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Thote V, Dinesh S, Sharma S. Prediction of deleterious non-synonymous SNPs of human MDC1 gene: an in silico approach. Syst Biol Reprod Med 2024; 70:101-112. [PMID: 38630598 DOI: 10.1080/19396368.2024.2325699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/24/2024] [Indexed: 04/19/2024]
Abstract
MDC1 (Mediator of DNA damage Checkpoint protein 1) functions to facilitate the localization of numerous DNA damage response (DDR) components to DNA double-strand break sites. MDC1 is an integral component in preserving genomic stability and appropriate DDR regulation. There haven't been systematic investigations of MDC1 mutations that induce cancer and genomic instability. Variations in nsSNPs have the potential to modify the protein chemistry and their function. Describing functional SNPs in disease-associated genes presents a significant conundrum for investigators, it is possible to assess potential functional SNPs before conducting larger population examinations. Multiple sequences and structure-based bioinformatics strategies were implemented in the current in-silico investigation to discern potential nsSNPs of the MDC1 genes. The nsSNPs were identified with SIFT, SNAP2, Align GVGD, PolyPhen-2, and PANTHER, and their stability was determined with MUpro. The conservation, solvent accessibility, and structural effects of the mutations were identified with ConSurf, NetSurfP-2.0, and SAAFEC-SEQ respectively. Cancer-related analysis of the nsSNPs was conducted using cBioPortal and TCGA web servers. The present study appraised five nsSNPs (P1426T, P69S, P194R, P203L, and H131Y) as probably mutilating due to their existence in highly conserved regions and propensity to deplete protein stability. The nsSNPs P194R, P203L, and H131Y were concluded as deleterious and possibly damaging from the 5 prediction tools. The functional nsSNP P194R mutation is associated with skin cutaneous melanoma while no significant records were found for other nsSNPs. The present study concludes that the highly deleterious P194R mutations can potentially induce genomic instability and contribute to various cancers' pathogenesis. Developing drugs targeting these mutations can undoubtedly be advantageous in large population-based studies, particularly in the development of precision medicine.
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Affiliation(s)
| | - Susha Dinesh
- Department of Bioinformatics, BioNome, Bengaluru, India
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bengaluru, India
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2
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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3
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Scherzer M, Giordano F, Ferran MS, Ström L. Recruitment of Scc2/4 to double-strand breaks depends on γH2A and DNA end resection. Life Sci Alliance 2022; 5:e202101244. [PMID: 35086935 PMCID: PMC8807874 DOI: 10.26508/lsa.202101244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination enables cells to overcome the threat of DNA double-strand breaks (DSBs), allowing for repair without the loss of genetic information. Central to the homologous recombination repair process is the de novo loading of cohesin around a DSB by its loader complex Scc2/4. Although cohesin's DSB accumulation has been explored in numerous studies, the prerequisites for Scc2/4 recruitment during the repair process are still elusive. To address this question, we combine chromatin immunoprecipitation-qPCR with a site-specific DSB in vivo, in Saccharomyces cerevisiae We find that Scc2 DSB recruitment relies on γH2A and Tel1, but as opposed to cohesin, not on Mec1. We further show that the binding of Scc2, which emanates from the break site, depends on and coincides with DNA end resection. Absence of chromatin remodeling at the DSB affects Scc2 binding and DNA end resection to a comparable degree, further indicating the latter to be a major driver for Scc2 recruitment. Our results shed light on the intricate DSB repair cascade leading to the recruitment of Scc2/4 and subsequent loading of cohesin.
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Affiliation(s)
- Martin Scherzer
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Fosco Giordano
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria Solé Ferran
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Lena Ström
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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4
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Yasuhara T, Kato R, Yamauchi M, Uchihara Y, Zou L, Miyagawa K, Shibata A. RAP80 suppresses the vulnerability of R-loops during DNA double-strand break repair. Cell Rep 2022; 38:110335. [PMID: 35108530 DOI: 10.1016/j.celrep.2022.110335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 12/08/2021] [Accepted: 01/12/2022] [Indexed: 01/15/2023] Open
Abstract
Single-stranded DNA (ssDNA) arising as an intermediate of cellular processes on DNA is a potential vulnerability of the genome unless it is appropriately protected. Recent evidence suggests that R-loops, consisting of ssDNA and DNA-RNA hybrids, can form in the proximity of DNA double-strand breaks (DSBs) within transcriptionally active regions. However, how the vulnerability of ssDNA in R-loops is overcome during DSB repair remains unclear. Here, we identify RAP80 as a factor suppressing the vulnerability of ssDNA in R-loops, chromosome translocations, and deletions during DSB repair. Mechanistically, RAP80 prevents unscheduled nucleolytic processing of ssDNA in R-loops by CtIP. This mechanism promotes efficient DSB repair via transcription-associated end joining dependent on BRCA1, Polθ, and LIG1/3. Thus, RAP80 suppresses the vulnerability of R-loops during DSB repair, thereby precluding genomic abnormalities in a critical component of the genome caused by deleterious R-loop processing.
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Affiliation(s)
- Takaaki Yasuhara
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan; Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
| | - Reona Kato
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Motohiro Yamauchi
- Hospital Campus Laboratory, Radioisotope Center, Central Institute of Radioisotope Science and Safety Management, Kyushu University, Fukuoka, Japan
| | - Yuki Uchihara
- Gunma University Initiative for Advanced Research, Gunma University, Maebashi, Gunma, Japan
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| | - Atsushi Shibata
- Gunma University Initiative for Advanced Research, Gunma University, Maebashi, Gunma, Japan.
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5
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Stefos GC, Szantai E, Konstantopoulos D, Samiotaki M, Fousteri M. aniFOUND: analysing the associated proteome and genomic landscape of the repaired nascent non-replicative chromatin. Nucleic Acids Res 2021; 49:e64. [PMID: 33693861 DOI: 10.1093/nar/gkab144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022] Open
Abstract
Specific capture of chromatin fractions with distinct and well-defined features has emerged as both challenging and a key strategy towards a comprehensive understanding of genome biology. In this context, we developed aniFOUND (accelerated native isolation of factors on unscheduled nascent DNA), an antibody-free method, which can label, capture, map and characterise nascent chromatin fragments that are synthesized in response to specific cues outside S-phase. We used the 'unscheduled' DNA synthesis (UDS) that takes place during the repair of UV-induced DNA lesions and coupled the captured chromatin to high-throughput analytical technologies. By mass-spectrometry we identified several factors with no previously known role in UVC-DNA damage response (DDR) as well as known DDR proteins. We experimentally validated the repair-dependent recruitment of the chromatin remodeller RSF1 and the cohesin-loader NIPBL at sites of UVC-induced photolesions. Developing aniFOUND-seq, a protocol for mapping UDS activity with high resolution, allowed us to monitor the landscape of UVC repair-synthesis events genome wide. We further resolved repair efficacy of the rather unexplored repeated genome, in particular rDNA and telomeres. In summary, aniFOUND delineates the proteome composition and genomic landscape of chromatin loci with specific features by integrating state-of-the-art 'omics' technologies to promote a comprehensive view of their function.
