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van den Heuvel D, Kim M, Wondergem AP, van der Meer PJ, Witkamp M, Lambregtse F, Kim HS, Kan F, Apelt K, Kragten A, González-Prieto R, Vertegaal ACO, Yeo JE, Kim BG, van Doorn R, Schärer OD, Luijsterburg MS. A disease-associated XPA allele interferes with TFIIH binding and primarily affects transcription-coupled nucleotide excision repair. Proc Natl Acad Sci U S A 2023; 120:e2208860120. [PMID: 36893274 PMCID: PMC10089173 DOI: 10.1073/pnas.2208860120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023] Open
Abstract
XPA is a central scaffold protein that coordinates the assembly of repair complexes in the global genome (GG-NER) and transcription-coupled nucleotide excision repair (TC-NER) subpathways. Inactivating mutations in XPA cause xeroderma pigmentosum (XP), which is characterized by extreme UV sensitivity and a highly elevated skin cancer risk. Here, we describe two Dutch siblings in their late forties carrying a homozygous H244R substitution in the C-terminus of XPA. They present with mild cutaneous manifestations of XP without skin cancer but suffer from marked neurological features, including cerebellar ataxia. We show that the mutant XPA protein has a severely weakened interaction with the transcription factor IIH (TFIIH) complex leading to an impaired association of the mutant XPA and the downstream endonuclease ERCC1-XPF with NER complexes. Despite these defects, the patient-derived fibroblasts and reconstituted knockout cells carrying the XPA-H244R substitution show intermediate UV sensitivity and considerable levels of residual GG-NER (~50%), in line with the intrinsic properties and activities of the purified protein. By contrast, XPA-H244R cells are exquisitely sensitive to transcription-blocking DNA damage, show no detectable recovery of transcription after UV irradiation, and display a severe deficiency in TC-NER-associated unscheduled DNA synthesis. Our characterization of a new case of XPA deficiency that interferes with TFIIH binding and primarily affects the transcription-coupled subpathway of nucleotide excision repair, provides an explanation of the dominant neurological features in these patients, and reveals a specific role for the C-terminus of XPA in TC-NER.
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Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Mihyun Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, 44919Ulsan, Republic of Korea
| | - Annelotte P. Wondergem
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Paula J. van der Meer
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Myrèse Witkamp
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Ferdy Lambregtse
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Folkert Kan
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
- Andalusian Center for Molecular Biology and Regenerative Medicine, University of Sevilla, 41092Seville, Spain
- Department of Cell Biology, University of Seville, 41012Seville, Spain
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Byung-Gyu Kim
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2333 ZALeiden, The Netherlands
| | - Orlando D. Schärer
- Center for Genomic Integrity, Institute for Basic Science, 44919Ulsan, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, 44919Ulsan, Republic of Korea
| | - Martijn S. Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, 2333 ZCLeiden, The Netherlands
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Schubert L, Hendriks IA, Hertz EPT, Wu W, Sellés‐Baiget S, Hoffmann S, Viswalingam KS, Gallina I, Pentakota S, Benedict B, Johansen J, Apelt K, Luijsterburg MS, Rasmussen S, Lisby M, Liu Y, Nielsen ML, Mailand N, Duxin JP. SCAI promotes error‐free repair of DNA interstrand crosslinks via the Fanconi anemia pathway. EMBO Rep 2022; 23:e53639. [PMID: 35156773 PMCID: PMC8982572 DOI: 10.15252/embr.202153639] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 01/05/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) are cytotoxic lesions that threaten genome integrity. The Fanconi anemia (FA) pathway orchestrates ICL repair during DNA replication, with ubiquitylated FANCI‐FANCD2 (ID2) marking the activation step that triggers incisions on DNA to unhook the ICL. Restoration of intact DNA requires the coordinated actions of polymerase ζ (Polζ)‐mediated translesion synthesis (TLS) and homologous recombination (HR). While the proteins mediating FA pathway activation have been well characterized, the effectors regulating repair pathway choice to promote error‐free ICL resolution remain poorly defined. Here, we uncover an indispensable role of SCAI in ensuring error‐free ICL repair upon activation of the FA pathway. We show that SCAI forms a complex with Polζ and localizes to ICLs during DNA replication. SCAI‐deficient cells are exquisitely sensitive to ICL‐inducing drugs and display major hallmarks of FA gene inactivation. In the absence of SCAI, HR‐mediated ICL repair is defective, and breaks are instead re‐ligated by polymerase θ‐dependent microhomology‐mediated end‐joining, generating deletions spanning the ICL site and radial chromosomes. Our work establishes SCAI as an integral FA pathway component, acting at the interface between TLS and HR to promote error‐free ICL repair.
