replication stress and genome instability in Caenorhabditis elegans. J Cell Sci 2021; 134:jcs258435. [PMID: 34553761 PMCID: PMC10658913 DOI: 10.1242/jcs.258435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 09/11/2021] [Indexed: 11/20/2022] Open
Abstract
Transcription is an essential process of DNA metabolism, yet it makes DNA more susceptible to DNA damage. THSC/TREX-2 is a conserved eukaryotic protein complex with a key role in mRNP biogenesis and maturation that prevents genome instability. One source of such instability is linked to transcription, as shown in yeast and human cells, but the underlying mechanism and whether this link is universal is still unclear. To obtain further insight into the putative role of the THSC/TREX-2 complex in genome integrity, we have used Caenorhabditis elegans mutants of the thp-1 and dss-1 components of THSC/TREX-2. These mutants show similar defective meiosis, DNA damage accumulation and activation of the DNA damage checkpoint. However, they differ from each other regarding replication defects, as determined by measuring dUTP incorporation in the germline. Interestingly, this specific thp-1 mutant phenotype can be partially rescued by overexpression of RNase H. Furthermore, both mutants show a mild increase in phosphorylation of histone H3 at Ser10 (H3S10P), a mark previously shown to be linked to DNA-RNA hybrid-mediated genome instability. These data support the view that both THSC/TREX-2 factors prevent transcription-associated DNA damage derived from DNA-RNA hybrid accumulation by separate means.
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Affiliation(s)
- Angelina Zheleva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Lola P. Camino
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Nuria Fernández-Fernández
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - María García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Peter Askjaer
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, 41013 Seville, Spain
| | - Tatiana García-Muse
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-Consejo Superior de Investigaciones Científicas-Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
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Katahira J, Senokuchi K, Hieda M. Human THO maintains the stability of repetitive DNA. Genes Cells 2020; 25:334-342. [PMID: 32065701 DOI: 10.1111/gtc.12760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/31/2023]
Abstract
The evolutionarily conserved multiprotein complex THO/TREX is required for pre-mRNA processing, mRNA export and the maintenance of genome stability. In this study, we analyzed the genome-wide distribution of human THOC7, a component of human THO, by chromatin immunoprecipitation sequencing. The analysis revealed that human THOC7 occupies repetitive sequences, which include microsatellite repeats in genic and intergenic regions and telomeric repeats. The majority of the THOC7 ChIP peaks overlapped with those of the elongating form of RNA polymerase II and R-loops, indicating that THOC7 accumulates in transcriptionally active repeat regions. Knocking down THOC5, an RNA-binding component of human THO, by siRNA induced the accumulation of γH2AX in the repeat regions. We also observed an aberration in the telomeres in the THOC5-depleted condition. These results suggest that human THO restrains the transcription-associated instability of repeat regions in the human genome.
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Affiliation(s)
- Jun Katahira
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Kohei Senokuchi
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Miki Hieda
- Graduate School of Health Sciences, Ehime Prefectural University of Health Sciences, Iyo-gun, Japan
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11
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Reduction of mRNA export unmasks different tissue sensitivities to low mRNA levels during Caenorhabditis elegans development. PLoS Genet 2019; 15:e1008338. [PMID: 31525188 PMCID: PMC6762213 DOI: 10.1371/journal.pgen.1008338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 09/26/2019] [Accepted: 07/31/2019] [Indexed: 12/25/2022] Open
Abstract
Animal development requires the execution of specific transcriptional programs in different sets of cells to build tissues and functional organs. Transcripts are exported from the nucleus to the cytoplasm where they are translated into proteins that, ultimately, carry out the cellular functions. Here we show that in Caenorhabditis elegans, reduction of mRNA export strongly affects epithelial morphogenesis and germline proliferation while other tissues remain relatively unaffected. Epithelialization and gamete formation demand a large number of transcripts in the cytoplasm for the duration of these processes. In addition, our findings highlight the existence of a regulatory feedback mechanism that activates gene expression in response to low levels of cytoplasmic mRNA. We expand the genetic characterization of nuclear export factor NXF-1 to other members of the mRNA export pathway to model mRNA export and recycling of NXF-1 back to the nucleus. Our model explains how mutations in genes involved in general processes, such as mRNA export, may result in tissue-specific developmental phenotypes. The Central Dogma of Biology schematically highlights the transmission of genetic information stored in DNA, through RNA, to the formation of proteins. This general flow implicates RNA export from the nucleus to the cytoplasm and proper protein localization within the eukaryotic cell. Ultimately, proteins are the cell’s structural and catalytic functional units. As a result, cells differentiate into one cell type or another (such as epithelial, muscle, neuron…) and exhibit specific shape and functionality. Here we describe, in a C. elegans model, how mutations in genes involved in a general and ubiquitous mechanism, such as mRNA export, may result in tissue-specific developmental phenotypes that show up in processes that are highly demanding of cytoplasmic transcripts like epithelialization and gamete formation. A deep understanding of the mechanisms underlying the "connectors" shown in the Central Dogma of Biology is key both to unravel the general genetic control of an organism’s development and, at the same time, contribute to a better understanding of tissue-specific diseases.