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Affiliation(s)
- Georgios C Stefos
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
| | - Eszter Szantai
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
| | | | | | - Maria Fousteri
- Institute for Fundamental Biomedical Research, BSRC 'Alexander Fleming', Vari 16672, Greece
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6
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Long Q, Liu Z, Gullerova M. Sweet Melody or Jazz? Transcription Around DNA Double-Strand Breaks. Front Mol Biosci 2021; 8:655786. [PMID: 33959637 PMCID: PMC8096065 DOI: 10.3389/fmolb.2021.655786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/22/2021] [Indexed: 12/23/2022] Open
Abstract
Genomic integrity is continuously threatened by thousands of endogenous and exogenous damaging factors. To preserve genome stability, cells developed comprehensive DNA damage response (DDR) pathways that mediate the recognition of damaged DNA lesions, the activation of signaling cascades, and the execution of DNA repair. Transcription has been understood to pose a threat to genome stability in the presence of DNA breaks. Interestingly, accumulating evidence in recent years shows that the transient transcriptional activation at DNA double-strand break (DSB) sites is required for efficient repair, while the rest of the genome exhibits temporary transcription silencing. This genomic shut down is a result of multiple signaling cascades involved in the maintenance of DNA/RNA homeostasis, chromatin stability, and genome fidelity. The regulation of transcription of protein-coding genes and non-coding RNAs has been extensively studied; however, the exact regulatory mechanisms of transcription at DSBs remain enigmatic. These complex processes involve many players such as transcription-associated protein complexes, including kinases, transcription factors, chromatin remodeling complexes, and helicases. The damage-derived transcripts themselves also play an essential role in DDR regulation. In this review, we summarize the current findings on the regulation of transcription at DSBs and discussed the roles of various accessory proteins in these processes and consequently in DDR.
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Affiliation(s)
| | | | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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7
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Qiao F, Zhang C, Wang Y, Liu G, Shao B, Hu P, Xu Z. Case Report: Prenatal Whole-Exome Sequencing to Identify a Novel Heterozygous Synonymous Variant in NIPBL in a Fetus With Cornelia de Lange Syndrome. Front Genet 2021; 12:628890. [PMID: 33633789 PMCID: PMC7900548 DOI: 10.3389/fgene.2021.628890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a genetically heterogeneous disorder characterized by a wide spectrum of abnormalities, including craniofacial dysmorphism, upper limb anomalies, pre- and post-natal growth restrictions, hirsutism and intellectual disability. Approximately 60% of cases are caused by NIPBL variants. Herein we report on a prenatal case presented with bilateral upper-extremity malformations and cardiac defects. Whole-exome sequencing (WES) was performed on the fetus–parental trio and a de novo heterozygous synonymous variant in NIPBL [chr5:37020979; NM_133433.4: c.5328G>A, p. (Gln1776=)] was identified. Reverse transcriptase–polymerase chain reaction (RT–PCR) was conducted to evaluate the potential splicing effect of this variant, which confirmed that the variant caused a deletion of exon 27 (103 bp) by disrupting the splice-donor site and changed the reading frame with the insertion of at least three stop codons. Our finding not only expands the mutation spectrum of NIPBL gene but also establishes the crucial role of WES in searching for underlying genetic variants. In addition, our research raises the important issue that synonymous mutations may be potential pathogenic variants and should not be neglected in clinical diagnoses.
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Affiliation(s)
- Fengchang Qiao
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Cuiping Zhang
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Gang Liu
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Binbin Shao
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Nanjing Maternity and Child Health Care Hospital, Women's Hospital of Nanjing Medical University, Nanjing, China
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8
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Lin H, Zhao X, Xia L, Lian J, You J. Clinicopathological and Prognostic Significance of CBX3 Expression in Human Cancer: a Systematic Review and Meta-analysis. DISEASE MARKERS 2020; 2020:2412741. [PMID: 33273987 PMCID: PMC7676940 DOI: 10.1155/2020/2412741] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 09/20/2020] [Accepted: 10/04/2020] [Indexed: 01/10/2023]
Abstract
BACKGROUND Chromebox protein homolog 3 (CBX3) as a member of the heterochromatin-associated protein 1 (HP1) family has been reported to be overexpressed in human cancer tissues. Numerous studies have shown the relationship between the CBX3 expression and clinicopathological factor or prognosis in malignant tumors, but their results are inconsistent. To address these results, a meta-analysis was described to investigate the prognostic value and clinicopathological significance of CBX3 expression in human malignant neoplasms. METHODS PubMed, Web of Science, Embase, and Chinese National Knowledge Infrastructure (CNKI) were used to search eligible literatures, including publications prior to September 2019. The role of CBX3 in cancer prognosis and clinicopathological characteristics was assessed by pooled hazard ratios (HRs) and odds ratios (ORs) with 95% confidence intervals (CIs). RESULTS Eleven studies with 1682 cancer patients were enrolled in this meta-analysis. This analysis demonstrated that the patients' increased CBX3 expression was significantly associated with poor overall survival (OS) (univariate analysis: HR = 1.81, 95% CI 1.46-2.25; multivariate analysis: HR = 1.95, 95% CI 1.63-2.34). Subgroups analysis by tumor type also indicated that high expression of CBX3 was correlated with poor OS in tongue squamous cell carcinoma (HR = 3.31, 95% CI 2.03-5.39), lung cancer (HR = 1.66, 95% CI 1.21-2.29), genitourinary cancer (HR = 2.03, 95% CI 1.15-3.58), and digestive cancer (HR = 1.48, 95% CI 1.23-1.79). For clinicopathological features, high expression of CBX3 was associated with lymph node metastasis (OR = 2.96, 95% CI 1.42-6.20) and lager tumor size (OR = 1.60, 95% CI 1.12-2.28). CONCLUSION The results of this meta-analysis indicated that CBX3 expression may be a novel biomarker for predicting patient prognosis and clinicopathological parameters in multiple human cancer.
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Affiliation(s)
- Hexin Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
- Laboratory of Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Xin Zhao
- Department of Medical Oncology, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Lu Xia
- Laboratory of Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- School of Clinical Medicine, Fujian Medical University, Fuzhou, China
| | - Jiabian Lian
- School of Clinical Medicine, Fujian Medical University, Fuzhou, China
- Department of laboratory medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Jun You
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China
- Laboratory of Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
- School of Clinical Medicine, Fujian Medical University, Fuzhou, China
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9
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Lin H, Lian J, Xia L, Guan G, You J. CBX3 Promotes Gastric Cancer Progression and Affects Factors Related to Immunotherapeutic Responses. Cancer Manag Res 2020; 12:10113-10125. [PMID: 33116867 PMCID: PMC7569062 DOI: 10.2147/cmar.s271807] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Chromobox 3 (CBX3) is a member of the chromobox family proteins, which plays a critical role in tumor progression, but the exact function of CBX3 in gastric cancer remains unknown. The current research mainly investigates the underlying mechanisms and clinical value of CBX3 in gastric cancer. Methods Gene expression cohorts from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) were analyzed to assess the effect of CBX3 in gastric cancer. CBX3 expression was further determined by immunohistochemistry (IHC). The function of CBX3 on proliferation, migration and the cell cycle was explored via colony-forming, cell cycle and transwell assays, respectively. Moreover, RNA sequencing (RNA-seq) in AGS cells and two cohorts was utilized to explore the specific mechanism of CBX3. Results CBX3 expression was upregulated in human gastric cancer tissues and the expression level was closely associated with adverse signs. Knockdown of CBX3 in gastric cancer cells significantly inhibited the malignant phenotype. In addition, RNA-seq analysis revealed that CBX3 regulates genes related to the cell cycle, mismatch repair and immune-related pathways. Furthermore, the expression of CBX3 was significantly and inversely related to the abundance of tumor-infiltrating lymphocytes (TILs), PDCD1 and PDCD1LG2 expression and immunotherapy responses. Moreover, CBX3 influences the effectiveness of chemotherapy, thereby impacting the prognosis of gastric cancer patients. Conclusion CBX3 contributes to gastric cancer progression and is associated with chemotherapy and immunotherapy response. CBX3 may serve as a new diagnostic biomarker and potential target for immunotherapy and chemotherapy in gastric cancer.
