1
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Xu X, Wang D, Xu W, Li H, Chen N, Li N, Yao Q, Chen W, Zhong J, Mao W. NIPBL-mediated RAD21 facilitates tumorigenicity by the PI3K pathway in non-small-cell lung cancer. Commun Biol 2024; 7:206. [PMID: 38378967 PMCID: PMC10879132 DOI: 10.1038/s42003-024-05801-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
It is urgent to identify novel early diagnostic markers and therapeutic targets for non-small-cell lung cancer (NSCLC), which accounts for 85% of lung cancer cases and has a 5-year survival rate of 4-17%. Here, chromatin immunoprecipitation (ChIP) was used to identify DNA‒protein interactions, RNA methylation was determined by methylated RNA immunoprecipitation (MeRIP), RNA stability was tested by an RNA decay assay. We showed that RAD21, a member of the cohesin complex, is upregulated in NSCLC tissues and cell lines and found to be an independent prognostic factor for overall survival (OS) of NSCLC patients. Mechanistically, the cohesin loading factor Nipped-B-Like Protein (NIPBL) promoted RAD21 gene transcription by enhancing histone H3 lysine 27 (H3K27) demethylation via recruiting lysine demethylase 6B (KDM6B) to the RAD21 gene promoter. RAD21 enhanced phosphatidylinositol 3-kinase (PI3K) gene transcription, and NIPBL reversed the effect of enhancer of zeste 2; catalytic subunit of polycomb repressive complex 2 (EZH2) on RAD21-mediated PI3K gene transcription by disrupting the association between EZH2 and RAD21. Moreover, NIPBL level was increased by stabilization of its transcripts through mRNA methylation. These findings highlight the oncogenic role of RAD21 in NSCLC and suggest its use as a potential diagnostic marker and therapeutic target for NSCLC.
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Affiliation(s)
- Xiaoling Xu
- Department of Radiation Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, 507 Zhengmin Road, Shanghai, China
| | - Ding Wang
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China
| | - Weizhen Xu
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China
| | - Huihui Li
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China
- The Second Clinical Medical College of Wenzhou Medical University, 268 West Xueyue Road, Wenzhou, China
| | - Ning Chen
- The Second Clinical Medical College of Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou, China
| | - Na Li
- The Second Clinical Medical College of Wenzhou Medical University, 268 West Xueyue Road, Wenzhou, China
| | - Qifeng Yao
- The Second Clinical Medical College of Wenzhou Medical University, 268 West Xueyue Road, Wenzhou, China
| | - Wei Chen
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China.
| | - Jianxiang Zhong
- School of Life Science and Technology, Southeast University, 2 Sipailou, Nanjing, China.
| | - Weimin Mao
- Key laboratory on Diagnosis and Treatment Technology on Thoracic Cancer, Zhejiang Cancer Research Institute, 38 Guangji Road, Hangzhou, China.
- The Second Clinical Medical College of Wenzhou Medical University, 268 West Xueyue Road, Wenzhou, China.
- Department of Thoracic Oncology, Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, 1 Banshan East Road, Hangzhou, China.
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2
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Choudhary K, Kupiec M. The cohesin complex of yeasts: sister chromatid cohesion and beyond. FEMS Microbiol Rev 2023; 47:6825453. [PMID: 36370456 DOI: 10.1093/femsre/fuac045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Each time a cell divides, it needs to duplicate the genome and then separate the two copies. In eukaryotes, which usually have more than one linear chromosome, this entails tethering the two newly replicated DNA molecules, a phenomenon known as sister chromatid cohesion (SCC). Cohesion ensures proper chromosome segregation to separate poles during mitosis. SCC is achieved by the presence of the cohesin complex. Besides its canonical function, cohesin is essential for chromosome organization and DNA damage repair. Surprisingly, yeast cohesin is loaded in G1 before DNA replication starts but only acquires its binding activity during DNA replication. Work in microorganisms, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe has greatly contributed to the understanding of cohesin composition and functions. In the last few years, much progress has been made in elucidating the role of cohesin in chromosome organization and compaction. Here, we discuss the different functions of cohesin to ensure faithful chromosome segregation and genome stability during the mitotic cell division in yeast. We describe what is known about its composition and how DNA replication is coupled with SCC establishment. We also discuss current models for the role of cohesin in chromatin loop extrusion and delineate unanswered questions about the activity of this important, conserved complex.
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Affiliation(s)
- Karan Choudhary
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Martin Kupiec
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Ramat Aviv 69978, Israel
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3
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Osadska M, Selicky T, Kretova M, Jurcik J, Sivakova B, Cipakova I, Cipak L. The Interplay of Cohesin and RNA Processing Factors: The Impact of Their Alterations on Genome Stability. Int J Mol Sci 2022; 23:3939. [PMID: 35409298 PMCID: PMC8999970 DOI: 10.3390/ijms23073939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 12/01/2022] Open
Abstract
Cohesin, a multi-subunit protein complex, plays important roles in sister chromatid cohesion, DNA replication, chromatin organization, gene expression, transcription regulation, and the recombination or repair of DNA damage. Recently, several studies suggested that the functions of cohesin rely not only on cohesin-related protein-protein interactions, their post-translational modifications or specific DNA modifications, but that some RNA processing factors also play an important role in the regulation of cohesin functions. Therefore, the mutations and changes in the expression of cohesin subunits or alterations in the interactions between cohesin and RNA processing factors have been shown to have an impact on cohesion, the fidelity of chromosome segregation and, ultimately, on genome stability. In this review, we provide an overview of the cohesin complex and its role in chromosome segregation, highlight the causes and consequences of mutations and changes in the expression of cohesin subunits, and discuss the RNA processing factors that participate in the regulation of the processes involved in chromosome segregation. Overall, an understanding of the molecular determinants of the interplay between cohesin and RNA processing factors might help us to better understand the molecular mechanisms ensuring the integrity of the genome.
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Affiliation(s)
- Michaela Osadska
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Miroslava Kretova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia;
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovakia; (M.O.); (T.S.); (M.K.); (J.J.)
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4
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Grabowska A, Sas-Nowosielska H, Wojtas B, Holm-Kaczmarek D, Januszewicz E, Yushkevich Y, Czaban I, Trzaskoma P, Krawczyk K, Gielniewski B, Martin-Gonzalez A, Filipkowski RK, Olszynski KH, Bernas T, Szczepankiewicz AA, Sliwinska MA, Kanhema T, Bramham CR, Bokota G, Plewczynski D, Wilczynski GM, Magalska A. Activation-induced chromatin reorganization in neurons depends on HDAC1 activity. Cell Rep 2022; 38:110352. [PMID: 35172152 DOI: 10.1016/j.celrep.2022.110352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 11/09/2021] [Accepted: 01/19/2022] [Indexed: 11/23/2022] Open
Abstract
Spatial chromatin organization is crucial for transcriptional regulation and might be particularly important in neurons since they dramatically change their transcriptome in response to external stimuli. We show that stimulation of neurons causes condensation of large chromatin domains. This phenomenon can be observed in vitro in cultured rat hippocampal neurons as well as in vivo in the amygdala and hippocampal neurons. Activity-induced chromatin condensation is an active, rapid, energy-dependent, and reversible process. It involves calcium-dependent pathways but is independent of active transcription. It is accompanied by the redistribution of posttranslational histone modifications and rearrangements in the spatial organization of chromosome territories. Moreover, it leads to the reorganization of nuclear speckles and active domains located in their proximity. Finally, we find that the histone deacetylase HDAC1 is the key regulator of this process. Our results suggest that HDAC1-dependent chromatin reorganization constitutes an important level of transcriptional regulation in neurons.
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Affiliation(s)
- Agnieszka Grabowska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Hanna Sas-Nowosielska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Dagmara Holm-Kaczmarek
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Elzbieta Januszewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Yana Yushkevich
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Iwona Czaban
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Pawel Trzaskoma
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Katarzyna Krawczyk
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Bartlomiej Gielniewski
- Laboratory of Sequencing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Ana Martin-Gonzalez
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, San Juan de Alicante, 03550 Alicante, Spain
| | - Robert Kuba Filipkowski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Krzysztof Hubert Olszynski
- Behavior and Metabolism Research Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Tytus Bernas
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland; Department of Anatomy and Neurology, VCU School of Medicine, Richmond, VA 23284, USA
| | - Andrzej Antoni Szczepankiewicz
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Malgorzata Alicja Sliwinska
- Laboratory of Imaging Tissue Structure and Function, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Tambudzai Kanhema
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5020 Bergen, Norway
| | - Clive R Bramham
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway; KG Jebsen Centre for Neuropsychiatric Disorders, University of Bergen, 5020 Bergen, Norway
| | - Grzegorz Bokota
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; Institute of Informatics, University of Warsaw, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland
| | - Grzegorz Marek Wilczynski
- Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Adriana Magalska
- Laboratory of Molecular Basis of Cell Motility, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland.
