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Jonnakuti VS, Wagner EJ, Maletić-Savatić M, Liu Z, Yalamanchili HK. PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data. CELL REPORTS METHODS 2024; 4:100707. [PMID: 38325383 PMCID: PMC10921021 DOI: 10.1016/j.crmeth.2024.100707] [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: 02/28/2023] [Revised: 04/13/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024]
Abstract
Alternative polyadenylation (APA) is a key post-transcriptional regulatory mechanism; yet, its regulation and impact on human diseases remain understudied. Existing bulk RNA sequencing (RNA-seq)-based APA methods predominantly rely on predefined annotations, severely impacting their ability to decode novel tissue- and disease-specific APA changes. Furthermore, they only account for the most proximal and distal cleavage and polyadenylation sites (C/PASs). Deconvoluting overlapping C/PASs and the inherent noisy 3' UTR coverage in bulk RNA-seq data pose additional challenges. To overcome these limitations, we introduce PolyAMiner-Bulk, an attention-based deep learning algorithm that accurately recapitulates C/PAS sequence grammar, resolves overlapping C/PASs, captures non-proximal-to-distal APA changes, and generates visualizations to illustrate APA dynamics. Evaluation on multiple datasets strongly evinces the performance merit of PolyAMiner-Bulk, accurately identifying more APA changes compared with other methods. With the growing importance of APA and the abundance of bulk RNA-seq data, PolyAMiner-Bulk establishes a robust paradigm of APA analysis.
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Affiliation(s)
- Venkata Soumith Jonnakuti
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric J Wagner
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Mirjana Maletić-Savatić
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
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2
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Buchwalter A. Intermediate, but not average: The unusual lives of the nuclear lamin proteins. Curr Opin Cell Biol 2023; 84:102220. [PMID: 37619289 DOI: 10.1016/j.ceb.2023.102220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
The nuclear lamins are polymeric intermediate filament proteins that scaffold the nucleus and organize the genome in nearly all eukaryotic cells. This review focuses on the dynamic regulation of lamin filaments through their biogenesis, assembly, disassembly, and degradation. The lamins are unusually long-lived proteins under homeostatic conditions, but their turnover can be induced in select contexts that are highlighted in this review. Finally, we discuss recent investigations into the influence of laminopathy-linked mutations on the assembly, folding, and stability of the nuclear lamins.
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Affiliation(s)
- Abigail Buchwalter
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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3
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Zhao L, Wu D, Qu Q, Li Z, Yin H. Karyopherin Subunit Alpha 1 Enhances the Malignant Behaviors of Colon Cancer Cells via Promoting Nuclear Factor-κB p65 Nuclear Translocation. Dig Dis Sci 2023:10.1007/s10620-023-07936-y. [PMID: 37038032 DOI: 10.1007/s10620-023-07936-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 03/20/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND/AIMS Aberrant nuclear factor-κB p65 (NF-κB p65) nuclear import commonly occurs in multiple cancers, including colon cancer. According to BioGRID, we noted that Karyopherin subunit alpha 1 (KPNA1), an important molecular transporter between the nucleus and the cytoplasm, may interact with NF-κB p65. KPNA1 itself is highly expressed in colon adenocarcinoma samples (N = 286) based on The Cancer Genome Atlas (TCGA) database. We aimed to explore the role of KPNA1 in colonic carcinogenesis and to determine whether NF-κB p65 nuclear translocation was involved. METHODS KPNA1 expressions at mRNA and protein levels were analyzed in colon cancer tissues. The regulatory effect of KPNA1 on malignant biological properties was detected in SW480 and HCT116 colon cancer cells. Coimmunoprecipitation and immunofluorescence were performed to verify the relationship between KPNA1 and NF-κB p65. KPNA1 ubiquitination was also preliminarily investigated. RESULTS KPNA1 was firstly confirmed as a significantly upregulated gene in our collected clinical colon cancer samples (N = 35). KPNA1 depletion inhibited cell proliferation, induced cell cycle arrest, and diminished migratory and invasive capacity of SW480 and HCT116 cells. Colon cancer cells overexpressing KPNA1 acquired more aggressive behaviors. KPNA1 acted as a transporter to induce the nuclear accumulation of NF-κB p65, thereby activating NF-κB signaling pathway in colon cancer cells. Furthermore, HECT, C2, and WW Domain-Containing E3 Ubiquitin (HECW2) interacted with KPNA1 to induce its ubiquitination. KPNA1 labeled with polyubiquitins was degraded through ubiquitin-proteasome system. CONCLUSION The present study uncovers a role of KPNA1-NF-κB p65 axis in promoting colonic carcinogenesis.
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Affiliation(s)
- Lianrong Zhao
- Department of Infectious Diseases, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Di Wu
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Qiao Qu
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Zhilong Li
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Hongzhuan Yin
- Department of General Surgery, Shengjing Hospital of China Medical University, No. 36, Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China.