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Affiliation(s)
- Hexin Lin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China.,Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Jiabian Lian
- Department of Laboratory Medicine, Xiamen Key Laboratory of Genetic Testing, The First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China.,School of Clinical Medicine, Fujian Medical University, Fuzhou, People's Republic of China
| | - Lu Xia
- School of Clinical Medicine, Fujian Medical University, Fuzhou, People's Republic of China.,Laboratory of Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China
| | - Guoxian Guan
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Jun You
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, People's Republic of China.,School of Clinical Medicine, Fujian Medical University, Fuzhou, People's Republic of China
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10
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Mathison A, Milech De Assuncao T, Dsouza NR, Williams M, Zimmermann MT, Urrutia R, Lomberk G. Discovery, expression, cellular localization, and molecular properties of a novel, alternative spliced HP1γ isoform, lacking the chromoshadow domain. PLoS One 2020; 15:e0217452. [PMID: 32027651 PMCID: PMC7004349 DOI: 10.1371/journal.pone.0217452] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
By reading the H3K9Me3 mark through their N-terminal chromodomain (CD), HP1 proteins play a significant role in cancer-associated processes, including cell proliferation, differentiation, chromosomal stability, and DNA repair. Here, we used a combination of bioinformatics-based methodologies, as well as experimentally-derived datasets, that reveal the existence of a novel short HP1γ (CBX3) isoform, named here sHP1γ, generated by alternative splicing of the CBX3 locus. The sHP1γ mRNA encodes a protein composed of 101 residues and lacks the C-terminal chromoshadow domain (CSD) that is required for dimerization and heterodimerization in the previously described 183 a. a HP1γ protein. Fold recognition, order-to-disorder calculations, threading, homology-based molecular modeling, docking, and molecular dynamic simulations show that the sHP1γ is comprised of a CD flanked by intrinsically disordered regions (IDRs) with an IDR-CD-IDR domain organization and likely retains the ability to bind to the H3K9Me3. Both qPCR analyses and mRNA-seq data derived from large-scale studies confirmed that sHP1γ mRNA is expressed in the majority of human tissues at approximately constant ratios with the chromoshadow domain containing isoform. However, sHP1γ mRNA levels appear to be dysregulated in different cancer types. Thus, our data supports the notion that, due to the existence of functionally different isoforms, the regulation of HP1γ-mediated functions is more complex than previously anticipated.
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Affiliation(s)
- Angela Mathison
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Thiago Milech De Assuncao
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Nikita R. Dsouza
- Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Monique Williams
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael T. Zimmermann
- Bioinformatics Research and Development Laboratory, and Precision Medicine Simulation Unit, Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Raul Urrutia
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Gwen Lomberk
- Genomics and Precision Medicine Center (GSPMC), Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Division of Research, Department of Surgery, Medical College of Wisconsin, WI Center, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
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11
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Korsholm LM, Gál Z, Lin L, Quevedo O, Ahmad DA, Dulina E, Luo Y, Bartek J, Larsen DH. Double-strand breaks in ribosomal RNA genes activate a distinct signaling and chromatin response to facilitate nucleolar restructuring and repair. Nucleic Acids Res 2019; 47:8019-8035. [PMID: 31184714 PMCID: PMC6735822 DOI: 10.1093/nar/gkz518] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 12/21/2022] Open
Abstract
The nucleolus is a nuclear sub-domain containing the most highly transcribed genes in the genome. Hundreds of human ribosomal RNA (rRNA) genes, located in the nucleolus, rely on constant maintenance. DNA double-strand breaks (DSBs) in rRNA genes activate the ATM kinase, repress rRNA transcription and induce nucleolar cap formation. Yet how ribosomal-DNA (rDNA) lesions are detected and processed remains elusive. Here, we use CRISPR/Cas9-mediated induction of DSBs and report a chromatin response unique to rDNA depending on ATM-phosphorylation of the nucleolar protein TCOF1 and recruitment of the MRE11-RAD50-NBS1 (MRN) complex via the NBS1-subunit. NBS1- and MRE11-depleted cells fail to suppress rRNA transcription and to translocate rDNA into nucleolar caps. Furthermore, the DNA damage response (DDR) kinase ATR operates downstream of the ATM-TCOF1-MRN interplay and is required to fully suppress rRNA transcription and complete DSB-induced nucleolar restructuring. Unexpectedly, we find that DSBs in rDNA neither activate checkpoint kinases CHK1/CHK2 nor halt cell-cycle progression, yet the nucleolar-DDR protects against genomic aberrations and cell death. Our data highlight the concept of a specialized nucleolar DNA damage response (n-DDR) with a distinct protein composition, spatial organization and checkpoint communication. The n-DDR maintains integrity of ribosomal RNA genes, with implications for cell physiology and disease.
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Affiliation(s)
- Lea M Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
| | - Oliver Quevedo
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Diana A Ahmad
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, 266555 Qingdao, China
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology, Karolinska Institutet, SE-171 65 Solna, Sweden
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
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12
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Arnould C, Legube G. The Secret Life of Chromosome Loops upon DNA Double-Strand Break. J Mol Biol 2019; 432:724-736. [PMID: 31401119 PMCID: PMC7057266 DOI: 10.1016/j.jmb.2019.07.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/24/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022]
Abstract
DNA double-strand breaks (DSBs) are harmful lesions that severely challenge genomic integrity, and recent evidence suggests that DSBs occur more frequently on the genome than previously thought. These lesions activate a complex and multilayered response called the DNA damage response, which allows to coordinate their repair with the cell cycle progression. While the mechanistic details of repair processes have been narrowed, thanks to several decades of intense studies, our knowledge of the impact of DSB on chromatin composition and chromosome architecture is still very sparse. However, the recent development of various tools to induce DSB at annotated loci, compatible with next-generation sequencing-based approaches, is opening a new framework to tackle these questions. Here we discuss the influence of initial and DSB-induced chromatin conformation and the strong potential of 3C-based technologies to decipher the contribution of chromosome architecture during DSB repair.
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Affiliation(s)
- Coline Arnould
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Integrative (CBI), CNRS, Université de Toulouse, UT3, Toulouse, France.
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13
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Ravi M, Ramanathan S, Krishna K. Factors, mechanisms and implications of chromatin condensation and chromosomal structural maintenance through the cell cycle. J Cell Physiol 2019; 235:758-775. [PMID: 31264212 DOI: 10.1002/jcp.29038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/12/2019] [Indexed: 12/16/2022]
Abstract
A series of well-orchestrated events help in the chromatin condensation and the formation of chromosomes. Apart from the formation of chromosomes, maintenance of their structure is important, especially for the cell division. The structural maintenance of chromosome (SMC) proteins, the non-SMC proteins and the SMC complexes are critical for the maintenance of chromosome structure. While condensins have roles for the DNA compaction, organization, and segregation, the cohesin functions in a cyclic manner through the cell cycle, as a "cohesin cycle." Specific mechanisms maintain the architecture of the centromere, the kinetochore and the telomeres which are in tandem with the cell cycle checkpoints. The presence of chromosomal territories and compactness differences through the length of the chromosomes might have implications on selective susceptibility of specific chromosomes for induced genotoxicity.