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5
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Parenti I, Kaiser FJ. Cornelia de Lange Syndrome as Paradigm of Chromatinopathies. Front Neurosci 2021; 15:774950. [PMID: 34803598 PMCID: PMC8603810 DOI: 10.3389/fnins.2021.774950] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
Chromatinopathies can be defined as a class of neurodevelopmental disorders caused by mutations affecting proteins responsible for chromatin remodeling and transcriptional regulation. The resulting dysregulation of gene expression favors the onset of a series of clinical features such as developmental delay, intellectual disability, facial dysmorphism, and behavioral disturbances. Cornelia de Lange syndrome (CdLS) is a prime example of a chromatinopathy. It is caused by mutations affecting subunits or regulators of the cohesin complex, a multisubunit protein complex involved in various molecular mechanisms such as sister chromatid cohesion, transcriptional regulation and formation of topologically associated domains. However, disease-causing variants in non-cohesin genes with overlapping functions have also been described in association with CdLS. Notably, the majority of these genes had been previously found responsible for distinct neurodevelopmental disorders that also fall within the category of chromatinopathies and are frequently considered as differential diagnosis for CdLS. In this review, we provide a systematic overview of the current literature to summarize all mutations in non-cohesin genes identified in association with CdLS phenotypes and discuss about the interconnection of proteins belonging to the chromatinopathies network.
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Affiliation(s)
- Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
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6
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Spreafico M, Mangano E, Mazzola M, Consolandi C, Bordoni R, Battaglia C, Bicciato S, Marozzi A, Pistocchi A. The Genome-Wide Impact of Nipblb Loss-of-Function on Zebrafish Gene Expression. Int J Mol Sci 2020; 21:E9719. [PMID: 33352756 PMCID: PMC7766774 DOI: 10.3390/ijms21249719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/31/2022] Open
Abstract
Transcriptional changes normally occur during development but also underlie differences between healthy and pathological conditions. Transcription factors or chromatin modifiers are involved in orchestrating gene activity, such as the cohesin genes and their regulator NIPBL. In our previous studies, using a zebrafish model for nipblb knockdown, we described the effect of nipblb loss-of-function in specific contexts, such as central nervous system development and hematopoiesis. However, the genome-wide transcriptional impact of nipblb loss-of-function in zebrafish embryos at diverse developmental stages remains under investigation. By RNA-seq analyses in zebrafish embryos at 24 h post-fertilization, we examined genome-wide effects of nipblb knockdown on transcriptional programs. Differential gene expression analysis revealed that nipblb loss-of-function has an impact on gene expression at 24 h post fertilization, mainly resulting in gene inactivation. A similar transcriptional effect has also been reported in other organisms, supporting the use of zebrafish as a model to understand the role of Nipbl in gene regulation during early vertebrate development. Moreover, we unraveled a connection between nipblb-dependent differential expression and gene expression patterns of hematological cell populations and AML subtypes, enforcing our previous evidence on the involvement of NIPBL-related transcriptional dysregulation in hematological malignancies.
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Affiliation(s)
- Marco Spreafico
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Eleonora Mangano
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Mara Mazzola
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Roberta Bordoni
- Institute of Biomedical Technologies, Italian National Research Council (ITB-CNR), Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (E.M.); (C.C.); (R.B.)
| | - Cristina Battaglia
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio-Emilia, Via G. Campi 287, 41125 Modena, Italy;
| | - Anna Marozzi
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
| | - Anna Pistocchi
- Department of Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, LITA, Via Fratelli Cervi 93, Segrate, 20090 Milano, Italy; (M.S.); (M.M.); (C.B.); (A.M.)
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7
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Zhang S, Zhou Y, Wang Q, Donahue K, Feng J, Yao Y, Chen A, Li X, Hong L. Nipped-B-like Protein Sensitizes Esophageal Squamous Cell Carcinoma Cells to Cisplatin via Upregulation of PUMA. Technol Cancer Res Treat 2020; 19:1533033820960726. [PMID: 33034274 PMCID: PMC7592177 DOI: 10.1177/1533033820960726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nipped-B-like protein plays a pivotal role as a cohesin loading factor in the segregation of chromosomes when cells divide. Accumulating evidence indicates that alterations of this protein are involved in human carcinogenesis, especially in the regulation of chemotherapeutic drug response. However, the role of Nipped-B-like protein in esophageal squamous cell carcinoma remains unknown. In this study, we investigated the relevance of Nipped-B-like protein in the regulation of cisplatin sensitivity in esophageal squamous cell carcinoma. Ectopic expression of Nipped-B-like protein inhibited the growth of COLO-680N cells with low endogenous expression levels of Nipped-B-like protein, and increased sensitivity to cisplatin, a commonly used chemotherapy drug for patients with esophageal squamous cell carcinoma. In contrast, loss of Nipped-B-like protein stimulated the growth of EC9706 and Eca-109 cells with high levels of the protein, and resulted in resistance to cisplatin. P53-upregulated modulator of apoptosis, which is essential in the modulation of cisplatin sensitivity in a variety of cancers, acts as a downstream effector of Nipped-B-like protein. Restoration of this pro-apoptotic protein in Nipped-B-like protein-overexpressing esophageal squamous cell carcinoma cells effectively increased cisplatin sensitivity. Conversely, the silencing of P53-upregulated modulator of apoptosis in Nipped-B-like protein-depleted esophageal squamous cell carcinoma rendered cells resistant to cisplatin. Moreover, Nipped-B-like protein could bind directly to the promoter region of P53-upregulated modulator of apoptosis. In summary, our study addresses the involvement of Nipped-B-like protein in the development of esophageal squamous cell carcinoma, and the modulation of cisplatin sensitivity via regulation of P53-upregulated modulator of apoptosis.
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Affiliation(s)
- Shengjie Zhang
- Experimental Research Center, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang Province, China.,Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Hangzhou, Zhejiang Province, China
| | - Yun Zhou
- Experimental Research Center, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang Province, China.,Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Hangzhou, Zhejiang Province, China
| | - Qinchuan Wang
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Kristine Donahue
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Jianguo Feng
- Experimental Research Center, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang Province, China.,Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Hangzhou, Zhejiang Province, China
| | - Yinli Yao
- Department of Medicine, The Children's Hospital, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Aiping Chen
- Experimental Research Center, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang Province, China.,Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Hangzhou, Zhejiang Province, China
| | - Xia Li
- Experimental Research Center, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang Province, China.,Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Hangzhou, Zhejiang Province, China
| | - Lianlian Hong
- Experimental Research Center, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang Province, China.,Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Hangzhou, Zhejiang Province, China
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8
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Thanh DC, Ngoc CTB, Nguyen NL, Vu CD, Tung NV, Nguyen HH. De novo NIPBL Mutations in Vietnamese Patients with Cornelia de Lange Syndrome. ACTA ACUST UNITED AC 2020; 56:medicina56020076. [PMID: 32074972 PMCID: PMC7073647 DOI: 10.3390/medicina56020076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 01/29/2020] [Accepted: 02/10/2020] [Indexed: 11/16/2022]
Abstract
Cornelia de Lange Syndrome (CdLS) is a rare congenital genetic disease causing abnormal unique facial phenotypes, several defects in organs and body parts, and mental disorder or intellectual disorder traits. Main causes of CdLS have been reported as variants in cohesin complex genes, in which mutations in the NIPBL gene have been estimated to account for up to 80%. Our study included three Vietnamese patients with typical CdLS phenotypes. Whole exome sequencing revealed two known heterozygous mutations c.6697G>A (p.Val2233Met) and c.2602C>T (p.Arg868X), and a novel heterozygous mutation c.4504delG (p.Val1502fsX87) in the NIPBL gene of the three patients. In silico analyses of the identified mutations predicted possible damaging and truncating effects on the NIPBL protein. Inherited analyses in the patients' families showed that all of the mutations are de novo. Our results lead a definitive diagnosis of patients with CdLS and expand the spectrum of mutations in the NIPBL gene. These findings also confirm whole exome sequencing is an efficient tool for genetic screening of CdLS.
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Affiliation(s)
- Duong Chi Thanh
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam; (D.C.T.); (N.-L.N.); (N.V.T.)
| | - Can Thi Bich Ngoc
- Center for Rare Diseases and Newborn Screening, Department of Endocrinology, Metabolism and Genetics, Vietnam National Hospital of Pediatrics, 18/879 La Thanh str., Dong Da, Hanoi 100000, Vietnam; (C.T.B.N.); (C.D.V.)
| | - Ngoc-Lan Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam; (D.C.T.); (N.-L.N.); (N.V.T.)
| | - Chi Dung Vu
- Center for Rare Diseases and Newborn Screening, Department of Endocrinology, Metabolism and Genetics, Vietnam National Hospital of Pediatrics, 18/879 La Thanh str., Dong Da, Hanoi 100000, Vietnam; (C.T.B.N.); (C.D.V.)
| | - Nguyen Van Tung
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam; (D.C.T.); (N.-L.N.); (N.V.T.)
| | - Huy Hoang Nguyen
- Institute of Genome Research, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet str., Cau Giay, Hanoi 100000, Vietnam; (D.C.T.); (N.-L.N.); (N.V.T.)