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4
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Jonnakuti VS, Wagner EJ, Maletić-Savatić M, Liu Z, Yalamanchili HK. PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.523471. [PMID: 36747700 PMCID: PMC9900750 DOI: 10.1101/2023.01.23.523471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
More than half of human genes exercise alternative polyadenylation (APA) and generate mRNA transcripts with varying 3' untranslated regions (UTR). However, current computational approaches for identifying cleavage and polyadenylation sites (C/PASs) and quantifying 3'UTR length changes from bulk RNA-seq data fail to unravel tissue- and disease-specific APA dynamics. Here, we developed a next-generation bioinformatics algorithm and application, PolyAMiner-Bulk, that utilizes an attention-based machine learning architecture and an improved vector projection-based engine to infer differential APA dynamics accurately. When applied to earlier studies, PolyAMiner-Bulk accurately identified more than twice the number of APA changes in an RBM17 knockdown bulk RNA-seq dataset compared to current generation tools. Moreover, on a separate dataset, PolyAMiner-Bulk revealed novel APA dynamics and pathways in scleroderma pathology and identified differential APA in a gene that was identified as being involved in scleroderma pathogenesis in an independent study. Lastly, we used PolyAMiner-Bulk to analyze the RNA-seq data of post-mortem prefrontal cortexes from the ROSMAP data consortium and unraveled novel APA dynamics in Alzheimer's Disease. Our method, PolyAMiner-Bulk, creates a paradigm for future alternative polyadenylation analysis from bulk RNA-seq data.
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Affiliation(s)
- Venkata Soumith Jonnakuti
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Mirjana Maletić-Savatić
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
| | - Zhandong Liu
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
- Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hari Krishna Yalamanchili
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, 77030, USA
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5
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Rodríguez-García ME, Cotrina-Vinagre FJ, Bellusci M, Hernández-Sánchez L, de Aragón AM, López-Laso E, Martín-Hernández E, Martínez-Azorín F. First splicing variant in HECW2 with an autosomal recessive pattern of inheritance and associated with NDHSAL. Hum Mutat 2022; 43:1361-1367. [PMID: 35753050 DOI: 10.1002/humu.24426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 11/07/2022]
Abstract
We report the clinical and genetic features of a Caucasian girl who presented a severe neurodevelopmental disorder with drug-resistant epilepsy, hypotonia, severe gastro-esophageal reflux and brain MRI anomalies. WES uncovered a novel variant in homozygosis (g.197092814_197092824delinsC) in HECW2 gene that encodes the E3 ubiquitin-protein ligase HECW2. This protein induces ubiquitination and is implicated in the regulation of several important pathways involved in neurodevelopment and neurogenesis. Furthermore, de novo heterozygous missense variants in this gene have been associated with NDHSAL. The homozygous variant of our patient disrupts the splice donor site of intron 22 and causes the elimination of exon 22 (r.3766_3917+1del) leading to an in-frame deletion of the protein (p.Leu1256_Trp1306del). Functional studies showed a two-fold increase of its RNA expression, while the protein expression level was reduced by 60%, suggesting a partial LOF mechanism of pathogenesis. Thus, this is the first patient with NDHSAL caused by an autosomal recessive splicing variant in HECW2. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- María Elena Rodríguez-García
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN) Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), E-28041, Madrid, Spain
| | - Francisco Javier Cotrina-Vinagre
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN) Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041, Madrid, Spain
| | - Marcello Bellusci
- Unidad Pediátrica de Enfermedades Raras, Enfermedades Mitocondriales y Metabólicas Hereditarias, Hospital 12 de Octubre, E-28041, Madrid, Spain
| | - Laura Hernández-Sánchez
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN) Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041, Madrid, Spain
| | | | - Eduardo López-Laso
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), E-28041, Madrid, Spain.,Unidad de Neurología Pediátrica, Hospital Universitario Reina Sofia IMIBIC, E-14004, Córdoba, Spain
| | - Elena Martín-Hernández
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN) Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), E-28041, Madrid, Spain.,Unidad Pediátrica de Enfermedades Raras, Enfermedades Mitocondriales y Metabólicas Hereditarias, Hospital 12 de Octubre, E-28041, Madrid, Spain
| | - Francisco Martínez-Azorín
- Grupo de Enfermedades Raras, Mitocondriales y Neuromusculares (ERMN) Instituto de Investigación Hospital 12 de Octubre (i+12), E-28041, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), E-28041, Madrid, Spain
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6
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Zheng M, Jin G, Zhou Z. Post-Translational Modification of Lamins: Mechanisms and Functions. Front Cell Dev Biol 2022; 10:864191. [PMID: 35656549 PMCID: PMC9152177 DOI: 10.3389/fcell.2022.864191] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/17/2022] [Indexed: 12/22/2022] Open
Abstract
Lamins are the ancient type V intermediate filament proteins contributing to diverse biological functions, such as the maintenance of nuclear morphology, stabilization of chromatin architecture, regulation of cell cycle progression, regulation of spatial-temporal gene expressions, and transduction of mechano-signaling. Deregulation of lamins is associated with abnormal nuclear morphology and chromatin disorganization, leading to a variety of diseases such as laminopathy and premature aging, and might also play a role in cancer. Accumulating evidence indicates that lamins are functionally regulated by post-translational modifications (PTMs) including farnesylation, phosphorylation, acetylation, SUMOylation, methylation, ubiquitination, and O-GlcNAcylation that affect protein stabilization and the association with chromatin or associated proteins. The mechanisms by which these PTMs are modified and the relevant functionality become increasingly appreciated as understanding of these changes provides new insights into the molecular mechanisms underlying the laminopathies concerned and novel strategies for the management. In this review, we discussed a range of lamin PTMs and their roles in both physiological and pathological processes, as well as potential therapeutic strategies by targeting lamin PTMs.