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Affiliation(s)
- Maddaly Ravi
- Department of Human Genetics, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - Srishti Ramanathan
- Department of Human Genetics, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - Krupa Krishna
- Department of Human Genetics, Faculty of Biomedical Sciences, Technology and Research, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
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14
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Litwin I, Pilarczyk E, Wysocki R. The Emerging Role of Cohesin in the DNA Damage Response. Genes (Basel) 2018; 9:genes9120581. [PMID: 30487431 PMCID: PMC6316000 DOI: 10.3390/genes9120581] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/23/2022] Open
Abstract
Faithful transmission of genetic material is crucial for all organisms since changes in genetic information may result in genomic instability that causes developmental disorders and cancers. Thus, understanding the mechanisms that preserve genome integrity is of fundamental importance. Cohesin is a multiprotein complex whose canonical function is to hold sister chromatids together from S-phase until the onset of anaphase to ensure the equal division of chromosomes. However, recent research points to a crucial function of cohesin in the DNA damage response (DDR). In this review, we summarize recent advances in the understanding of cohesin function in DNA damage signaling and repair. First, we focus on cohesin architecture and molecular mechanisms that govern sister chromatid cohesion. Next, we briefly characterize the main DDR pathways. Finally, we describe mechanisms that determine cohesin accumulation at DNA damage sites and discuss possible roles of cohesin in DDR.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Ewa Pilarczyk
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
| | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland.
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15
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Abstract
Constitutive heterochromatin is a major component of the eukaryotic nucleus and is essential for the maintenance of genome stability. Highly concentrated at pericentromeric and telomeric domains, heterochromatin is riddled with repetitive sequences and has evolved specific ways to compartmentalize, silence, and repair repeats. The delicate balance between heterochromatin epigenetic maintenance and cellular processes such as mitosis and DNA repair and replication reveals a highly dynamic and plastic chromatin domain that can be perturbed by multiple mechanisms, with far-reaching consequences for genome integrity. Indeed, heterochromatin dysfunction provokes genetic turmoil by inducing aberrant repeat repair, chromosome segregation errors, transposon activation, and replication stress and is strongly implicated in aging and tumorigenesis. Here, we summarize the general principles of heterochromatin structure and function, discuss the importance of its maintenance for genome integrity, and propose that more comprehensive analyses of heterochromatin roles in tumorigenesis will be integral to future innovations in cancer treatment.
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Affiliation(s)
- Aniek Janssen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Serafin U. Colmenares
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
| | - Gary H. Karpen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
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16
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Human Rad52 Promotes XPG-Mediated R-loop Processing to Initiate Transcription-Associated Homologous Recombination Repair. Cell 2018; 175:558-570.e11. [DOI: 10.1016/j.cell.2018.08.056] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 05/02/2018] [Accepted: 08/22/2018] [Indexed: 12/22/2022]
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17
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Gao D, Zhu B, Cao X, Zhang M, Wang X. Roles of NIPBL in maintenance of genome stability. Semin Cell Dev Biol 2018; 90:181-186. [PMID: 30096364 DOI: 10.1016/j.semcdb.2018.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/06/2018] [Indexed: 12/24/2022]
Abstract
A cohesin-loading factor (NIPBL) is one of important regulatory factors in the maintenance of 3D genome organization and function, by interacting with a large number of factors, e.g. cohesion, CCCTC-binding factor (CTCF) or cohesin complex component. The present article overviews the critical and regulatory roles of NIBPL in cohesion loading on chromotin and in gene expression and transcriptional signaling. We explore molecular mechanisms by which NIPBL recruits endogenous histone deacetylase (HDAC) to induce histone deacetylation and influence multi-dimensions of genome, through which NIPBL "hop" movement in chromatin regulates gene expression and alters genome folding. NIPBL regulates the process of CTCF and cohesion into chromatin loops and topologically associated domains, binding of cohesion and H3K4mes3 through interaction among promoters and enhancers. HP1 recruits NIPBL to DNA damage site through RNF8/RNF168 ubiquitylation pathway. NIPBL contributes to regulation of genome-controlled gene expression through the influence of cohesin in chromosome structure. NIPBL interacts with cohesin and then increases transcriptional activities of REC8 promoter, leading to up-regulation of gene expression. NIPBL movement among chromosomal loops regulates gene expression through dynamic alterations of genome organization. Thus, we expect a new and deep insight to understand dynamics of chromosome and explore potential strategies of therapiesc on basis of NIPBL.
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Affiliation(s)
- Danyan Gao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Bijun Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xin Cao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Miaomiao Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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18
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Zheng L, Zhou H, Guo L, Xu X, Zhang S, Xu W, Mao W. Inhibition of NIPBL enhances the chemosensitivity of non-small-cell lung cancer cells via the DNA damage response and autophagy pathway. Onco Targets Ther 2018; 11:1941-1948. [PMID: 29670369 PMCID: PMC5896680 DOI: 10.2147/ott.s158655] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background Previously, we reported that high expression of nipped-B-like protein (NIPBL) was strongly correlated with poor prognosis, tumor differentiation, and lymph node metastasis. Survival analysis indicated that NIPBL expression was a potential prognostic factor for non-small cell lung cancer (NSCLC). Moreover, loss of NIPBL decreased lung cancer cells proliferation, migration, invasion and promoted apoptosis as well as sensitivity to chemotherapeutic agents. However, the deep mechanisms were not explored. Purpose The objective of this study was to identify the role of NIPBL in DNA damage response, as well as autophagy pathway, so as to interpret the mechanisms of how NIPBL knockdown enhances the chemosensitivity of lung cancer cell. Methods Cells (NCI-H1299 and NCI-H1650) were transfected by specific siRNAs before immunofluorescence and single-cell gel electrophoresis, which were mainly used to observe the differences of DNA damage in different groups. Additionally, protein were obtained and then analyzed by western blot and mass spectroscopy. Results In this study, we found that knockdown of NIPBL resulted in accumulation of phosphorylated H2AX (γ-H2AX) foci and higher levels of DNA damage, as revealed by comet assay. Western blot assay revealed that loss of NIPBL decreased expression of ATM/ATR, Rad3-related protein and Ku70/Ku80, but increased expression of LC3-B and depletion of p62. Using mass spectroscopy, we identified eight proteins that were significantly differentially expressed upon NIPBL knockdown. Gene Ontology analysis revealed that these proteins are mainly involved in DNA repair, mismatch repair, and binding to damaged DNA. The expression changes in two of the proteins, MSH2 and STAT1, were verified by Western blotting in NIPBL-knockdown cells. Conclusions In summary, these results reflected that loss of NIPBL impairs the DNA damage response and promotes autophagy. And NIPBL suppression may represent a novel strategy for preventing chemotherapy resistance in lung cancer.
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Affiliation(s)
- Lei Zheng
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Huanhuan Zhou
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Liwei Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoling Xu
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Shengjie Zhang
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Weizhen Xu
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Weimin Mao
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang, China.,Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China.,Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology of Zhejiang Province, Hangzhou, Zhejiang, China
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19
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Zhou H, Zheng L, Lu K, Gao Y, Guo L, Xu W, Wang X. Downregulation of Cohesin Loading Factor Nipped-B-Like Protein (NIPBL) Induces Cell Cycle Arrest, Apoptosis, and Autophagy of Breast Cancer Cell Lines. Med Sci Monit 2017; 23:4817-4825. [PMID: 28987049 PMCID: PMC5642644 DOI: 10.12659/msm.906583] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/12/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The cohesin loading factor, nipped-B-like protein (NIPBL), is also known as the sister chromatid cohesion 2 (SCC2) human homolog. Recently, we have studied the role of expression levels of NIPBL in cell proliferation and chemotherapy resistance of non-small cell lung cancer (NSCLC) cells in vitro. The aim of this study was to investigate the effects of expression of the cohesin loading factor, NIPBL, on the cell cycle, apoptosis, and autophagy of breast cancer cell lines in vitro. MATERIAL AND METHODS Expression levels of the NIPBL in the breast cancer cell lines, MCF7, Bcap37, MDA-MB 453 and MDA-MB 231, were measured using Western blot and flow cytometry. Small interfering RNA (si-RNA) was used to study the biological functions of NIPBL. The cell counting kit-8 (CCK-8) assay and the colony formation assay were used to measure cell proliferation; the wound scratching assay and transwell chamber assay were used to investigate cell invasion and migration. RESULTS NIPBL gene and protein expression were upregulated in the MCF7 and Bcap37 cells; si-NIPBL transfection inhibited cell proliferation, invasion, and migration of breast cancer cells. Downregulation of NIPBL arrested cells in the G0/G1 phase of the cell cycle and induced apoptosis and autophagy of breast cancer cells through the caspase3 and mammalian target of rapamycin (mTOR) signaling pathways. CONCLUSIONS [color=black]Downregulation of cohesin loading factor NIPBL arrested breast cancer cells in vitro in the G0/G1 phase of the cell cycle and induced apoptosis and autophagy. [/color].