- Correspondence: ; Tel.: +84-243-7918012
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9
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Sarogni P, Palumbo O, Servadio A, Astigiano S, D'Alessio B, Gatti V, Cukrov D, Baldari S, Pallotta MM, Aretini P, Dell'Orletta F, Soddu S, Carella M, Toietta G, Barbieri O, Fontanini G, Musio A. Overexpression of the cohesin-core subunit SMC1A contributes to colorectal cancer development. J Exp Clin Cancer Res 2019; 38:108. [PMID: 30823889 PMCID: PMC6397456 DOI: 10.1186/s13046-019-1116-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/21/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Cancer cells are characterized by chromosomal instability (CIN) and it is thought that errors in pathways involved in faithful chromosome segregation play a pivotal role in the genesis of CIN. Cohesin forms a large protein ring that binds DNA strands by encircling them. In addition to this central role in chromosome segregation, cohesin is also needed for DNA repair, gene transcription regulation and chromatin architecture. Though mutations in both cohesin and cohesin-regulator genes have been identified in many human cancers, the contribution of cohesin to cancer development is still under debate. METHODS Normal mucosa, early adenoma, and carcinoma samples deriving from 16 subjects affected by colorectal cancer (CRC) were analyzed by OncoScan for scoring both chromosome gains and losses (CNVs) and loss of heterozygosity (LOH). Then the expression of SMC1A was analyzed by immunochemistry in 66 subjects affected by CRC. The effects of SMC1A overexpression and mutated SMC1A were analyzed in vivo using immunocompromised mouse models. Finally, we measured global gene expression profiles in induced-tumors by RNA-seq. RESULTS Here we showed that SMC1A cohesin core gene was present as extra-copies, mutated, and overexpressed in human colorectal carcinomas. We then demonstrated that cohesin overexpression led to the development of aggressive cancers in immunocompromised mice through gene expression dysregulation. CONCLUSION Collectively, these results support a role of defective cohesin in the development of human colorectal cancer.
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Affiliation(s)
- Patrizia Sarogni
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Orazio Palumbo
- Division of Medical Genetics, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Adele Servadio
- Division of Pathology, Department of Surgery, University of Pisa, Pisa, Italy
| | - Simonetta Astigiano
- IRCCS Ospedale Policlinico San Martino, Department of Translational Oncology, Genoa, Italy
| | - Barbara D'Alessio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Veronica Gatti
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy.,Present address: Institute of Cell Biology and Neurobiology, National Research Council (CNR), Monterotondo, Italy
| | - Dubravka Cukrov
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Silvia Baldari
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Maria Michela Pallotta
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy
| | - Paolo Aretini
- Fondazione Pisana per la Scienza ONLUS, San Giuliano Terme, Italy
| | - Felice Dell'Orletta
- Institute for Computational Linguistics (ILC) "A. Zampolli", National Research Council (CNR), Pisa, Italy
| | - Silvia Soddu
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Massimo Carella
- Division of Medical Genetics, IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Gabriele Toietta
- IRCCS Regina Elena National Cancer Institute, Department of Research, Advanced Diagnostic and Technological Innovation, Rome, Italy
| | - Ottavia Barbieri
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Gabriella Fontanini
- Division of Pathology, Department of Surgery, University of Pisa, Pisa, Italy
| | - Antonio Musio
- Institute for Genetic and Biomedical Research (IRGB), National Research Council (CNR), Via Moruzzi, 1, 56124, Pisa, Italy.
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Krawczynska N, Wierzba J, Jasiecki J, Wasag B. Molecular characterization of two novel intronic variants of NIPBL gene detected in unrelated Cornelia de Lange syndrome patients. BMC MEDICAL GENETICS 2019; 20:1. [PMID: 30606125 PMCID: PMC6318863 DOI: 10.1186/s12881-018-0738-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 12/21/2018] [Indexed: 11/17/2022]
Abstract
Background Cornelia de Lange syndrome (CdLS), a rare, multisystemic disorder, has been linked to genetic alterations in NIPBL, SMC1A, SMC3, HDAC8, and RAD21 genes. Approximately 60% of CdLS patients harbor various NIPBL variants. Genetic changes predicted to affect NIPBL gene splicing represent 15% of all NIPBL genetic abnormalities. Yet, only a few studies have investigated the molecular consequences of such variants. Case presentation This study reports two novel, intronic NIPBL genetic variants in unrelated CdLS patients with the characteristic phenotype. A c.6954 + 3A > C substitution and a c.5862 + 1delG deletion were identified, one of each, in a 6 year-old boy and 39 month-old girl. Further studies confirmed that both variants introduce premature termination codons, resulting in the formation of truncated proteins p.(Ser2255LeufsTer20) and p.(Leu1955Ter), respectively. Conclusion Single nucleotide alterations located within the conserved splice-donor site of intronic regions of the NIPBL gene can give rise to a premature termination of the translation and cause significant changes in the sequence of mRNA transcripts and NIPBL protein structure and function. The latter underline development of Cornelia de Lange syndrome phenotype. Electronic supplementary material The online version of this article (10.1186/s12881-018-0738-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Natalia Krawczynska
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland.,Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Jolanta Wierzba
- Department of Pediatrics, Hematology and Oncology, Medical University of Gdansk, Gdansk, Poland.,Department of General Nursery, Medical University of Gdansk, Gdansk, Poland
| | - Jacek Jasiecki
- Department of Pharmaceutical Microbiology, Medical University of Gdansk, Gdansk, Poland
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland. .,Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland.
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11
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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: 18] [Impact Index Per Article: 3.0] [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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12
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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: 13] [Impact Index Per Article: 2.2] [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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13
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Hirayama T, Yagi T. Regulation of clustered protocadherin genes in individual neurons. Semin Cell Dev Biol 2017; 69:122-130. [PMID: 28591566 DOI: 10.1016/j.semcdb.2017.05.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 02/06/2023]
Abstract
Individual neurons are basic functional units in the complex system of the brain. One aspect of neuronal individuality is generated by stochastic and combinatorial expression of diverse clustered protocadherins (Pcdhs), encoded by the Pcdha, Pcdhb, and Pcdhg gene clusters, that are critical for several aspects of neural circuit formation. Each clustered Pcdh gene has its own promoter containing conserved sequences and is transcribed by a promoter choice mechanism involving interaction between the promoter and enhancers. A CTCF/Cohesin complex induces this interaction by configuration of DNA-looping in the chromatin structure. At the same time, the semi-stochastic expression of clustered Pcdh genes is regulated in individual neurons by DNA methylation: the methyltransferase Dnmt3b regulates methylation state of individual clustered Pcdh genes during early embryonic stages prior to the establishment of neural stem cells. Several other factors, including Smchd1, also contribute to the regulation of clustered Pcdh gene expression. In addition, psychiatric diseases and early life experiences of individuals can influence expression of clustered Pcdh genes in the brain, through epigenetic alterations. Clustered Pcdh gene expression is thus a significant and highly regulated step in establishing neuronal individuality and generating functional neural circuits in the brain.
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Affiliation(s)
- Teruyoshi Hirayama
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Yagi
- KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
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14
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Chao WCH, Murayama Y, Muñoz S, Jones AW, Wade BO, Purkiss AG, Hu XW, Borg A, Snijders AP, Uhlmann F, Singleton MR. Structure of the cohesin loader Scc2. Nat Commun 2017; 8:13952. [PMID: 28059076 PMCID: PMC5227109 DOI: 10.1038/ncomms13952] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/16/2016] [Indexed: 01/07/2023] Open
Abstract
The functions of cohesin are central to genome integrity, chromosome organization and transcription regulation through its prevention of premature sister-chromatid separation and the formation of DNA loops. The loading of cohesin onto chromatin depends on the Scc2-Scc4 complex; however, little is known about how it stimulates the cohesion-loading activity. Here we determine the large 'hook' structure of Scc2 responsible for catalysing cohesin loading. We identify key Scc2 surfaces that are crucial for cohesin loading in vivo. With the aid of previously determined structures and homology modelling, we derive a pseudo-atomic structure of the full-length Scc2-Scc4 complex. Finally, using recombinantly purified Scc2-Scc4 and cohesin, we performed crosslinking mass spectrometry and interaction assays that suggest Scc2-Scc4 uses its modular structure to make multiple contacts with cohesin.
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Affiliation(s)
- William C. H. Chao
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Yasuto Murayama
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew W. Jones
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Benjamin O. Wade
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrew G. Purkiss
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Xiao-Wen Hu
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Aaron Borg
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ambrosius P. Snijders
- Protein Analysis and Proteomics Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Martin R. Singleton
- Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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15
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Identification and Functional Characterization of Two Intronic NIPBL Mutations in Two Patients with Cornelia de Lange Syndrome. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8742939. [PMID: 26925417 PMCID: PMC4746300 DOI: 10.1155/2016/8742939] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 11/16/2015] [Indexed: 12/03/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a rare genetically heterogeneous disorder with a high phenotypic variability including mental retardation, developmental delay, and limb malformations. The genetic causes in about 30% of patients with CdLS are still unknown. We report on the functional characterization of two intronic NIPBL mutations in two patients with CdLS that do not affect a conserved splice-donor or acceptor site. Interestingly, mRNA analyses showed aberrantly spliced transcripts missing exon 28 or 37, suggesting the loss of the branch site by the c.5329-15A>G transition and a disruption of the polypyrimidine by the c.6344del(-13)_(-8) deletion. While the loss of exon 28 retains the reading frame of the NIBPL transcript resulting in a shortened protein, the loss of exon 37 shifts the reading frame with the consequence of a premature stop of translation. Subsequent quantitative PCR analysis demonstrated a 30% decrease of the total NIPBL mRNA levels associated with the frameshift transcript. Consistent with our results, this patient shows a more severe phenotype compared to the patient with the aberrant transcript that retains its reading frame. Thus, intronic variants identified by sequencing analysis in CdLS diagnostics should carefully be examined before excluding them as nonrelevant to disease.