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Affiliation(s)
- Mingyue Zheng
- Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Guoxiang Jin
- Medical Research Center, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhongjun Zhou
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong SAR, China
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7
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Transcription of the Envelope Protein by 1-L Protein–RNA Recognition Code Leads to Genes/Proteins That Are Relevant to the SARS-CoV-2 Life Cycle and Pathogenesis. Curr Issues Mol Biol 2022; 44:791-816. [PMID: 35723340 PMCID: PMC8928949 DOI: 10.3390/cimb44020055] [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: 12/07/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
The theoretical protein–RNA recognition code was used in this study to research the compatibility of the SARS-CoV-2 envelope protein (E) with mRNAs in the human transcriptome. According to a review of the literature, the spectrum of identified genes showed that the virus post-transcriptionally promotes or represses the genes involved in the SARS-CoV-2 life cycle. The identified genes/proteins are also involved in adaptive immunity, in the function of the cilia and wound healing (EMT and MET) in the pulmonary epithelial tissue, in Alzheimer’s and Parkinson’s disease and in type 2 diabetes. For example, the E-protein promotes BHLHE40, which switches off the IL-10 inflammatory “brake” and inhibits antiviral THαβ cells. In the viral cycle, E supports the COPII-SCAP-SREBP-HSP90α transport complex by the lowering of cholesterol in the ER and by the repression of insulin signaling, which explains the positive effect of HSP90 inhibitors in COVID-19 (geldanamycin), and E also supports importin α/β-mediated transport to the nucleus, which explains the positive effect of ivermectin, a blocker of importins α/β. In summary, transcription of the envelope protein by the 1-L protein–RNA recognition code leads to genes/proteins that are relevant to the SARS-CoV-2 life cycle and pathogenesis.
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8
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Acharya A, Kavus H, Dunn P, Nasir A, Folk L, Withrow K, Wentzensen IM, Ruzhnikov MRZ, Fallot C, Smol T, Rama M, Brown K, Whalen S, Ziegler A, Barth M, Chassevent A, Smith-Hicks C, Afenjar A, Courtin T, Heide S, Font-Montgomery E, Heid C, Hamm JA, Love DR, Thabet F, Misra VK, Cunningham M, Leal SM, Jarvela I, Normand EA, Zou F, Helal M, Keren B, Torti E, Chung WK, Schrauwen I. Delineating the genotypic and phenotypic spectrum of HECW2-related neurodevelopmental disorders. J Med Genet 2021; 59:669-677. [PMID: 34321324 DOI: 10.1136/jmedgenet-2021-107871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/06/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Variants in HECW2 have recently been reported to cause a neurodevelopmental disorder with hypotonia, seizures and impaired language; however, only six variants have been reported and the clinical characteristics have only broadly been defined. METHODS Molecular and clinical data were collected from clinical and research cohorts. Massive parallel sequencing was performed and identified individuals with a HECW2-related neurodevelopmental disorder. RESULTS We identified 13 novel missense variants in HECW2 in 22 unpublished cases, of which 18 were confirmed to have a de novo variant. In addition, we reviewed the genotypes and phenotypes of previously reported and new cases with HECW2 variants (n=35 cases). All variants identified are missense, and the majority of likely pathogenic and pathogenic variants are located in or near the C-terminal HECT domain (88.2%). We identified several clustered variants and four recurrent variants (p.(Arg1191Gln);p.(Asn1199Lys);p.(Phe1327Ser);p.(Arg1330Trp)). Two variants, (p.(Arg1191Gln);p.(Arg1330Trp)), accounted for 22.9% and 20% of cases, respectively. Clinical characterisation suggests complete penetrance for hypotonia with or without spasticity (100%), developmental delay/intellectual disability (100%) and developmental language disorder (100%). Other common features are behavioural problems (88.9%), vision problems (83.9%), motor coordination/movement (75%) and gastrointestinal issues (70%). Seizures were present in 61.3% of individuals. Genotype-phenotype analysis shows that HECT domain variants are more frequently associated with cortical visual impairment and gastrointestinal issues. Seizures were only observed in individuals with variants in or near the HECT domain. CONCLUSION We provide a comprehensive review and expansion of the genotypic and phenotypic spectrum of HECW2 disorders, aiding future molecular and clinical diagnosis and management.