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Affiliation(s)
- Lisa Schubert
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Ivo A Hendriks
- Proteomics Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Emil P T Hertz
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Wei Wu
- Center for Chromosome Stability Department of Cellular and Molecular Medicine University of Copenhagen Copenhagen Denmark
| | - Selene Sellés‐Baiget
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Saskia Hoffmann
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | | | - Irene Gallina
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Satyakrishna Pentakota
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Bente Benedict
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Joachim Johansen
- Disease Systems Biology Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Katja Apelt
- Department of Human Genetics Leiden University Medical Center Leiden The Netherlands
| | | | - Simon Rasmussen
- Disease Systems Biology Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Michael Lisby
- Center for Chromosome Stability Department of Cellular and Molecular Medicine University of Copenhagen Copenhagen Denmark
- Department of Biology University of Copenhagen Copenhagen Denmark
| | - Ying Liu
- Center for Chromosome Stability Department of Cellular and Molecular Medicine University of Copenhagen Copenhagen Denmark
| | - Michael L Nielsen
- Proteomics Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
| | - Niels Mailand
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
- Center for Chromosome Stability Department of Cellular and Molecular Medicine University of Copenhagen Copenhagen Denmark
| | - Julien P Duxin
- Protein Signaling Program Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark
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3
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Niederacher G, Urwin D, Dijkwel Y, Tremethick DJ, Rosengren KJ, Becker CFW, Conibear AC. Site-specific modification and segmental isotope labelling of HMGN1 reveals long-range conformational perturbations caused by posttranslational modifications. RSC Chem Biol 2021; 2:537-550. [PMID: 34458797 PMCID: PMC8341956 DOI: 10.1039/d0cb00175a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/16/2020] [Indexed: 01/03/2023] Open
Abstract
Interactions between histones, which package DNA in eukaryotes, and nuclear proteins such as the high mobility group nucleosome-binding protein HMGN1 are important for regulating access to DNA. HMGN1 is a highly charged and intrinsically disordered protein (IDP) that is modified at several sites by posttranslational modifications (PTMs) - acetylation, phosphorylation and ADP-ribosylation. These PTMs are thought to affect cellular localisation of HMGN1 and its ability to bind nucleosomes; however, little is known about how these PTMs regulate the structure and function of HMGN1 at a molecular level. Here, we combine the chemical biology tools of protein semi-synthesis and site-specific modification to generate a series of unique HMGN1 variants bearing precise PTMs at their N- or C-termini with segmental isotope labelling for NMR spectroscopy. With access to these precisely-defined variants, we show that PTMs in both the N- and C-termini cause changes in the chemical shifts and conformational populations in regions distant from the PTM sites; up to 50-60 residues upstream of the PTM site. The PTMs investigated had only minor effects on binding of HMGN1 to nucleosome core particles, suggesting that they have other regulatory roles. This study demonstrates the power of combining protein semi-synthesis for introduction of site-specific PTMs with segmental isotope labelling for structural biology, allowing us to understand the role of PTMs with atomic precision, from both structural and functional perspectives.
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Affiliation(s)
- Gerhard Niederacher
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna Währinger Straße 38 1090 Vienna Austria
| | - Debra Urwin
- John Curtin School of Medical Research, Department of Genome Sciences, The Australian National University ACT 2601 Australia
| | - Yasmin Dijkwel
- John Curtin School of Medical Research, Department of Genome Sciences, The Australian National University ACT 2601 Australia
| | - David J Tremethick
- John Curtin School of Medical Research, Department of Genome Sciences, The Australian National University ACT 2601 Australia
| | - K Johan Rosengren
- School of Biomedical Sciences, The University of Queensland Brisbane QLD 4072 Australia +61-7-3365-1738
| | - Christian F W Becker
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna Währinger Straße 38 1090 Vienna Austria
| | - Anne C Conibear
- School of Biomedical Sciences, The University of Queensland Brisbane QLD 4072 Australia +61-7-3365-1738
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4
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van den Heuvel D, van der Weegen Y, Boer DEC, Ogi T, Luijsterburg MS. Transcription-Coupled DNA Repair: From Mechanism to Human Disorder. Trends Cell Biol 2021; 31:359-371. [PMID: 33685798 DOI: 10.1016/j.tcb.2021.02.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
DNA lesions pose a major obstacle during gene transcription by RNA polymerase II (RNAPII) enzymes. The transcription-coupled DNA repair (TCR) pathway eliminates such DNA lesions. Inherited defects in TCR cause severe clinical syndromes, including Cockayne syndrome (CS). The molecular mechanism of TCR and the molecular origin of CS have long remained enigmatic. Here we explore new advances in our understanding of how TCR complexes assemble through cooperative interactions between repair factors stimulated by RNAPII ubiquitylation. Mounting evidence suggests that RNAPII ubiquitylation activates TCR complex assembly during repair and, in parallel, promotes processing and degradation of RNAPII to prevent prolonged stalling. The fate of stalled RNAPII is therefore emerging as a crucial link between TCR and associated human diseases.
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Affiliation(s)
- Diana van den Heuvel
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Yana van der Weegen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Daphne E C Boer
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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5
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Li D, Lin H, Li L. Multiple Feature Selection Strategies Identified Novel Cardiac Gene Expression Signature for Heart Failure. Front Physiol 2020; 11:604241. [PMID: 33304275 PMCID: PMC7693561 DOI: 10.3389/fphys.2020.604241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/15/2020] [Indexed: 02/02/2023] Open
Abstract
Heart failure (HF) is a serious condition in which the support of blood pumped by the heart is insufficient to meet the demands of body at a normal cardiac filling pressure. Approximately 26 million patients worldwide are suffering from heart failure and about 17–45% of patients with heart failure die within 1-year, and the majority die within 5-years admitted to a hospital. The molecular mechanisms underlying the progression of heart failure have been poorly studied. We compared the gene expression profiles between patients with heart failure (n = 177) and without heart failure (n = 136) using multiple feature selection strategies and identified 38 HF signature genes. The support vector machine (SVM) classifier based on these 38 genes evaluated with leave-one-out cross validation (LOOCV) achieved great performance with sensitivity of 0.983 and specificity of 0.963. The network analysis suggested that the hub gene SMOC2 may play important roles in HF. Other genes, such as FCN3, HMGN2, and SERPINA3, also showed great promises. Our results can facilitate the early detection of heart failure and can reveal its molecular mechanisms.
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Affiliation(s)
- Dan Li
- Department of Cardiovascular Medicine, First Hospital Affiliated to Harbin Medical University, Harbin, China
| | - Hong Lin
- Internal Medicine-Cardiovascular Department, Harbin Chest Hospital, Harbin, China
| | - Luyifei Li
- Department of Cardiovascular Medicine, First Hospital Affiliated to Harbin Medical University, Harbin, China
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