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Affiliation(s)
- Huanhuan Zhou
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Lei Zheng
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Kongbeng Lu
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Yun Gao
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Liwei Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, P.R. China
| | - Weizhen Xu
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
| | - Xiaojia Wang
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, P.R. China
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20
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Tsekrekou M, Stratigi K, Chatzinikolaou G. The Nucleolus: In Genome Maintenance and Repair. Int J Mol Sci 2017; 18:ijms18071411. [PMID: 28671574 PMCID: PMC5535903 DOI: 10.3390/ijms18071411] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 11/16/2022] Open
Abstract
The nucleolus is the subnuclear membrane-less organelle where rRNA is transcribed and processed and ribosomal assembly occurs. During the last 20 years, however, the nucleolus has emerged as a multifunctional organelle, regulating processes that go well beyond its traditional role. Moreover, the unique organization of rDNA in tandem arrays and its unusually high transcription rates make it prone to unscheduled DNA recombination events and frequent RNA:DNA hybrids leading to DNA double strand breaks (DSBs). If not properly repaired, rDNA damage may contribute to premature disease onset and aging. Deregulation of ribosomal synthesis at any level from transcription and processing to ribosomal subunit assembly elicits a stress response and is also associated with disease onset. Here, we discuss how genome integrity is maintained within nucleoli and how such structures are functionally linked to nuclear DNA damage response and repair giving an emphasis on the newly emerging roles of the nucleolus in mammalian physiology and disease.
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Affiliation(s)
- Maria Tsekrekou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013 Heraklion, Crete, Greece.
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Crete, Greece.
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013 Heraklion, Crete, Greece.
- Department of Biology, University of Crete, Vassilika Vouton, 71409 Heraklion, Crete, Greece.
| | - Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013 Heraklion, Crete, Greece.
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21
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Bot C, Pfeiffer A, Giordano F, Manjeera DE, Dantuma NP, Ström L. Independent mechanisms recruit the cohesin loader protein NIPBL to sites of DNA damage. J Cell Sci 2017; 130:1134-1146. [PMID: 28167679 PMCID: PMC5358341 DOI: 10.1242/jcs.197236] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/30/2017] [Indexed: 12/21/2022] Open
Abstract
NIPBL is required to load the cohesin complex on to DNA. While the canonical role of cohesin is to couple replicated sister chromatids together until the onset of mitosis, it also promotes tolerance to DNA damage. Here, we show that NIPBL is recruited to DNA damage throughout the cell cycle via independent mechanisms, influenced by type of damage. First, the heterochromatin protein HP1γ (also known as CBX3) recruits NIPBL to DNA double-strand breaks (DSBs) through the corresponding HP1-binding motif within the N-terminus. By contrast, the C-terminal HEAT repeat domain is unable to recruit NIPBL to DSBs but independently targets NIPBL to laser microirradiation-induced DNA damage. Each mechanism is dependent on the RNF8 and RNF168 ubiquitylation pathway, while the recruitment of the HEAT repeat domain requires further ATM or ATR activity. Thus, NIPBL has evolved a sophisticated response to damaged DNA that is influenced by the form of damage, suggesting a highly dynamic role for NIPBL in maintaining genomic stability.
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Affiliation(s)
- Christopher Bot
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm 171 77, Sweden
| | - Annika Pfeiffer
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm 171 77, Sweden
| | - Fosco Giordano
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm 171 77, Sweden
| | - Dharani E Manjeera
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm 171 77, Sweden
| | - Nico P Dantuma
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm 171 77, Sweden
| | - Lena Ström
- Karolinska Institutet, Department of Cell and Molecular Biology, Stockholm 171 77, Sweden
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22
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Abstract
The kollerin complex, consisting of Scc2/Scc4 in yeast and Nipbl/Mau2 in vertebrates, is crucial for the chromatin-association of the cohesin complex and therefore for the critical functions of cohesin in cell division, transcriptional regulation and chromatin organisation. Despite the recent efforts to determine the genomic localization of the kollerin complex in different cell lines, major questions still remain unresolved, for instance where cohesin is actually loaded onto chromatin. Further, Nipbl seems to have also additional roles, for instance as transcription factor.This chapter summarizes our current knowledge on kollerin function and the recent studies on the genomic localization of Scc2, highlighting and critically discussing controversial data.
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Affiliation(s)
- Kerstin S Wendt
- Department of Cell Biology, Erasmus MC, Faculty Building, Room Ee1020, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
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23
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Cramer D, Serrano L, Schaefer MH. A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference. eLife 2016; 5. [PMID: 27831464 PMCID: PMC5122459 DOI: 10.7554/elife.16519] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 11/02/2016] [Indexed: 01/22/2023] Open
Abstract
Copy number alterations (CNAs) in cancer patients show a large variability in their number, length and position, but the sources of this variability are not known. CNA number and length are linked to patient survival, suggesting clinical relevance. We have identified genes that tend to be mutated in samples that have few or many CNAs, which we term CONIM genes (COpy Number Instability Modulators). CONIM proteins cluster into a densely connected subnetwork of physical interactions and many of them are epigenetic modifiers. Therefore, we investigated how the epigenome of the tissue-of-origin influences the position of CNA breakpoints and the properties of the resulting CNAs. We found that the presence of heterochromatin in the tissue-of-origin contributes to the recurrence and length of CNAs in the respective cancer type. DOI:http://dx.doi.org/10.7554/eLife.16519.001 Cancer is a genetic disease that develops when a cell’s DNA becomes altered. There are several different types of DNA alterations and one that is frequently seen in cancer cells is known as a “copy number alteration” (or CNA for short). These CNAs arise when breaks in the DNA are repaired incorrectly, leading to some pieces of DNA being multiplied while others are lost. Ultimately, CNAs contribute to cancer growth either by providing extra copies of genes that drive tumour development or by deleting genes that normally protect against cancer. However, it is not known why patients with some types of cancer tend to have more CNAs than others and why some DNA regions are particularly susceptible to this type of alteration. Cramer et al. asked whether cancer patients have any other genetic mutations that might be linked with having many or few CNAs. Analysing datasets from almost 6000 patients with 20 different types of cancer showed that mutations in several genes are linked to a higher or lower number of CNAs in patients. Cramer et al. called the proteins encoded by these genes “copy number instability modulators” (or CONIMs for short). Further investigation revealed that several of these CONIM proteins can change the way DNA is packaged inside cells. Furthermore, many of the regions of DNA that are vulnerable to CNAs in cancer cells are tightly packaged within healthy cells. These data suggest that the three-dimensional arrangement of DNA in cells influences where CNAs occur. The next step following on from this work is to find out exactly how the CONIM proteins influence the formation of CNAs. DOI:http://dx.doi.org/10.7554/eLife.16519.002
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Affiliation(s)
- Dina Cramer
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Martin H Schaefer
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
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24
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Gelot C, Guirouilh-Barbat J, Le Guen T, Dardillac E, Chailleux C, Canitrot Y, Lopez BS. The Cohesin Complex Prevents the End Joining of Distant DNA Double-Strand Ends. Mol Cell 2016; 61:15-26. [PMID: 26687679 DOI: 10.1016/j.molcel.2015.11.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 09/25/2015] [Accepted: 11/02/2015] [Indexed: 02/07/2023]
Abstract
The end joining of distant DNA double-strand ends (DSEs) can produce potentially deleterious rearrangements. We show that depletion of cohesion complex proteins specifically stimulates the end joining (both C-NHEJ and A-EJ) of distant, but not close, I-SceI-induced DSEs in S/G2 phases. At the genome level, whole-exome sequencing showed that ablation of RAD21 or Sororin produces large chromosomal rearrangements (translocation, duplication, deletion). Moreover, cytogenetic analysis showed that RAD21 silencing leads to the formation of chromosome fusions synergistically with replication stress, which generates distant single-ended DSEs. These data reveal a role for the cohesin complex in protecting against genome rearrangements arising from the ligation of distant DSEs in S/G2 phases (both long-range DSEs and those that are only a few kilobases apart), while keeping end joining fully active for close DSEs. Therefore, this role likely involves limitation of DSE motility specifically in S phase, rather than inhibition of the end-joining machinery itself.