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Affiliation(s)
- Anushree Acharya
- Center for Statistical Genetics, Gertrude H. Sergievsky Center and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Haluk Kavus
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Patrick Dunn
- The George Washington University, Washington, District of Columbia, USA
| | - Abdul Nasir
- Department of Molecular Science and Technology, Ajou University, Suwon, The Republic of Korea
| | | | | | | | - Maura R Z Ruzhnikov
- Neurology and Neurological Sciences, Pediatrics, Division of Medical Genetics, Stanford University and Lucile Packard Children's Hospital, Palo Alto, California, USA
| | | | - Thomas Smol
- Institut de Génétique, Univ Lille, EA7364 RADEME, CHU Lille, Lille, France
| | | | - Kathleen Brown
- Pediatrics-Clinical Genetics and Metabolism, School of Medicine, University of Colorado-Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sandra Whalen
- UF de génétique Clinique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Assistance Publique-Hôpitaux de Paris (APHP) Sorbonne Université, Hôpital Armand Trousseau, ERN-ITHACA, Paris, France
| | - Alban Ziegler
- Department of Genetics, Angers University Hospital, Angers, France
| | - Magali Barth
- Department of Genetics, Angers University Hospital, Angers, France
| | - Anna Chassevent
- Division of Neurogenetics, Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Constance Smith-Hicks
- Division of Neurogenetics, Kennedy Krieger Institute, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Alexandra Afenjar
- Assistance Publique-Hôpitaux de Paris (APHP) Sorbonne Université, Centre de Référence Malformations et maladies congénitales du cervelet et déficiences intellectuelles de causes rares, département de génétique et embryologie médicale, Hôpital Trousseau, Paris, France
| | - Thomas Courtin
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Solveig Heide
- Department of Genetics, Pitié-Salpêtrière Hospital, Referral Center for Intellectual Disabilities of Rare Causes, Assistance Publique-Hôpitaux de Paris (APHP) Sorbonne Université, Paris, France
| | | | - Caleb Heid
- University Hospital Medical Genetics Clinic, University of Missouri, Columbia, Missouri, USA
| | - J Austin Hamm
- Pediatric Genetics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | | | - Farouq Thabet
- Pediatric Neurology Division, Sidra Medicine, Doha, Qatar
| | - Vinod K Misra
- Department of Pediatrics, Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan, Detroit, Michigan, USA.,Discipline of Pediatrics, Central Michigan University, Mount Pleasant, Michigan, USA
| | - Mitch Cunningham
- Department of Pediatrics, Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Gertrude H. Sergievsky Center and the Department of Neurology, Columbia University Medical Center, New York, New York, USA.,Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, New York, USA
| | - Irma Jarvela
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | | | | | - Mayada Helal
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Boris Keren
- Département de génétique, Hôpital Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | | | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, New York, USA .,Department of Medicine, Columbia University, New York, New York, USA
| | - Isabelle Schrauwen
- Center for Statistical Genetics, Gertrude H. Sergievsky Center and the Department of Neurology, Columbia University Medical Center, New York, New York, USA
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9
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Murray-Nerger LA, Cristea IM. Lamin post-translational modifications: emerging toggles of nuclear organization and function. Trends Biochem Sci 2021; 46:832-847. [PMID: 34148760 DOI: 10.1016/j.tibs.2021.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/03/2021] [Accepted: 05/18/2021] [Indexed: 01/03/2023]
Abstract
Nuclear lamins are ancient type V intermediate filaments with diverse functions that include maintaining nuclear shape, mechanosignaling, tethering and stabilizing chromatin, regulating gene expression, and contributing to cell cycle progression. Despite these numerous roles, an outstanding question has been how lamins are regulated. Accumulating work indicates that a range of lamin post-translational modifications (PTMs) control their functions both in homeostatic cells and in disease states such as progeria, muscular dystrophy, and viral infection. Here, we review the current knowledge of the diverse types of PTMs that regulate lamins in a site-specific manner. We highlight methods that can be used to characterize lamin PTMs whose functions are currently unknown and provide a perspective on the future of the lamin PTM field.