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16
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Yuen KC, Xu B, Krantz ID, Gerton JL. NIPBL Controls RNA Biogenesis to Prevent Activation of the Stress Kinase PKR. Cell Rep 2015; 14:93-102. [PMID: 26725122 PMCID: PMC4904785 DOI: 10.1016/j.celrep.2015.12.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/27/2015] [Accepted: 11/23/2015] [Indexed: 12/30/2022] Open
Abstract
NIPBL, a cohesin loader, has been implicated in transcriptional control and genome organization. Mutations in NIPBL, cohesin, and its deacetylase HDAC8 result in Cornelia de Lange syndrome. We report activation of the RNA-sensing kinase PKR in human lymphoblastoid cell lines carrying NIPBL or HDAC8 mutations, but not SMC1A or SMC3 mutations. PKR activation can be triggered by unmodified RNAs. Gene expression profiles in NIPBL-deficient lymphoblastoid cells and mouse embryonic stem cells reveal lower expression of genes involved in RNA processing and modification. NIPBL mutant lymphoblastoid cells show reduced proliferation and protein synthesis with increased apoptosis, all of which are partially reversed by a PKR inhibitor. Non-coding RNAs from an NIPBL mutant line had less m6A modification and activated PKR activity in vitro. This study provides insight into the molecular pathology of Cornelia de Lange syndrome by establishing a relationship between NIPBL and HDAC8 mutations and PKR activation.
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Affiliation(s)
- Kobe C Yuen
- Stowers Institute for Medical Research (SIMR), 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Baoshan Xu
- Stowers Institute for Medical Research (SIMR), 1000 East 50(th) Street, Kansas City, MO 64110, USA
| | - Ian D Krantz
- Children's Hospital of Philadelphia, Division of Human Genetics, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research (SIMR), 1000 East 50(th) Street, Kansas City, MO 64110, USA; University of Kansas School of Medicine, Department of Biochemistry and Molecular Biology, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA.
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17
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Zakari M, Yuen K, Gerton JL. Etiology and pathogenesis of the cohesinopathies. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2015; 4:489-504. [PMID: 25847322 PMCID: PMC6680315 DOI: 10.1002/wdev.190] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 01/12/2023]
Abstract
Cohesin is a chromosome-associated protein complex that plays many important roles in chromosome function. Genetic screens in yeast originally identified cohesin as a key regulator of chromosome segregation. Subsequently, work by various groups has identified cohesin as critical for additional processes such as DNA damage repair, insulator function, gene regulation, and chromosome condensation. Mutations in the genes encoding cohesin and its accessory factors result in a group of developmental and intellectual impairment diseases termed 'cohesinopathies.' How mutations in cohesin genes cause disease is not well understood as precocious chromosome segregation is not a common feature in cells derived from patients with these syndromes. In this review, the latest findings concerning cohesin's function in the organization of chromosome structure and gene regulation are discussed. We propose that the cohesinopathies are caused by changes in gene expression that can negatively impact translation. The similarities and differences between cohesinopathies and ribosomopathies, diseases caused by defects in ribosome biogenesis, are discussed. The contribution of cohesin and its accessory proteins to gene expression programs that support translation suggests that cohesin provides a means of coupling chromosome structure with the translational output of cells.
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Affiliation(s)
- Musinu Zakari
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Universite Pierre et Marie Curie, Paris, France
| | - Kobe Yuen
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS, USA
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18
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Xu W, Ying Y, Shan L, Feng J, Zhang S, Gao Y, Xu X, Yao Y, Zhu C, Mao W. Enhanced expression of cohesin loading factor NIPBL confers poor prognosis and chemotherapy resistance in non-small cell lung cancer. J Transl Med 2015; 13:153. [PMID: 25963978 PMCID: PMC4438579 DOI: 10.1186/s12967-015-0503-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 04/22/2015] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND NIPBL, the sister chromatid cohesion 2 (SCC2) human homolog, is a cohesin loading factor which is essential for deposition of cohesin onto the sister chromatid. Recent studies have shown that NIPBL contribute to sister chromatid cohesion and plays a critical role in development, DNA repair, and gene regulation. In this study, we measured the expression of NIPBL in clinical non-small cell lung cancer specimens, and determined its effects on cellular processes and chemosensitivity in vitro. METHODS NIPBL immunohistochemistry was performed on 123 lung adenocarcinoma samples. Through knockdown of NIPBL protein expression, non-small cell lung cancer cell lines were used to test the potential involvement of NIPBL silencing on cell proliferation, migration, invasion, and apoptosis. Chemosensitivity was assessed with clonogenic assays, and chromatin immunoprecipitation assays were performed to analyze the relationship between NIPBL and signal transducers and activators of transcription 3 (STAT3). RESULTS Immunohistochemical analysis showed that high expression of NIPBL was strongly correlated with poor prognosis, tumor differentiation, and lymph node metastasis. Survival analysis further indicated that NIPBL expression was a potential prognostic factor for non-small cell lung cancer. Knockdown of NIPBL in non-small cell lung cancer cell lines significantly reduced cellular proliferation, migration, and invasion, and enhanced cellular apoptosis and sensitivity to cisplatin, paclitaxel, and gemcitabine hydrochloride. NIPBL bound to the promoter region of the STAT3 gene, directly regulating the expression of STAT3. CONCLUSIONS These data suggested that NIPBL played a significant role in lung carcinogenesis. NIPBL expression conferred poor prognosis and resistance to chemotherapy in non-small cell lung cancer, suggesting that NIPBL may be a novel therapeutic target.
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Affiliation(s)
- Weizhen Xu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Yinyin Ying
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Lihong Shan
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Jianguo Feng
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Shengjie Zhang
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Yun Gao
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Xiaoling Xu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Yinli Yao
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Chihong Zhu
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
| | - Weimin Mao
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Cancer Research Institute, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
- Department of Thoracic Surgery, Zhejiang Cancer Hospital, 38, Guangji Load, Hangzhou, Zhejiang, 310022, China.
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Upadhyay M, Priya GK, Ramesh P, Madhavi MB, Rath S, Bal V, George A, Vaidya T. CD40 signaling drives B lymphocytes into an intermediate memory-like state, poised between naïve and plasma cells. J Cell Physiol 2014; 229:1387-96. [PMID: 24482285 DOI: 10.1002/jcp.24572] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 01/16/2014] [Indexed: 01/18/2023]
Abstract
Immunological memory comprising of antigen-specific B and T cells contributes to the acquisition of long-term resistance to pathogens. Interactions between CD40 on B cells and CD40L on T cells are responsible for several aspects of acquired immune responses including generation of memory B cells. In order to gain insights into events leading to memory B cell formation, we analyzed the genome-wide expression profile of murine naive B cells stimulated in the presence of anti-CD40. We have identified over 8,000 genes whose expression is altered minimally 1.5-fold at least at one time point over a 3-day time course. The array analysis indicates that changes in expression level of maximum number of these genes occur within 24 h of anti-CD40 treatment. In parallel, we have studied the events following CD40 ligation by examining the expression of known regulators of naive B cell to plasma cell transition, including Pax5 and BLIMP1. The expression profile of these regulatory genes indicates firstly, that CD40 signaling activates naïve B cells to a phenotype that is intermediate between the naive and plasma cell stages of the B cell differentiation. Secondly, the major known regulator of plasma cell differentiation, BLIMP1, gets irreversibly downregulated upon anti-CD40 treatment. Additionally, our data reveal that CD40 signaling mediated BLIMP1 downregulation occurs by non-Pax5/non-Bcl6 dependent mechanisms, indicating novel mechanisms at work that add to the complexity of understanding of B cell master regulatory molecules like BLIMP1 and Pax5.