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Affiliation(s)
- Camille Gelot
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Josée Guirouilh-Barbat
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Tangui Le Guen
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Elodie Dardillac
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France
| | - Catherine Chailleux
- Université de Toulouse UPS, CNRS UMR 5088, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), 31062 Toulouse, France
| | - Yvan Canitrot
- Université de Toulouse UPS, CNRS UMR 5088, Laboratoire de Biologie Cellulaire et Moléculaire du Contrôle de la Prolifération (LBCMCP), 31062 Toulouse, France
| | - Bernard S Lopez
- Centre National de la Recherche Scientifique (CNRS) UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, 114 Rue Edouard Vaillant, 94805 Villejuif, France.
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Kracker S, Di Virgilio M, Schwartzentruber J, Cuenin C, Forveille M, Deau MC, McBride KM, Majewski J, Gazumyan A, Seneviratne S, Grimbacher B, Kutukculer N, Herceg Z, Cavazzana M, Jabado N, Nussenzweig MC, Fischer A, Durandy A. An inherited immunoglobulin class-switch recombination deficiency associated with a defect in the INO80 chromatin remodeling complex. J Allergy Clin Immunol 2015; 135:998-1007.e6. [PMID: 25312759 PMCID: PMC4382329 DOI: 10.1016/j.jaci.2014.08.030] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/31/2014] [Accepted: 08/05/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND Immunoglobulin class-switch recombination defects (CSR-D) are rare primary immunodeficiencies characterized by impaired production of switched immunoglobulin isotypes and normal or elevated IgM levels. They are caused by impaired T:B cooperation or intrinsic B cell defects. However, many immunoglobulin CSR-Ds are still undefined at the molecular level. OBJECTIVE This study's objective was to delineate new causes of immunoglobulin CSR-Ds and thus gain further insights into the process of immunoglobulin class-switch recombination (CSR). METHODS Exome sequencing in 2 immunoglobulin CSR-D patients identified variations in the INO80 gene. Functional experiments were performed to assess the function of INO80 on immunoglobulin CSR. RESULTS We identified recessive, nonsynonymous coding variations in the INO80 gene in 2 patients affected by defective immunoglobulin CSR. Expression of wild-type INO80 in patients' fibroblastic cells corrected their hypersensitivity to high doses of γ-irradiation. In murine CH12-F3 cells, the INO80 complex accumulates at Sα and Eμ regions of the IgH locus, and downregulation of INO80 as well as its partners Reptin and Pontin impaired CSR. In addition, Reptin and Pontin were shown to interact with activation-induced cytidine deaminase. Finally, an abnormal separation of sister chromatids was observed upon INO80 downregulation in CH12-F3 cells, pinpointing its role in cohesin activity. CONCLUSION INO80 deficiency appears to be associated with defective immunoglobulin CSR. We propose that the INO80 complex modulates cohesin function that may be required during immunoglobulin switch region synapsis.
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Affiliation(s)
- Sven Kracker
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Michela Di Virgilio
- Laboratory of Molecular Immunology, Howard Hughes Medical Institute, the Rockefeller University, New York, NY
| | - Jeremy Schwartzentruber
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Cyrille Cuenin
- International Agency for Research on Cancer, F-69008 Lyon, Lyon, France
| | - Monique Forveille
- Center for Primary Immunodeficiencies, Hôpital Necker Enfants Malades, F-75015 Paris, Paris, France
| | - Marie-Céline Deau
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Kevin M McBride
- Laboratory of Molecular Immunology, Howard Hughes Medical Institute, the Rockefeller University, New York, NY
| | - Jacek Majewski
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, Howard Hughes Medical Institute, the Rockefeller University, New York, NY
| | - Suranjith Seneviratne
- UCL Institute of Immunity and Transplantation, Royal Free London NHS Foundation Tust, London, United Kingdom
| | - Bodo Grimbacher
- UCL Institute of Immunity and Transplantation, Royal Free London NHS Foundation Tust, London, United Kingdom; Centre of Chronic Immunodeficiency, University Medical Center Freiburg and University of Freiburg, D-79106 Freiburg, Freiburg, Germany
| | - Necil Kutukculer
- Ege University Faculty of Medicine, Department of Pediatric Immunology, 35100 Bornova, Izmir, Turkey
| | - Zdenko Herceg
- International Agency for Research on Cancer, F-69008 Lyon, Lyon, France
| | - Marina Cavazzana
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France; Department of Biotherapy, AP-HP Hôpital Necker Enfants Malades, F-75015 Paris, Paris, France; Clinical Investigation Center (CIC)-Biotherapy GHU Ouest, INSERM-APHP (Assistance Publique des Hôpitaux de Paris), Paris, France
| | - Nada Jabado
- Department of Pediatrics, McGill University and McGill University Health Center, Montreal, Quebec, Canada
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, Howard Hughes Medical Institute, the Rockefeller University, New York, NY
| | - Alain Fischer
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France; Department of Immunology and Hematology, Hôpital Necker Enfants Malades, F-75015 Paris, Paris, France; Collège de France, Paris, France
| | - Anne Durandy
- INSERM UMR 1163, The Human Lymphohematopoiesis Laboratory, Imagine Institute, Paris, France; Paris Descartes Sorbonne Paris Cité University, Imagine Institute, Paris, France; Department of Immunology and Hematology, Hôpital Necker Enfants Malades, F-75015 Paris, Paris, France.