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Affiliation(s)
- Laura A Murray-Nerger
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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10
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Yanagishita T, Hirade T, Shimojima Yamamoto K, Funatsuka M, Miyamoto Y, Maeda M, Yanagi K, Kaname T, Nagata S, Nagata M, Ishihara Y, Miyashita Y, Asano Y, Sakata Y, Kosaki K, Yamamoto T. HECW2-related disorder in four Japanese patients. Am J Med Genet A 2021; 185:2895-2902. [PMID: 34047014 DOI: 10.1002/ajmg.a.62363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/14/2021] [Accepted: 05/09/2021] [Indexed: 11/11/2022]
Abstract
The HECT, C2, and WW domain containing E3 ubiquitin protein ligase 2 gene (HECW2) is involved in protein ubiquitination. Several genes associated with protein ubiquitination have been linked to neurodevelopmental disorders. HECW2-related disorder has been established through the identification of de novo variants in HECW2 in patients with neurodevelopmental disorders with hypotonia, seizures, and absent language. Recently, we identified novel HECW2 variants in four Japanese patients with neurodevelopmental disorders. Regarding motor development, two of the patients cannot walk, whereas the other two can walk with an unsteady gait, owing to hypotonia. All HECW2 variants, including those that were previously reported, are missense, and no loss-of-function variants have been identified. Most of the identified variants are located around the HECT domain. These findings suggest that the dominant negative effects of missense variants around the HECT domain may be the mechanism underlying HECW2-related disorder.
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Affiliation(s)
- Tomoe Yanagishita
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan.,Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Takuya Hirade
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Keiko Shimojima Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan.,Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Tokyo, Japan
| | - Makoto Funatsuka
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Yusaku Miyamoto
- Department of Pediatrics, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Makiko Maeda
- Department of Pediatrics, Saga Medical and Welfare Center for the Challenged, Saga, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Satoru Nagata
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Miho Nagata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasuki Ishihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yohei Miyashita
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Legal Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
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11
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Qiu S, Jiang G, Cao L, Huang J. Replication Fork Reversal and Protection. Front Cell Dev Biol 2021; 9:670392. [PMID: 34041245 PMCID: PMC8141627 DOI: 10.3389/fcell.2021.670392] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
During genome replication, replication forks often encounter obstacles that impede their progression. Arrested forks are unstable structures that can give rise to collapse and rearrange if they are not properly processed and restarted. Replication fork reversal is a critical protective mechanism in higher eukaryotic cells in response to replication stress, in which forks reverse their direction to form a Holliday junction-like structure. The reversed replication forks are protected from nuclease degradation by DNA damage repair proteins, such as BRCA1, BRCA2, and RAD51. Some of these molecules work cooperatively, while others have unique functions. Once the stress is resolved, the replication forks can restart with the help of enzymes, including human RECQ1 helicase, but restart will not be considered here. Here, we review research on the key factors and mechanisms required for the remodeling and protection of stalled replication forks in mammalian cells.
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Affiliation(s)
- Shan Qiu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Guixing Jiang
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Huang
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
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12
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Sferra A, Fortugno P, Motta M, Aiello C, Petrini S, Ciolfi A, Cipressa F, Moroni I, Leuzzi V, Pieroni L, Marini F, Boespflug Tanguy O, Eymard-Pierre E, Danti FR, Compagnucci C, Zambruno G, Brusco A, Santorelli FM, Chiapparini L, Francalanci P, Loizzo AL, Tartaglia M, Cestra G, Bertini E. Biallelic mutations in RNF220 cause laminopathies featuring leukodystrophy, ataxia and deafness. Brain 2021; 144:3020-3035. [PMID: 33964137 DOI: 10.1093/brain/awab185] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/14/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Leukodystrophies are a heterogeneous group of rare inherited disorders that involve preferentially the white matter of the central nervous system (CNS). These conditions are characterized by a primary glial cell and myelin sheath pathology of variable etiology, which causes secondary axonal degeneration, generally emerging with disease progression. Whole exome sequencing performed in 5 large consanguineous nuclear families allowed to identify homozygosity for two recurrent missense variants affecting highly conserved residues of RNF220 as the causative event underlying a novel form of leukodystrophy with ataxia and sensorineural deafness. We report on two homozygous missense variants (p.R363Q and p.R365Q) in the ubiquitin E3 ligase RNF220 as the cause underlying a novel form of leukodystrophy with ataxia and sensorineural deafness having fibrotic cardiomyopathy and hepatopathy as associated features, in seven consanguineous families. Mass spectrometry analysis identified lamin B1 as RNF220 binding protein and co-immunoprecipitation experiments demonstrated reduced binding of both RNF220 mutants to lamin B1. We demonstrate that RNF220 silencing in Drosophila melanogaster specifically affects proper localization of lamin Dm0, the fly lamin B1 orthologue, promotes its aggregation, and causes a neurodegenerative phenotype, strongly supporting the functional link between RNF220 and lamin B1. Finally, we demonstrate that RNF220 plays a crucial role in the maintenance of nuclear morphology: mutations primary skin fibroblasts determine nuclear abnormalities such as blebs, herniations and invaginations, which are typically observed in cells of patients affected by laminopathies. Overall, our data identify RNF220 as a gene implicated in leukodystrophy with ataxia and sensorineural deafness, and document a critical role of RNF220 in the regulation of nuclear lamina. Our findings provide further evidence on the direct link between nuclear lamina dysfunction and neurodegeneration.