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Affiliation(s)
- Mala Upadhyay
- Centre for Cellular and Molecular Biology, Hyderabad, 500007, India
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20
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Functional characterization of NIPBL physiological splice variants and eight splicing mutations in patients with Cornelia de Lange syndrome. Int J Mol Sci 2014; 15:10350-64. [PMID: 24918291 PMCID: PMC4100155 DOI: 10.3390/ijms150610350] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/12/2014] [Accepted: 05/20/2014] [Indexed: 02/05/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a congenital developmental disorder characterized by distinctive craniofacial features, growth retardation, cognitive impairment, limb defects, hirsutism, and multisystem involvement. Mutations in five genes encoding structural components (SMC1A, SMC3, RAD21) or functionally associated factors (NIPBL, HDAC8) of the cohesin complex have been found in patients with CdLS. In about 60% of the patients, mutations in NIPBL could be identified. Interestingly, 17% of them are predicted to change normal splicing, however, detailed molecular investigations are often missing. Here, we report the first systematic study of the physiological splicing of the NIPBL gene, that would reveal the identification of four new splicing isoforms ΔE10, ΔE12, ΔE33,34, and B’. Furthermore, we have investigated nine mutations affecting splice-sites in the NIPBL gene identified in twelve CdLS patients. All mutations have been examined on the DNA and RNA level, as well as by in silico analyses. Although patients with mutations affecting NIPBL splicing show a broad clinical variability, the more severe phenotypes seem to be associated with aberrant transcripts resulting in a shift of the reading frame.
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21
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Woodman J, Fara T, Dzieciatkowska M, Trejo M, Luong N, Hansen KC, Megee PC. Cell cycle-specific cleavage of Scc2 regulates its cohesin deposition activity. Proc Natl Acad Sci U S A 2014; 111:7060-5. [PMID: 24778232 PMCID: PMC4024903 DOI: 10.1073/pnas.1321722111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sister chromatid cohesion (SCC), efficient DNA repair, and the regulation of some metazoan genes require the association of cohesins with chromosomes. Cohesins are deposited by a conserved heterodimeric loading complex composed of the Scc2 and Scc4 proteins in Saccharomyces cerevisiae, but how the Scc2/Scc4 deposition complex regulates the spatiotemporal association of cohesin with chromosomes is not understood. We examined Scc2 chromatin association during the cell division cycle and found that the affinity of Scc2 for chromatin increases biphasically during the cell cycle, increasing first transiently in late G1 phase and then again later in G2/M. Inactivation of Scc2 following DNA replication reduces cellular viability, suggesting that this post S-phase increase in Scc2 chromatin binding affinity is biologically relevant. Interestingly, high and low Scc2 chromatin binding levels correlate strongly with the presence of full-length or amino-terminally cleaved forms of Scc2, respectively, and the appearance of the cleaved Scc2 species is promoted in vitro either by treatment with specific cell cycle-staged cellular extracts or by dephosphorylation. Importantly, Scc2 cleavage eliminates Scc2-Scc4 physical interactions, and an scc2 truncation mutant that mimics in vivo Scc2 cleavage is defective for cohesin deposition. These observations suggest a previously unidentified mechanism for the spatiotemporal regulation of cohesin association with chromosomes through cell cycle regulation of Scc2 cohesin deposition activity by Scc2 dephosphorylation and cleavage.
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Affiliation(s)
- Julie Woodman
- Molecular Biology Program, andDepartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Tyler Fara
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Michael Trejo
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Nancy Luong
- Molecular Biology Program, andDepartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
| | - Paul C Megee
- Molecular Biology Program, andDepartment of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045
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22
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Smith TG, Laval S, Chen F, Rock MJ, Strachan T, Peters H. Neural crest cell-specific inactivation ofNipblorMau2during mouse development results in a late onset of craniofacial defects. Genesis 2014; 52:687-94. [DOI: 10.1002/dvg.22780] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 03/24/2014] [Accepted: 04/02/2014] [Indexed: 01/21/2023]
Affiliation(s)
- Terence Gordon Smith
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway; Newcastle upon Tyne NE1 3BZ United Kingdom
| | - Steve Laval
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway; Newcastle upon Tyne NE1 3BZ United Kingdom
| | - Fangli Chen
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway; Newcastle upon Tyne NE1 3BZ United Kingdom
| | - Matthew James Rock
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway; Newcastle upon Tyne NE1 3BZ United Kingdom
| | - Tom Strachan
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway; Newcastle upon Tyne NE1 3BZ United Kingdom
| | - Heiko Peters
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway; Newcastle upon Tyne NE1 3BZ United Kingdom
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23
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Zuin J, Franke V, van IJcken WFJ, van der Sloot A, Krantz ID, van der Reijden MIJA, Nakato R, Lenhard B, Wendt KS. A cohesin-independent role for NIPBL at promoters provides insights in CdLS. PLoS Genet 2014; 10:e1004153. [PMID: 24550742 PMCID: PMC3923681 DOI: 10.1371/journal.pgen.1004153] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 12/16/2013] [Indexed: 01/28/2023] Open
Abstract
The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture. The NIPBL protein is required for the loading of cohesin onto chromatin, but how and where cohesin is loaded in vertebrate cells is unclear. Heterozygous mutations of NIPBL were found in 50% of the cases of Cornelia de Lange Syndrome (CdLS), a human developmental syndrome with a complex phenotype. However, no defects in the mitotic function of cohesin have been observed so far and the links between NIPBL mutations and the observed developmental defects are unclear. We show that NIPBL binds to chromatin in somatic cells with a different timing than cohesin. Further, we observe that high-affinity NIPBL binding sites localize to different regions than cohesin and almost exclusively to the promoters of active genes. NIPBL or cohesin knockdown reduce transcription of these genes differently, suggesting a cohesin-independent role of NIPBL for transcription. Motif analysis and comparison to published data show that NIPBL co-localizes with a specific set of other transcription factors. In cells derived from CdLS patients NIPBL binding levels are reduced and several of the NIPBL-bound genes have previously been observed to be mis-expressed in CdLS. In summary, our observations indicate that NIPBL mutations might cause developmental defects in different ways. First, defects of NIPBL might lead to cohesin-loading defects and thereby alter gene expression and second, NIPBL deficiency might affect genes directly via its role at the respective promoters.
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Affiliation(s)
- Jessica Zuin
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands
| | - Vedran Franke
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
| | | | | | - Ian D. Krantz
- The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Ryuichiro Nakato
- Laboratory of Genome Structure and Function, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan
| | - Boris Lenhard
- Computational Biology Unit, Uni Computing, Uni Research AS, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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24
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Lindgren E, Hägg S, Giordano F, Björkegren J, Ström L. Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break. Cell Cycle 2014; 13:3645-58. [PMID: 25483075 PMCID: PMC4612677 DOI: 10.4161/15384101.2014.964108] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 09/07/2014] [Indexed: 11/19/2022] Open
Abstract
Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding.
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Affiliation(s)
- Emma Lindgren
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm, Sweden
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics; Karolinska Institutet; Stockholm, Sweden
- Molecular Epidemiology and Science for Life Laboratory; Department of Medical Sciences; Uppsala University; Uppsala, Sweden
| | - Fosco Giordano
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm, Sweden
| | - Johan Björkegren
- Department of Medical Biochemistry and Biophysics; Vascular Biology Unit; Karolinska Institutet; Stockholm, Sweden
- Department of Medical Pathology and Forensic Medicine; University of Tartu; Tartu, Estonia
- Department of Genetics and Genomic Sciences; Icahn Institute for Genomics and Multiscale Biology; Icahn School of Medicine at Mount Sinai; New York, NY USA
| | - Lena Ström
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm, Sweden
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25
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Mannini L, Cucco F, Quarantotti V, Krantz ID, Musio A. Mutation spectrum and genotype-phenotype correlation in Cornelia de Lange syndrome. Hum Mutat 2013; 34:1589-96. [PMID: 24038889 PMCID: PMC3880228 DOI: 10.1002/humu.22430] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/20/2013] [Indexed: 12/22/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a clinically and genetically heterogeneous developmental disorder. Clinical features include growth retardation, intellectual disability, limb defects, typical facial dysmorphism, and other systemic involvement. The increased understanding of the genetic basis of CdLS has led to diagnostic improvement and expansion of the phenotype. Mutations in five genes (NIPBL, SMC1A, SMC3, RAD21, and HDAC8), all regulators or structural components of cohesin, have been identified. Approximately 60% of CdLS cases are due to NIPBL mutations, 5% caused by mutations in SMC1A, RAD21, and HDAC8 and one proband was found to carry a mutation in SMC3. To date, 311 CdLS-causing mutations are known including missense, nonsense, small deletions and insertions, splice site mutations, and genomic rearrangements. Phenotypic variability is seen both intra- and intergenically. This article reviews the spectrum of CdLS mutations with a particular emphasis on their correlation to the clinical phenotype.