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Merlo DF, Agramunt S, Anna L, Besselink H, Botsivali M, Brady NJ, Ceppi M, Chatzi L, Chen B, Decordier I, Farmer PB, Fleming S, Fontana V, Försti A, Fthenou E, Gallo F, Georgiadis P, Gmuender H, Godschalk RW, Granum B, Hardie LJ, Hemminki K, Hochstenbach K, Knudsen LE, Kogevinas M, Kovács K, Kyrtopoulos SA, Løvik M, Nielsen JK, Nygaard UC, Pedersen M, Rydberg P, Schoket B, Segerbäck D, Singh R, Sunyer J, Törnqvist M, van Loveren H, van Schooten FJ, Vande Loock K, von Stedingk H, Wright J, Kleinjans JC, Kirsch-Volders M, van Delft JHM. Micronuclei in cord blood lymphocytes and associations with biomarkers of exposure to carcinogens and hormonally active factors, gene polymorphisms, and gene expression: the NewGeneris cohort. ENVIRONMENTAL HEALTH PERSPECTIVES 2014; 122:193-200. [PMID: 24252472 PMCID: PMC3914866 DOI: 10.1289/ehp.1206324] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 11/18/2013] [Indexed: 05/15/2023]
Abstract
BACKGROUND Leukemia incidence has increased in recent decades among European children, suggesting that early-life environmental exposures play an important role in disease development. OBJECTIVES We investigated the hypothesis that childhood susceptibility may increase as a result of in utero exposure to carcinogens and hormonally acting factors. Using cord blood samples from the NewGeneris cohort, we examined associations between a range of biomarkers of carcinogen exposure and hormonally acting factors with micronuclei (MN) frequency as a proxy measure of cancer risk. Associations with gene expression and genotype were also explored. METHODS DNA and protein adducts, gene expression profiles, circulating hormonally acting factors, and GWAS (genome-wide association study) data were investigated in relation to genomic damage measured by MN frequency in lymphocytes from 623 newborns enrolled between 2006 and 2010 across Europe. RESULTS Malondialdehyde DNA adducts (M1dG) were associated with increased MN frequency in binucleated lymphocytes (MNBN), and exposure to androgenic, estrogenic, and dioxin-like compounds was associated with MN frequency in mononucleated lymphocytes (MNMONO), although no monotonic exposure-outcome relationship was observed. Lower frequencies of MNBN were associated with a 1-unit increase expression of PDCD11, LATS2, TRIM13, CD28, SMC1A, IL7R, and NIPBL genes. Gene expression was significantly higher in association with the highest versus lowest category of bulky and M1dG-DNA adducts for five and six genes, respectively. Gene expression levels were significantly lower for 11 genes in association with the highest versus lowest category of plasma AR CALUX® (chemically activated luciferase expression for androgens) (8 genes), ERα CALUX® (for estrogens) (2 genes), and DR CALUX® (for dioxins). Several SNPs (single-nucleotide polymorphisms) on chromosome 11 near FOLH1 significantly modified associations between androgen activity and MNBN frequency. Polymorphisms in EPHX1/2 and CYP2E1 were associated with MNBN. CONCLUSION We measured in utero exposure to selected environmental carcinogens and circulating hormonally acting factors and detected associations with MN frequency in newborns circulating T lymphocytes. The results highlight mechanisms that may contribute to carcinogen-induced leukemia and require further research.
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Affiliation(s)
- Domenico Franco Merlo
- Epidemiology, Biostatistics, and Clinical Trials, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-Istituto Nazionale per la Ricerca sul Cancro (IST), Genoa, Italy
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27
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Kong X, Ball AR, Pham HX, Zeng W, Chen HY, Schmiesing JA, Kim JS, Berns M, Yokomori K. Distinct functions of human cohesin-SA1 and cohesin-SA2 in double-strand break repair. Mol Cell Biol 2014; 34:685-98. [PMID: 24324008 PMCID: PMC3911484 DOI: 10.1128/mcb.01503-13] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/02/2013] [Indexed: 11/20/2022] Open
Abstract
Cohesin is an essential multiprotein complex that mediates sister chromatid cohesion critical for proper segregation of chromosomes during cell division. Cohesin is also involved in DNA double-strand break (DSB) repair. In mammalian cells, cohesin is involved in both DSB repair and the damage checkpoint response, although the relationship between these two functions is unclear. Two cohesins differing by one subunit (SA1 or SA2) are present in somatic cells, but their functional specificities with regard to DNA repair remain enigmatic. We found that cohesin-SA2 is the main complex corecruited with the cohesin-loading factor NIPBL to DNA damage sites in an S/G(2)-phase-specific manner. Replacing the diverged C-terminal region of SA1 with the corresponding region of SA2 confers this activity on SA1. Depletion of SA2 but not SA1 decreased sister chromatid homologous recombination repair and affected repair pathway choice, indicating that DNA repair activity is specifically associated with cohesin recruited to damage sites. In contrast, both cohesin complexes function in the intra-S checkpoint, indicating that cell cycle-specific damage site accumulation is not a prerequisite for cohesin's intra-S checkpoint function. Our findings reveal the unique ways in which cohesin-SA1 and cohesin-SA2 participate in the DNA damage response, coordinately protecting genome integrity in human cells.
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Affiliation(s)
- Xiangduo Kong
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
| | - Alexander R. Ball
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
| | - Hoang Xuan Pham
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
| | - Weihua Zeng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
| | - Hsiao-Yuan Chen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
| | - John A. Schmiesing
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
| | - Jong-Soo Kim
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
| | - Michael Berns
- Beckman Laser Institute, University of California, Irvine, California, USA
- Department of Biomedical Engineering, Samueli School of Engineering, University of California, Irvine, California, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California, USA
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28
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Enervald E, Du L, Visnes T, Björkman A, Lindgren E, Wincent J, Borck G, Colleaux L, Cormier-Daire V, van Gent DC, Pie J, Puisac B, de Miranda NFCC, Kracker S, Hammarström L, de Villartay JP, Durandy A, Schoumans J, Ström L, Pan-Hammarström Q. A regulatory role for the cohesin loader NIPBL in nonhomologous end joining during immunoglobulin class switch recombination. J Exp Med 2013; 210:2503-13. [PMID: 24145515 PMCID: PMC3832922 DOI: 10.1084/jem.20130168] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/30/2013] [Indexed: 11/30/2022] Open
Abstract
DNA double strand breaks (DSBs) are mainly repaired via homologous recombination (HR) or nonhomologous end joining (NHEJ). These breaks pose severe threats to genome integrity but can also be necessary intermediates of normal cellular processes such as immunoglobulin class switch recombination (CSR). During CSR, DSBs are produced in the G1 phase of the cell cycle and are repaired by the classical NHEJ machinery. By studying B lymphocytes derived from patients with Cornelia de Lange Syndrome, we observed a strong correlation between heterozygous loss-of-function mutations in the gene encoding the cohesin loading protein NIPBL and a shift toward the use of an alternative, microhomology-based end joining during CSR. Furthermore, the early recruitment of 53BP1 to DSBs was reduced in the NIPBL-deficient patient cells. Association of NIPBL deficiency and impaired NHEJ was also observed in a plasmid-based end-joining assay and a yeast model system. Our results suggest that NIPBL plays an important and evolutionarily conserved role in NHEJ, in addition to its canonical function in sister chromatid cohesion and its recently suggested function in HR.