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Affiliation(s)
- Antonella Sferra
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Paola Fortugno
- Department of Life, Health and Environmental Sciences University of L'Aquila, 00167 Rome, Italy.,Human Functional Genomics, IRCCS San Raffaele Pisana, 00166 Rome, Italy
| | - Marialetizia Motta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Chiara Aiello
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Laboratories, Ospedale Pediatrico Bambino Gesù, 00146 Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Francesca Cipressa
- University of Rome "Sapienza", Department of Biology and Biotechnology, 00185 Rome, Italy
| | - Isabella Moroni
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Vincenzo Leuzzi
- Department of Human Neuroscience, Unit of Child Neurology and Psychiatry, Sapienza University, 00185 Rome, Italy
| | | | - Federica Marini
- Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.,Department of Laboratory Diagnostic and Infectious Diseases, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Odile Boespflug Tanguy
- Service de Neurologie Pédiatrique, Centre de reference leucodystrophies et leucoencephalopathies de cause rare (LEUKOFRANCE), APHP Hopital Robert-Debré, 75019 Paris, France.,Université de Paris, NeuroDiderot, UMR 1141 INSERM 75651 Paris, France
| | - Eleonore Eymard-Pierre
- Service de Cytogénétique Médicale CHU de Clermont Ferrand, Hopital ESTAING 63003 CLERMONT FERRAND, France
| | - Federica Rachele Danti
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Claudia Compagnucci
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Giovanna Zambruno
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10124 Turin, Italy
| | | | - Luisa Chiapparini
- Neuroradiology Department, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Paola Francalanci
- Department of Laboratories, Pathology Unit, IRCCS Bambino Gesù Children's Hospital, 00165 Rome, Italy
| | - Anna Livia Loizzo
- DIDASCO Società Cooperativa Sociale- Centro di riabilitazione, 00185 Rome, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Gianluca Cestra
- University of Rome "Sapienza", Department of Biology and Biotechnology, 00185 Rome, Italy.,Santa Lucia IRCCS Foundation, 00179 Rome, Italy.,Institute of Biochemistry and Clinical Biochemistry, Università Cattolica del Sacro Cuore, 00168 Rome, Italy.,Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR) 00185 Rome, Italy
| | - Enrico Bertini
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
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13
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Lescouzères L, Bomont P. E3 Ubiquitin Ligases in Neurological Diseases: Focus on Gigaxonin and Autophagy. Front Physiol 2020; 11:1022. [PMID: 33192535 PMCID: PMC7642974 DOI: 10.3389/fphys.2020.01022] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a dynamic post-translational modification that regulates the fate of proteins and therefore modulates a myriad of cellular functions. At the last step of this sophisticated enzymatic cascade, E3 ubiquitin ligases selectively direct ubiquitin attachment to specific substrates. Altogether, the ∼800 distinct E3 ligases, combined to the exquisite variety of ubiquitin chains and types that can be formed at multiple sites on thousands of different substrates confer to ubiquitination versatility and infinite possibilities to control biological functions. E3 ubiquitin ligases have been shown to regulate behaviors of proteins, from their activation, trafficking, subcellular distribution, interaction with other proteins, to their final degradation. Largely known for tagging proteins for their degradation by the proteasome, E3 ligases also direct ubiquitinated proteins and more largely cellular content (organelles, ribosomes, etc.) to destruction by autophagy. This multi-step machinery involves the creation of double membrane autophagosomes in which engulfed material is degraded after fusion with lysosomes. Cooperating in sustaining homeostasis, actors of ubiquitination, proteasome and autophagy pathways are impaired or mutated in wide range of human diseases. From initial discovery of pathogenic mutations in the E3 ligase encoding for E6-AP in Angelman syndrome and Parkin in juvenile forms of Parkinson disease, the number of E3 ligases identified as causal gene for neurological diseases has considerably increased within the last years. In this review, we provide an overview of these diseases, by classifying the E3 ubiquitin ligase types and categorizing the neurological signs. We focus on the Gigaxonin-E3 ligase, mutated in giant axonal neuropathy and present a comprehensive analysis of the spectrum of mutations and the recent biological models that permitted to uncover novel mechanisms of action. Then, we discuss the common functions shared by Gigaxonin and the other E3 ligases in cytoskeleton architecture, cell signaling and autophagy. In particular, we emphasize their pivotal roles in controlling multiple steps of the autophagy pathway. In light of the various targets and extending functions sustained by a single E3 ligase, we finally discuss the challenge in understanding the complex pathological cascade underlying disease and in designing therapeutic approaches that can apprehend this complexity.