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Affiliation(s)
- Linda Mannini
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Francesco Cucco
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Valentina Quarantotti
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Ian D. Krantz
- Division of Human Genetics, The Children’s Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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26
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Localisation of the SMC loading complex Nipbl/Mau2 during mammalian meiotic prophase I. Chromosoma 2013; 123:239-52. [PMID: 24287868 PMCID: PMC4031387 DOI: 10.1007/s00412-013-0444-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 10/28/2013] [Accepted: 11/05/2013] [Indexed: 12/25/2022]
Abstract
Evidence from lower eukaryotes suggests that the chromosomal associations of all the structural maintenance of chromosome (SMC) complexes, cohesin, condensin and Smc5/6, are influenced by the Nipbl/Mau2 heterodimer. Whether this function is conserved in mammals is currently not known. During mammalian meiosis, very different localisation patterns have been reported for the SMC complexes, and the localisation of Nipbl/Mau2 has just recently started to be investigated. Here, we show that Nipbl/Mau2 binds on chromosomal axes from zygotene to mid-pachytene in germ cells of both sexes. In spermatocytes, Nipbl/Mau2 then relocalises to chromocenters, whereas in oocytes it remains bound to chromosomal axes throughout prophase to dictyate arrest. The localisation pattern of Nipbl/Mau2, together with those seen for cohesin, condensin and Smc5/6 subunits, is consistent with a role as a loading factor for cohesin and condensin I, but not for Smc5/6. We also demonstrate that Nipbl/Mau2 localises next to Rad51 and γH2AX foci. NIPBL gene deficiencies are associated with the Cornelia de Lange syndrome in humans, and we find that haploinsufficiency of the orthologous mouse gene results in an altered distribution of double-strand breaks marked by γH2AX during prophase I. However, this is insufficient to result in major meiotic malfunctions, and the chromosomal associations of the synaptonemal complex proteins and the three SMC complexes appear cytologically indistinguishable in wild-type and Nipbl+/− spermatocytes.
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27
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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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28
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Abstract
Cohesin is a ring-form multifunctional protein complex, which was discovered during a search for molecules that keep sister chromatids together during segregation of chromosomes during cell division. In the past decade, a large number of results have also demonstrated a need for the cohesin complex in other crucial events in the life cycle of the cell, including DNA duplication, heterochromatin formation, DNA double-strand break repair, and control of gene expression. The dynamics of the cohesin ring are modulated by a number of accessory and regulatory proteins, known as cohesin cofactors. Loss of function of the cohesin complex is incompatible with life; however, mutations in the genes encoding for cohesin subunits and/or cohesin cofactors, which have very little or a null effect on chromosome segregation, represent a newly recognized class of human genetic disorders known as cohesinopathies. A number of genetic, biochemical, and clinical approaches, and importantly, animal models, can help us to determine the underlying mechanisms for these human diseases.
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Affiliation(s)
- José L Barbero
- Cellular and Molecular Biology Department, Biological Research Center, Madrid, Spain
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29
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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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30
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Rudra S, Skibbens RV. Cohesin codes - interpreting chromatin architecture and the many facets of cohesin function. J Cell Sci 2013; 126:31-41. [PMID: 23516328 PMCID: PMC3603509 DOI: 10.1242/jcs.116566] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Sister chromatid tethering is maintained by cohesin complexes that minimally contain Smc1, Smc3, Mcd1 and Scc3. During S-phase, chromatin-associated cohesins are modified by the Eco1/Ctf7 family of acetyltransferases. Eco1 proteins function during S phase in the context of replicated sister chromatids to convert chromatin-bound cohesins to a tethering-competent state, but also during G2 and M phases in response to double-stranded breaks to promote error-free DNA repair. Cohesins regulate transcription and are essential for ribosome biogenesis and complete chromosome condensation. Little is known, however, regarding the mechanisms through which cohesin functions are directed. Recent findings reveal that Eco1-mediated acetylation of different lysine residues in Smc3 during S phase promote either cohesion or condensation. Phosphorylation and SUMOylation additionally impact cohesin functions. Here, we posit the existence of a cohesin code, analogous to the histone code introduced over a decade ago, and speculate that there is a symphony of post-translational modifications that direct cohesins to function across a myriad of cellular processes. We also discuss evidence that outdate the notion that cohesion defects are singularly responsible for cohesion-mutant-cell inviability. We conclude by proposing that cohesion establishment is linked to chromatin formation.
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Affiliation(s)
| | - Robert V. Skibbens
- Department of Biological Sciences, 111 Research Drive, Lehigh University, Bethlehem, PA 18015, USA
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31
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Novara F, Alfei E, D'Arrigo S, Pantaleoni C, Beri S, Achille V, Sciacca FL, Giorda R, Zuffardi O, Ciccone R. 5p13 microduplication syndrome: a new case and better clinical definition of the syndrome. Eur J Med Genet 2012; 56:54-8. [PMID: 23085304 DOI: 10.1016/j.ejmg.2012.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 10/05/2012] [Indexed: 10/27/2022]
Abstract
Chromosome 5p13 duplication syndrome (OMIM #613174), a contiguous gene syndrome involving duplication of several genes on chromosome 5p13 including NIPBL (OMIM 608667), has been described in rare patients with developmental delay and learning disability, behavioral problems and peculiar facial dysmorphisms. 5p13 duplications described so far present with variable sizes, from 0.25 to 13.6 Mb, and contain a variable number of genes. Here we report another patient with 5p13 duplication syndrome including NIPBL gene only. Proband's phenotype overlapped that reported in patients with 5p13 microduplication syndrome and especially that of subjects with smaller duplications. Moreover, we better define genotype-phenotype relationship associated with this duplication and confirmed that NIPBL was likely the major dosage sensitive gene for the 5p13 microduplication phenotype.
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Affiliation(s)
- Francesca Novara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
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32
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Chen Z, McCroskey S, Guo W, Li H, Gerton JL. A genetic screen to discover pathways affecting cohesin function in Schizosaccharomyces pombe identifies chromatin effectors. G3 (BETHESDA, MD.) 2012; 2:1161-8. [PMID: 23050226 PMCID: PMC3464108 DOI: 10.1534/g3.112.003327] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 07/23/2012] [Indexed: 11/23/2022]
Abstract
Cohesion, the force that holds sister chromatids together from the time of DNA replication until separation at the metaphase to anaphase transition, is mediated by the cohesin complex. This complex is also involved in DNA damage repair, chromosomes condensation, and gene regulation. To learn more about the cellular functions of cohesin, we conducted a genetic screen in Schizosaccharomyces pombe with two different cohesin mutants (eso1-G799D and mis4-242). We found synthetic negative interactions with deletions of genes involved in DNA replication and heterochromatin formation. We also found a few gene deletions that rescued the growth of eso1-G799D at the nonpermissive temperature, and these genes partially rescue the lagging chromosome phenotype. These genes are all chromatin effectors. Overall, our screen revealed an intimate association between cohesin and chromatin.
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Affiliation(s)
- Zhiming Chen
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Scott McCroskey
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Weichao Guo
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Hua Li
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
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33
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Li Y, Xu X, Song L, Hou Y, Li Z, Tsang S, Li F, Im KM, Wu K, Wu H, Ye X, Li G, Wang L, Zhang B, Liang J, Xie W, Wu R, Jiang H, Liu X, Yu C, Zheng H, Jian M, Nie L, Wan L, Shi M, Sun X, Tang A, Guo G, Gui Y, Cai Z, Li J, Wang W, Lu Z, Zhang X, Bolund L, Kristiansen K, Wang J, Yang H, Dean M, Wang J. Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer. Gigascience 2012; 1:12. [PMID: 23587365 PMCID: PMC3626503 DOI: 10.1186/2047-217x-1-12] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/02/2012] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Cancers arise through an evolutionary process in which cell populations are subjected to selection; however, to date, the process of bladder cancer, which is one of the most common cancers in the world, remains unknown at a single-cell level. RESULTS We carried out single-cell exome sequencing of 66 individual tumor cells from a muscle-invasive bladder transitional cell carcinoma (TCC). Analyses of the somatic mutant allele frequency spectrum and clonal structure revealed that the tumor cells were derived from a single ancestral cell, but that subsequent evolution occurred, leading to two distinct tumor cell subpopulations. By analyzing recurrently mutant genes in an additional cohort of 99 TCC tumors, we identified genes that might play roles in the maintenance of the ancestral clone and in the muscle-invasive capability of subclones of this bladder cancer, respectively. CONCLUSIONS This work provides a new approach of investigating the genetic details of bladder tumoral changes at the single-cell level and a new method for assessing bladder cancer evolution at a cell-population level.