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Affiliation(s)
- Elin Enervald
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Likun Du
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Torkild Visnes
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Andrea Björkman
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Emma Lindgren
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Josephine Wincent
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Guntram Borck
- Department of Genetics, Institut National de la Santé et de la Recherche Médicale U781, Hospital Necker, 75743 Paris, France
- Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany
| | - Laurence Colleaux
- Department of Genetics, Institut National de la Santé et de la Recherche Médicale U781, Hospital Necker, 75743 Paris, France
| | - Valerie Cormier-Daire
- Department of Genetics, Institut National de la Santé et de la Recherche Médicale U781, Hospital Necker, 75743 Paris, France
| | - Dik C. van Gent
- Department of Cell Biology and Genetics, Cancer Genomics Center, Erasmus Medical Center, 3000 CA Rotterdam, The Netherlands
| | - Juan Pie
- Unit of Clinical Genetics and functional Genomics, Medical Faculty, Zaragosa University, 50009 Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and functional Genomics, Medical Faculty, Zaragosa University, 50009 Zaragoza, Spain
| | - Noel FCC de Miranda
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Sven Kracker
- National Institutes of Health and Medical Research INSERM U768, Hopital Necker Enfants Malades and Medical Faculty, Descartes-Sorbone Paris Cité University of Paris, 75743 Paris, France
| | - Lennart Hammarström
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jean-Pierre de Villartay
- Université Paris-Descartes, Faculté de Médicine René Descartes, Site Necker, Institut Fédératif de Recherche, F-71015 Paris, France
| | - Anne Durandy
- National Institutes of Health and Medical Research INSERM U768, Hopital Necker Enfants Malades and Medical Faculty, Descartes-Sorbone Paris Cité University of Paris, 75743 Paris, France
| | - Jacqueline Schoumans
- Department of Medical Genetics Cancer Cytogenetic Unit, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Lena Ström
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Qiang Pan-Hammarström
- Department of Cell and Molecular Biology, Department of Laboratory Medicine, Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 77 Stockholm, Sweden
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NIPBL, a cohesion loading factor, is somatically mutated in gastric and colorectal cancers with high microsatellite instability. Dig Dis Sci 2013; 58:3376-8. [PMID: 23912250 DOI: 10.1007/s10620-013-2808-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/15/2013] [Indexed: 12/24/2022]
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Nolen LD, Boyle S, Ansari M, Pritchard E, Bickmore WA. Regional chromatin decompaction in Cornelia de Lange syndrome associated with NIPBL disruption can be uncoupled from cohesin and CTCF. Hum Mol Genet 2013; 22:4180-93. [PMID: 23760082 PMCID: PMC3781641 DOI: 10.1093/hmg/ddt265] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/03/2013] [Indexed: 01/09/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a developmental disorder caused by mutations in NIPBL, a protein which has functionally been associated with the cohesin complex. Mutations in core cohesin complex components have also been reported in individuals with CdLS-like phenotypes. In addition to its role in sister chromatid cohesion, cohesin is thought to play a role in regulating gene expression during development. The mechanism of this gene regulation remains unclear, but NIPBL and cohesin have been reported to affect long-range chromosomal interactions, both independently and through interactions with CTCF. We used fluorescence in situ hybridization to investigate whether the disruption of NIPBL affects chromosome architecture. We show that cells from CdLS patients exhibit visible chromatin decompaction, that is most pronounced across gene-rich regions of the genome. Cells carrying mutations predicted to have a more severe effect on NIPBL function show more extensive chromatin decompaction than those carrying milder mutations. This cellular phenotype was reproduced in normal cells depleted for NIPBL with siRNA, but was not seen following the knockdown of either the cohesin component SMC3, or CTCF. We conclude that NIPBL has a function in modulating chromatin architecture, particularly for gene-rich areas of the chromosome, that is not dependent on SMC3/cohesin or CTCF, raising the possibility that the aetiology of disorders associated with the mutation of core cohesin components is distinct from that associated with the disruption of NIPBL itself in classical CdLS.
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Affiliation(s)
| | | | | | | | - Wendy A. Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
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31
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Kuleszewicz K, Fu X, Kudo NR. Cohesin loading factor Nipbl localizes to chromosome axes during mammalian meiotic prophase. Cell Div 2013; 8:12. [PMID: 23967866 PMCID: PMC3765518 DOI: 10.1186/1747-1028-8-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/12/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sister chromatid cohesion mediated by the cohesin complex is essential for accurate chromosome segregation during mitosis and meiosis. Loading of cohesin onto chromosomes is dependent on another protein complex called kollerin, containing Nipbl/Scc2 and Mau2/Scc4. Nipbl is an evolutionarily conserved large protein whose haploinsufficiency in humans causes a developmental disorder called Cornelia de Lange syndrome. Although the function of Nipbl homologues for chromosome cohesion in meiotic cells of non-vertebrate models has been elucidated, Nipbl has not been characterized so far in mammalian spermatocytes or oocytes. FINDINGS Here we describe our analyses on the expression and localization of Nipbl in nuclei of mouse spermatocytes and oocytes at different stages of meiotic prophase. In both spermatocytes and oocytes we found that Nipbl is associated with the axial/lateral element of the synaptonemal complex (AE/LE) to which cohesin also localizes. Interestingly, Nipbl in spermatocytes, but not in oocytes, dissociates from the AE/LE at mid-pachytene stage coincident with completion of DNA double-strand break repair. CONCLUSIONS Our data propose that cohesin loading activity is maintained during early stages of meiotic prophase in mammalian spermatocytes and oocytes.
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Affiliation(s)
- Katarzyna Kuleszewicz
- IRDB, Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN, UK.
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32
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de Braekeleer E, Auffret R, García JRG, Padilla JMS, Fletes CC, Morel F, Douet-Guilbert N, de Braekeleer M. Identification of NIPBL, a new ETV6 partner gene in t(5;12) (p13;p13)-associated acute megakaryoblastic leukemia. Leuk Lymphoma 2013; 54:423-4. [PMID: 22734863 DOI: 10.3109/10428194.2012.706288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Abstract
The cohesin complex, named for its key role in sister chromatid cohesion, also plays critical roles in gene regulation and DNA repair. It performs all three functions in single cell eukaryotes such as yeasts, and in higher organisms such as man. Minor disruption of cohesin function has significant consequences for human development, even in the absence of measurable effects on chromatid cohesion or chromosome segregation. Here we survey the roles of cohesin in gene regulation and DNA repair, and how these functions vary from yeast to man.
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Affiliation(s)
- Dale Dorsett
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
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Luijsterburg MS, van Attikum H. Close encounters of the RNF8th kind: when chromatin meets DNA repair. Curr Opin Cell Biol 2012; 24:439-47. [PMID: 22464734 DOI: 10.1016/j.ceb.2012.03.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/22/2012] [Accepted: 03/11/2012] [Indexed: 12/16/2022]
Abstract
Cells counteract the adverse effects of chromosome breakage by activating the DNA damage response (DDR), which entails a coordinated series of events that regulate cell cycle progression and repair of DNA lesions. The packaging of genomic DNA into condensed, often inaccessible chromatin severely complicates efficient DNA damage repair in living cells. Recent studies implicate a large number of chromatin-modifying enzymes in the DDR, suggesting a stepwise model in which chromatin is continually reconfigured to accommodate the association and action of repair factors during the different stages of the DDR. Emerging evidence suggests that the histone ubiquitin ligases RNF8/RNF168 act in concert with ATP-dependent chromatin remodelling enzymes to orchestrate the signalling and repair of DNA lesions in specific chromatin topologies.
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Affiliation(s)
- Martijn S Luijsterburg
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
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35
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Soria G, Almouzni G. Differential contribution of HP1 proteins to DNA end resection and homology-directed repair. Cell Cycle 2012; 12:422-9. [PMID: 23287531 DOI: 10.4161/cc.23215] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Heterochromatin protein 1 paralogs (HP1α, β and γ in mammals) are not only central in heterochromatin organization, but have also been linked to transcriptional activation at euchromatic regions, maintenance of telomere stability and, most recently, to the DNA damage response (DDR). However, how HP1 proteins contribute to the DDR at a molecular level, and whether HP1 paralogs within the same organism, as well as their respective orthologs, have overlapping or unique roles in the DDR, remain to be elucidated. Herein, we have combined the analysis of the efficiency and kinetics of recruitment of key repair proteins to sites of DNA damage with specific DNA repair assays to demonstrate that human HP1 paralogs differentially modulate homology-directed repair (HDR) pathways, including homologous recombination (HR) and single-strand annealing (SSA). We find that while HP1α and β stimulate HR and SSA, HP1γ has an inhibitory role. In addition, we show that the stimulatory role of HP1α and β in HDR is linked to the DNA-end resection step of DNA breaks, through the promotion of RPA loading and phosphorylation at damage sites. Altogether, our findings provide mechanistic insight into how human HP1 proteins participate in the recombination process, emerging as important chromatin regulators during HDR.
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Affiliation(s)
- Gaston Soria
- Laboratory of Chromatin Dynamics, Institut Curie Section Recherche, Paris, France
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