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Affiliation(s)
- Léa Lescouzères
- ATIP-Avenir Team, INM, INSERM, University of Montpellier, Montpellier, France
| | - Pascale Bomont
- ATIP-Avenir Team, INM, INSERM, University of Montpellier, Montpellier, France
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14
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15
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Blank M. Targeted Regulation of Nuclear Lamins by Ubiquitin and Ubiquitin-Like Modifiers. Cells 2020; 9:cells9061340. [PMID: 32471220 PMCID: PMC7348791 DOI: 10.3390/cells9061340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023] Open
Abstract
Nuclear lamins (NLs) are essential components of the animal cell nucleus involved in the regulation of a plethora of molecular and cellular processes. These include the nuclear envelope assembly and stability, mechanotransduction and chromatin organization, transcription, DNA replication, damage repair, and genomic integrity maintenance. Mutations in NLs can lead to the development of a wide range of distinct disease phenotypes, laminopathies, consisting of cardiac, neuromuscular, metabolic and premature aging syndromes. In addition, alterations in the expression of nuclear lamins were associated with different types of neoplastic diseases. Despite the importance and critical roles that NLs play in the diverse cellular activities, we only recently started to uncover the complexity of regulatory mechanisms governing their expression, localization and functions. This integrative review summarizes and discusses the recent findings on the emerging roles of ubiquitin and ubiquitin-like modifiers (ULMs) in the regulation of NLs, highlighting the intriguing molecular associations and cross-talks occurring between NLs and these regulatory molecules under physiological conditions and in the disease states.
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Affiliation(s)
- Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
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16
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Wang Y, Argiles-Castillo D, Kane EI, Zhou A, Spratt DE. HECT E3 ubiquitin ligases - emerging insights into their biological roles and disease relevance. J Cell Sci 2020; 133:133/7/jcs228072. [PMID: 32265230 DOI: 10.1242/jcs.228072] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Homologous to E6AP C-terminus (HECT) E3 ubiquitin ligases play a critical role in various cellular pathways, including but not limited to protein trafficking, subcellular localization, innate immune response, viral infections, DNA damage responses and apoptosis. To date, 28 HECT E3 ubiquitin ligases have been identified in humans, and recent studies have begun to reveal how these enzymes control various cellular pathways by catalyzing the post-translational attachment of ubiquitin to their respective substrates. New studies have identified substrates and/or interactors with different members of the HECT E3 ubiquitin ligase family, particularly for E6AP and members of the neuronal precursor cell-expressed developmentally downregulated 4 (NEDD4) family. However, there still remains many unanswered questions about the specific roles that each of the HECT E3 ubiquitin ligases have in maintaining cellular homeostasis. The present Review discusses our current understanding on the biological roles of the HECT E3 ubiquitin ligases in the cell and how they contribute to disease development. Expanded investigations on the molecular basis for how and why the HECT E3 ubiquitin ligases recognize and regulate their intracellular substrates will help to clarify the biochemical mechanisms employed by these important enzymes in ubiquitin biology.
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Affiliation(s)
- Yaya Wang
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, Shanxi, China 710054.,Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA
| | - Diana Argiles-Castillo
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA
| | - Emma I Kane
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA
| | - Anning Zhou
- College of Chemistry and Chemical Engineering, Xi'an University of Science and Technology, Xi'an, Shanxi, China 710054
| | - Donald E Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main St., Worcester, MA 01610, USA
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17
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Dubois ML, Meller A, Samandi S, Brunelle M, Frion J, Brunet MA, Toupin A, Beaudoin MC, Jacques JF, Lévesque D, Scott MS, Lavigne P, Roucou X, Boisvert FM. UBB pseudogene 4 encodes functional ubiquitin variants. Nat Commun 2020; 11:1306. [PMID: 32161257 PMCID: PMC7066184 DOI: 10.1038/s41467-020-15090-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/18/2020] [Indexed: 02/06/2023] Open
Abstract
Pseudogenes are mutated copies of protein-coding genes that cannot be translated into proteins, but a small subset of pseudogenes has been detected at the protein level. Although ubiquitin pseudogenes represent one of the most abundant pseudogene families in many organisms, little is known about their expression and signaling potential. By re-analyzing public RNA-sequencing and proteomics datasets, we here provide evidence for the expression of several ubiquitin pseudogenes including UBB pseudogene 4 (UBBP4), which encodes UbKEKS (Q2K, K33E, Q49K, N60S). The functional consequences of UbKEKS conjugation appear to differ from canonical ubiquitylation. Quantitative proteomics shows that UbKEKS modifies specific proteins including lamins. Knockout of UBBP4 results in slower cell division, and accumulation of lamin A within the nucleolus. Our work suggests that a subset of proteins reported as ubiquitin targets may instead be modified by ubiquitin variants that are the products of wrongly annotated pseudogenes and induce different functional effects. Ubiquitin pseudogenes are present in many organisms but whether they encode functional proteins has remained unclear. Here, the authors show that human UBB pseudogene 4 produces ubiquitin variants with amino acid compositions and cellular functions that are distinct from canonical ubiquitin.