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Affiliation(s)
- Yingrui Li
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Xun Xu
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Luting Song
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 32# Jiao-chang Road, Kunming, Yunnan, 650223, People’s Republic of China
- Graduate University of the Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People’s Republic of China
- College of Life Sciences, Wuhan University, Luojia Hill, Wuhan, 430072, People’s Republic of China
| | - Yong Hou
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
- School of Biological Science and Medical Engineering, Southeast University, Sipailou 2#, Nanjing, 210096, People’s Republic of China
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2#, Nanjing, 210096, People’s Republic of China
| | - Zesong Li
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, People’s Republic of China
- Department of Urology, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
- The Institute of Urogenital Diseases, Shenzhen University, Shenzhen, 518060, People’s Republic of China
| | - Shirley Tsang
- BioMatrix, LLC, 3029 Windy Knoll Court, Rockville, MD, 20850, USA
| | - Fuqiang Li
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Kate McGee Im
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Building 560, Frederick, MD, 21702, USA
| | - Kui Wu
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Hanjie Wu
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
- School of Bioscience and Biotechnology, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou, 510006, People’s Republic of China
| | - Xiaofei Ye
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Guibo Li
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Linlin Wang
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Bo Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Jie Liang
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Wei Xie
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
- School of Biological Science and Medical Engineering, Southeast University, Sipailou 2#, Nanjing, 210096, People’s Republic of China
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2#, Nanjing, 210096, People’s Republic of China
| | - Renhua Wu
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Hui Jiang
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Xiao Liu
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Chang Yu
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Hancheng Zheng
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Min Jian
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Liping Nie
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Shenzhen PKU-HKUST Medical Center, Peking University Shenzhen Hospital, 1120 Lian Hua Road, Futian District, Shenzhen, 518036, People’s Republic of China
| | - Lei Wan
- Department of Urology, Longgang Central Hospital, Shenhui Road, Longgang Town, Shenzhen, 518116, People’s Republic of China
| | - Min Shi
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Shenzhen PKU-HKUST Medical Center, Peking University Shenzhen Hospital, 1120 Lian Hua Road, Futian District, Shenzhen, 518036, People’s Republic of China
| | - Xiaojuan Sun
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, People’s Republic of China
- Department of Urology, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
- The Institute of Urogenital Diseases, Shenzhen University, Shenzhen, 518060, People’s Republic of China
| | - Aifa Tang
- Shenzhen Key Laboratory of Genitourinary Tumor, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, People’s Republic of China
- Department of Urology, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
- The Institute of Urogenital Diseases, Shenzhen University, Shenzhen, 518060, People’s Republic of China
| | - Guangwu Guo
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Yaoting Gui
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Shenzhen PKU-HKUST Medical Center, Peking University Shenzhen Hospital, 1120 Lian Hua Road, Futian District, Shenzhen, 518036, People’s Republic of China
| | - Zhiming Cai
- Department of Urology, Shenzhen Second People’s Hospital, Shenzhen, 518035, People’s Republic of China
- The Institute of Urogenital Diseases, Shenzhen University, Shenzhen, 518060, People’s Republic of China
- Guangdong and Shenzhen Key Laboratory of Male Reproductive Medicine and Genetics, Institute of Urology, Shenzhen PKU-HKUST Medical Center, Peking University Shenzhen Hospital, 1120 Lian Hua Road, Futian District, Shenzhen, 518036, People’s Republic of China
| | - Jingxiang Li
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Wen Wang
- CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 32# Jiao-chang Road, Kunming, Yunnan, 650223, People’s Republic of China
| | - Zuhong Lu
- School of Biological Science and Medical Engineering, Southeast University, Sipailou 2#, Nanjing, 210096, People’s Republic of China
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2#, Nanjing, 210096, People’s Republic of China
| | - Xiuqing Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Lars Bolund
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
- Institute of Human Genetics, University of Aarhus, Aarhus, 8100, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK, 2200, Denmark
| | - Jian Wang
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
| | - Michael Dean
- Cancer and Inflammation Program, National Cancer Institute at Frederick, Building 560, Frederick, MD, 21702, USA
| | - Jun Wang
- BGI-Shenzhen, Beishan Industrial Zone, Beishan Road, Yantian, Shenzhen, 518083, People’s Republic of China
- The Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK, 2200, Denmark
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK, 2200, Denmark
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Chien R, Zeng W, Ball AR, Yokomori K. Cohesin: a critical chromatin organizer in mammalian gene regulation. Biochem Cell Biol 2011; 89:445-58. [PMID: 21851156 PMCID: PMC4056987 DOI: 10.1139/o11-039] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cohesins are evolutionarily conserved essential multi-protein complexes that are important for higher-order chromatin organization. They play pivotal roles in the maintenance of genome integrity through mitotic chromosome regulation, DNA repair and replication, as well as gene regulation critical for proper development and cellular differentiation. In this review, we will discuss the multifaceted functions of mammalian cohesins and their apparent functional hierarchy in the cell, with particular focus on their actions in gene regulation and their relevance to human developmental disorders.
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Affiliation(s)
- Richard Chien
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697-1700, USA
| | - Weihua Zeng
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697-1700, USA
| | - Alexander R. Ball
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697-1700, USA
| | - Kyoko Yokomori
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, California 92697-1700, USA
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Muto A, Calof AL, Lander AD, Schilling TF. Multifactorial origins of heart and gut defects in nipbl-deficient zebrafish, a model of Cornelia de Lange Syndrome. PLoS Biol 2011; 9:e1001181. [PMID: 22039349 PMCID: PMC3201921 DOI: 10.1371/journal.pbio.1001181] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 09/13/2011] [Indexed: 12/31/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is the founding member of a class of multi-organ system birth defect syndromes termed cohesinopathies, named for the chromatin-associated protein complex cohesin, which mediates sister chromatid cohesion. Most cases of CdLS are caused by haploinsufficiency for Nipped-B-like (Nipbl), a highly conserved protein that facilitates cohesin loading. Consistent with recent evidence implicating cohesin and Nipbl in transcriptional regulation, both CdLS cell lines and tissues of Nipbl-deficient mice show changes in the expression of hundreds of genes. Nearly all such changes are modest, however--usually less than 1.5-fold--raising the intriguing possibility that, in CdLS, severe developmental defects result from the collective action of many otherwise innocuous perturbations. As a step toward testing this hypothesis, we developed a model of nipbl-deficiency in zebrafish, an organism in which we can quantitatively investigate the combinatorial effects of gene expression changes. After characterizing the structure and embryonic expression of the two zebrafish nipbl genes, we showed that morpholino knockdown of these genes produces a spectrum of specific heart and gut/visceral organ defects with similarities to those in CdLS. Analysis of nipbl morphants further revealed that, as early as gastrulation, expression of genes involved in endodermal differentiation (sox32, sox17, foxa2, and gata5) and left-right patterning (spaw, lefty2, and dnah9) is altered. Experimental manipulation of the levels of several such genes--using RNA injection or morpholino knockdown--implicated both additive and synergistic interactions in causing observed developmental defects. These findings support the view that birth defects in CdLS arise from collective effects of quantitative changes in gene expression. Interestingly, both the phenotypes and gene expression changes in nipbl morphants differed from those in mutants or morphants for genes encoding cohesin subunits, suggesting that the transcriptional functions of Nipbl cannot be ascribed simply to its role in cohesin loading.
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Affiliation(s)
- Akihiko Muto
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Anne L. Calof
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
- Department of Anatomy and Neurobiology, University of California, Irvine, California, United States of America
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
| | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- Center for Complex Biological Systems, University of California, Irvine, California, United States of America
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Isolated NIBPL missense mutations that cause Cornelia de Lange syndrome alter MAU2 interaction. Eur J Hum Genet 2011; 20:271-6. [PMID: 21934712 DOI: 10.1038/ejhg.2011.175] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS; or Brachmann-de Lange syndrome) is a dominantly inherited congenital malformation disorder with features that include characteristic facies, cognitive delays, growth retardation and limb anomalies. Mutations in nearly 60% of CdLS patients have been identified in NIPBL, which encodes a regulator of the sister chromatid cohesion complex. NIPBL, also known as delangin, is a homolog of yeast and amphibian Scc2 and C. elegans PQN-85. Although the exact mechanism of NIPBL function in sister chromatid cohesion is unclear, in vivo yeast and C. elegans experiments and in vitro vertebrate cell experiments have demonstrated that NIPBL/Scc2 functionally interacts with the MAU2/Scc4 protein to initiate loading of cohesin onto chromatin. To test the significance of this model in the clinical setting of CdLS, we fine-mapped the NIBPL-MAU2 interaction domain and tested the functional significance of missense mutations and variants in NIPBL and MAU2 identified in these minimal domains in a cohort of patients with CdLS. We demonstrate that specific novel mutations at the N-terminus of the MAU2-interacting domain of NIBPL result in markedly reduced MAU2 binding, although we appreciate no consistent clinical difference in the small group of patients with these mutations. These data suggest that factors in addition to MAU2 are essential in determining the clinical features and severity of CdLS.
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Oka Y, Suzuki K, Yamauchi M, Mitsutake N, Yamashita S. Recruitment of the cohesin loading factor NIPBL to DNA double-strand breaks depends on MDC1, RNF168 and HP1γ in human cells. Biochem Biophys Res Commun 2011; 411:762-7. [PMID: 21784059 DOI: 10.1016/j.bbrc.2011.07.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 07/06/2011] [Indexed: 01/01/2023]
Abstract
The cohesin loading factor NIPBL is required for cohesin to associate with chromosomes and plays a role in DNA double-strand break (DSB) repair. Although the NIPBL homolog Scc2 is recruited to an enzymatically generated DSB and promotes cohesin-dependent DSB repair in yeast, the mechanism of the recruitment remains poorly understood. Here we show that the human NIPBL is recruited to the sites of DNA damage generated by micro-irradiation as well as to the sites of DSBs induced by homing endonuclease, I-PpoI. The recruitment of NIPBL was impaired by RNAi-mediated knockdown of MDC1 or RNF168, both of which also accumulate at DSBs. We also show that the recruitment of NIPBL to the sites of DNA damage is mediated by its C-terminal region containing HEAT repeats and Heterochromatin protein 1 (HP1) interacting motif. Furthermore, NIPBL accumulation at damaged sites was also compromised by HP1γ depletion. Taken together, our study reveals that human NIPBL is a novel protein recruited to DSB sites, and the recruitment is controlled by MDC1, RNF168 and HP1γ.