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12
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Accogli A, Scala M, Calcagno A, Castello R, Torella A, Musacchia F, Allegri AME, Mancardi MM, Maghnie M, Severino M, Nigro V, Capra V. Novel CNS malformations and skeletal anomalies in a patient with Beaulieu-boycott-Innes syndrome. Am J Med Genet A 2018; 176:2835-2840. [PMID: 30238602 DOI: 10.1002/ajmg.a.40534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022]
Abstract
THO/TREX (transcription/export) is a conserved eukaryotic complex that plays a crucial role in gene expression and prevents DNA damage during mitosis and meiosis. In mammals, TREX is essential during embryogenesis, determining stem cell fate specification by regulating posttranscriptional self-renewal and differentiation in several tissues. It is composed of a core called THO, consisting of THOC1, 2, 5, 6, 7, and additional proteins. Bi-allelic mutations in THOC6 have been associated to Beaulieu-Boycott-Innes syndrome (BBIS), a syndromic form of intellectual disability (ID). To date, nine patients harbouring homozygous or compound heterozygous mutations in THOC6 have been reported. Despite the clinical heterogenity and subtle dysmorphic features in some individuals, distinctive facial features are tall forehead, short and upslanting palpebral fissures, deep set eyes, flat philtrum, and malocclusion. Nonlife threatening congenital anomalies are common, including cardiac and renal malformations, anteriorly displaced anus, cryptorchidism in males, submucous cleft palate, and corpus callosum dysgenesis. Affected patients usually have short stature, mild microcephaly, and mild to moderate ID. Here, we describe an Italian patient with BBIS, carrying two compound heterozygous loss-of-function (LoF) variants in THOC6 (c.577C > T, p.R193* and c.792_793delCA, p.V264Vfs*48). In addition to the common phenotype, she displays cerebellar hypoplasia with severe vermian dysgenesis and hydrocephalus due to aqueductal stenosis, multiple skeletal anomalies and hypergonadotropic hypogonadism. Thus, we review the previous cases and discuss the phenotypic spectrum of BBIS, providing further evidence regarding the pivotal role of TREX complex in human development.
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Affiliation(s)
- Andrea Accogli
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genoa, Italy.,Università degli studi di Genova, Italy
| | - Marcello Scala
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genoa, Italy.,Università degli studi di Genova, Italy
| | - Annalisa Calcagno
- UOC Clinica Pediatrica, Istituto Giannina Gaslini, Università di Genova, Genoa, Italy
| | | | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Anna M E Allegri
- UOC Clinica Pediatrica, Istituto Giannina Gaslini, Università di Genova, Genoa, Italy
| | - Maria M Mancardi
- UOC Neuropsichiatria Infantile-Centro Epilessia, Istituto Giannina Gaslini, Genoa, Italy
| | - Mohamad Maghnie
- UOC Clinica Pediatrica, Istituto Giannina Gaslini, Università di Genova, Genoa, Italy
| | | | | | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Valeria Capra
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genoa, Italy
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Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability. Nat Genet 2016; 48:1385-1395. [DOI: 10.1038/ng.3672] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 08/22/2016] [Indexed: 12/14/2022]
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14
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Castellano-Pozo M, García-Muse T, Aguilera A. Correction: The Caenorhabditis elegans THO Complex Is Required for the Mitotic Cell Cycle and Development. PLoS One 2016; 11:e0160138. [PMID: 27441844 PMCID: PMC4956278 DOI: 10.1371/journal.pone.0160138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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15
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Mechanisms of genome instability induced by RNA-processing defects. Trends Genet 2014; 30:245-53. [PMID: 24794811 DOI: 10.1016/j.tig.2014.03.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/20/2022]
Abstract
The role of normal transcription and RNA processing in maintaining genome integrity is becoming increasingly appreciated in organisms ranging from bacteria to humans. Several mutations in RNA biogenesis factors have been implicated in human cancers, but the mechanisms and potential connections to tumor genome instability are not clear. Here, we discuss how RNA-processing defects could destabilize genomes through mutagenic R-loop structures and by altering expression of genes required for genome stability. A compelling body of evidence now suggests that researchers should be directly testing these mechanisms in models of human cancer.
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