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Affiliation(s)
| | - Anna Meller
- Department of Immunology and Cell Biology, Sherbrooke, QC, Canada
| | - Sondos Samandi
- Department of Biochemistry and Functional Genomics, Sherbrooke, QC, Canada
| | - Mylène Brunelle
- Department of Biochemistry and Functional Genomics, Sherbrooke, QC, Canada
| | - Julie Frion
- Department of Immunology and Cell Biology, Sherbrooke, QC, Canada
| | - Marie A Brunet
- Department of Biochemistry and Functional Genomics, Sherbrooke, QC, Canada
| | - Amanda Toupin
- Department of Biochemistry and Functional Genomics, Sherbrooke, QC, Canada
| | - Maxime C Beaudoin
- Department of Biochemistry and Functional Genomics, Sherbrooke, QC, Canada
| | | | | | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Sherbrooke, QC, Canada
| | - Pierre Lavigne
- Department of Biochemistry and Functional Genomics, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Sherbrooke, QC, Canada.
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18
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Genomic instability and innate immune responses to self-DNA in progeria. GeroScience 2019; 41:255-266. [PMID: 31280482 DOI: 10.1007/s11357-019-00082-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/21/2019] [Indexed: 12/15/2022] Open
Abstract
In the last decade, we have seen increasing evidence of the importance of structural nuclear proteins such as lamins in nuclear architecture and compartmentalization of genome function and in the maintenance of mechanical stability and genome integrity. With over 400 mutations identified in the LMNA gene (encoding for A-type lamins) associated with more than ten distinct degenerative disorders, the role of lamins as genome caretakers and the contribution of lamins dysfunction to disease are unarguable. However, the molecular mechanisms whereby lamins mutations cause pathologies remain less understood. Here, we review pathways and mechanisms recently identified as playing a role in the pathophysiology of laminopathies, with special emphasis in Hutchinson Gilford Progeria Syndrome (HGPS). This devastating incurable accelerated aging disease is caused by a silent mutation in the LMNA gene that generates a truncated lamin A protein "progerin" that exerts profound cellular toxicity and organismal decline. Patients usually die in their teens due to cardiovascular complications such as myocardial infarction or stroke. To date, there are no efficient therapies that ameliorate disease progression, stressing the need to understand molecularly disease mechanisms that can be targeted therapeutically. We will summarize data supporting that replication stress is a major cause of genomic instability in laminopathies, which contributes to the activation of innate immune responses to self-DNA that in turn accelerate the aging process.
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19
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Patrolling the nucleus: inner nuclear membrane-associated degradation. Curr Genet 2019; 65:1099-1106. [PMID: 31020383 PMCID: PMC6744382 DOI: 10.1007/s00294-019-00971-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 12/13/2022]
Abstract
Protein quality control and transport are important for the integrity of organelles such as the endoplasmic reticulum, but it is largely unknown how protein homeostasis is regulated at the nuclear envelope (NE) despite the connection between NE protein function and human disease. Elucidating mechanisms that regulate the NE proteome is key to understanding nuclear processes such as gene expression, DNA replication and repair as NE components, particularly proteins at the inner nuclear membrane (INM), are involved in the maintenance of nuclear structure, nuclear positioning and chromosome organization. Nuclear pore complexes control the entry and exit of proteins in and out of the nucleus, restricting movement across the nuclear membrane based on protein size, or the size of the extraluminal-facing domain of a transmembrane protein, providing one level of INM proteome regulation. Research in budding yeast has identified a protein quality control system that targets mislocalized and misfolded proteins at the INM. Here, we review what is known about INM-associated degradation, including recent evidence suggesting that it not only targets mislocalized or misfolded proteins, but also contributes to homeostasis of resident INM proteins.
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20
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Blank spots on the map: some current questions on nuclear organization and genome architecture. Histochem Cell Biol 2018; 150:579-592. [PMID: 30238154 DOI: 10.1007/s00418-018-1726-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear architecture and function, including the existence of chromatin domains of various sizes, the presence of a large number of non-membranous intranuclear bodies, non-random positioning of genes and chromosomes in 3D space, and a prominent role of the nuclear lamina in organizing genomes. Despite this tremendous progress in elucidating the biological properties of the cell nucleus, many questions remain. Here, we highlight some of the key open areas of investigation in the field of nuclear organization and genome architecture with a particular focus on the mechanisms and principles of higher-order genome organization, the emerging role of liquid phase separation in cellular organization, and the functional role of the nuclear lamina in physiological processes.
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21
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E3 ubiquitin ligase HECW2 mediates the proteasomal degradation of HP1 isoforms. Biochem Biophys Res Commun 2018; 503:2478-2484. [DOI: 10.1016/j.bbrc.2018.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/02/2018] [Indexed: 12/12/2022]
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