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Affiliation(s)
- Yasuyoshi Oka
- Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Graduate School of Biomedical Sciences, Japan.
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Galehdari H, Monajemzadeh R, Nazem H, Mohamadian G, Pedram M. Identification of a novel de novo mutation in the NIPBL gene in an Iranian patient with Cornelia de Lange syndrome: A case report. J Med Case Rep 2011; 5:242. [PMID: 21707975 PMCID: PMC3138439 DOI: 10.1186/1752-1947-5-242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 06/27/2011] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Cornelia de Lange syndrome is characterized by dysmorphic facial features, hirsutism, severe growth and developmental delay. Germline mutations in the NIPBL gene with an autosomal dominant pattern and in the SMC1A gene with an X-linked pattern have been identified in Cornelia de Lange syndrome. CASE PRESENTATION A two-month-old Iranian boy who showed multiple congenital anomalies was referred to the genetic center of a welfare organization in southwest Iran. He was the second child of a non-consanguineous marriage, born after full term with normal delivery. His birth weight was 3110 g, his length was 46 cm and his head circumference was 30 cm. Both parents were clinically asymptomatic, with no positive history of any deformity in their respective families. CONCLUSIONS Sequencing of the NIPBL gene from our patient revealed a single-base deletion of thymidine in exon 10 (c.516delT). This mutation presumably results in premature termination at codon 526. We did not observe this mutation in the parents of our patient with Cornelia de Lange syndrome. The results presented here enlarge the spectrum of NIPBL gene mutations associated with Cornelia de Lange syndrome by identifying a novel de novo mutation in an Iranian patient with Cornelia de Lange syndrome and further support the hypothesis that NIPBL mutations are disease-causing mutations leading to Cornelia de Lange syndrome.
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Affiliation(s)
- Hamid Galehdari
- Genetics Department, Shahid Chamran University, Ahwaz, Iran.
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Chien R, Zeng W, Kawauchi S, Bender MA, Santos R, Gregson HC, Schmiesing JA, Newkirk DA, Kong X, Ball AR, Calof AL, Lander AD, Groudine MT, Yokomori K. Cohesin mediates chromatin interactions that regulate mammalian β-globin expression. J Biol Chem 2011; 286:17870-8. [PMID: 21454523 PMCID: PMC3093862 DOI: 10.1074/jbc.m110.207365] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 03/17/2011] [Indexed: 11/06/2022] Open
Abstract
The β-globin locus undergoes dynamic chromatin interaction changes in differentiating erythroid cells that are thought to be important for proper globin gene expression. However, the underlying mechanisms are unclear. The CCCTC-binding factor, CTCF, binds to the insulator elements at the 5' and 3' boundaries of the locus, but these sites were shown to be dispensable for globin gene activation. We found that, upon induction of differentiation, cohesin and the cohesin loading factor Nipped-B-like (Nipbl) bind to the locus control region (LCR) at the CTCF insulator and distal enhancer regions as well as at the specific target globin gene that undergoes activation upon differentiation. Nipbl-dependent cohesin binding is critical for long-range chromatin interactions, both between the CTCF insulator elements and between the LCR distal enhancer and the target gene. We show that the latter interaction is important for globin gene expression in vivo and in vitro. Furthermore, the results indicate that such cohesin-mediated chromatin interactions associated with gene regulation are sensitive to the partial reduction of Nipbl caused by heterozygous mutation. This provides the first direct evidence that Nipbl haploinsufficiency affects cohesin-mediated chromatin interactions and gene expression. Our results reveal that dynamic Nipbl/cohesin binding is critical for developmental chromatin organization and the gene activation function of the LCR in mammalian cells.
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Affiliation(s)
| | | | | | - M. A. Bender
- the Department of Pediatrics, University of Washington, Seattle, Washington 98195, and
| | | | | | | | | | | | | | - Anne L. Calof
- Department of Anatomy and Neurobiology, School of Medicine
| | - Arthur D. Lander
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, California 92697-1700
| | - Mark T. Groudine
- the Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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Robb EA, Gitter CL, Cheng HH, Delany ME. Chromosomal mapping and candidate gene discovery of chicken developmental mutants and genome-wide variation analysis of MHC congenics. ACTA ACUST UNITED AC 2011; 102:141-56. [PMID: 21273214 DOI: 10.1093/jhered/esq122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The chicken has been widely used in experimental research given its importance to agriculture and its utility as a model for vertebrate biology and biomedical pursuits for over 100 years. Herein we used advanced technologies to investigate the genomic characteristics of specialized chicken congenic genetic resources developed on a highly inbred background. An Illumina 3K chicken single nucleotide polymorphism (SNP) array was utilized to study variation within and among major histocompatibility complex (MHC)-congenic lines as well as investigate line-specific genomic diversity, inbreeding coefficients, and MHC B haplotype-specific GGA 16 SNP profiles. We also investigated developmental mutant-congenic lines to map a number of single-gene mutations using both the Illumina 3K array and a recently developed Illumina 60K chicken SNP array. In addition to identifying the chromosomes and specific subregions, the mapping results affirmed prior analyses indicating recessive or dominant and autosomal or sex chromosome modes of inheritance. Priority candidate genes are described for each mutation based on association with similar phenotypes in other vertebrates. These single-gene mutations provide a means of studying amniote development and in particular serve as invaluable biomedical models for similar malformations found in human.
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Affiliation(s)
- Elizabeth A Robb
- Department of Animal Science, University of California, Davis, CA 95616, USA
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Oliveira J, Dias C, Redeker E, Costa E, Silva J, Reis Lima M, den Dunnen JT, Santos R. Development of NIPBL locus-specific database using LOVD: from novel mutations to further genotype-phenotype correlations in Cornelia de Lange Syndrome. Hum Mutat 2010; 31:1216-22. [PMID: 20824775 DOI: 10.1002/humu.21352] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The establishment of Locus Specific Databases (LSDB) is a crucial aspect for the Human Genetics field and one of the aims of the Human Variation Project. We report the development of a publicly accessible LSDB for the NIPBL gene (http://www.lovd.nl/NIPBL) implicated in Cornelia de Lange Syndrome (CdLS). This rare disorder is characterized by developmental and growth retardation, typical facial features, limb anomalies, and multiple organ involvement. Mutations in the NIPBL gene, the product of which is involved in control of the cohesion complex, account for over half of the patients currently characterized. The NIPBL LSDB adopted the Leiden Open Variation database (LOVD) software platform, which enables the comprehensive Web-based listing and curation of sequence variations and associated phenotypical information. The NIPBL-LOVD database contains 199 unique mutations reported in 246 patients (last accessed April 2010). Information on phenotypic characteristics included in the database enabled further genotype-phenotype correlations, the most evident being the severe form of CdLS associated with premature termination codons in the NIPBL gene. In addition to the NIPBL LSDB, 50 novel mutations are described in detail, resulting from a collaborative multicenter study.
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Affiliation(s)
- Jorge Oliveira
- Unidade de Genética Molecular, Centro de Genética Médica Dr. Jacinto Magalhães, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
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42
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Carretero M, Remeseiro S, Losada A. Cohesin ties up the genome. Curr Opin Cell Biol 2010; 22:781-7. [PMID: 20675112 DOI: 10.1016/j.ceb.2010.07.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 07/06/2010] [Accepted: 07/07/2010] [Indexed: 11/17/2022]
Abstract
Cohesin was originally identified as a mediator of sister chromatid cohesion both in mitosis and meiosis. Emerging evidences suggest that it also participates in the organization of interphase chromatin. The ring-shaped complex regulates gene expression by constraining chromatin topology in concert with factors such as the insulator CTCF, at least in certain loci. The global relevance of this function of cohesin remains to be assessed, but its contribution to the pathology of the Cornelia de Lange syndrome seems evident. Our current knowledge of the molecular mechanisms underlying cohesin behavior should now be considered from the perspective of its novel functions, which promise to be as relevant for cell viability as cohesion.
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Affiliation(s)
- María Carretero
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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43
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Kaiser FJ, Osmanoric A, Rakovic A, Erogullari A, Uflacker N, Braunholz D, Lohnau T, Orolicki S, Albrecht M, Gillessen-Kaesbach G, Klein C, Lohmann K. The dystonia gene DYT1 is repressed by the transcription factor THAP1 (DYT6). Ann Neurol 2010; 68:554-9. [DOI: 10.1002/ana.22157] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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Pié J, Gil-Rodríguez MC, Ciero M, López-Viñas E, Ribate MP, Arnedo M, Deardorff MA, Puisac B, Legarreta J, de Karam JC, Rubio E, Bueno I, Baldellou A, Calvo MT, Casals N, Olivares JL, Losada A, Hegardt FG, Krantz ID, Gómez-Puertas P, Ramos FJ. Mutations and variants in the cohesion factor genes NIPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lange syndrome. Am J Med Genet A 2010; 152A:924-9. [PMID: 20358602 DOI: 10.1002/ajmg.a.33348] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cornelia de Lange syndrome (CdLS) manifests facial dysmorphic features, growth and cognitive impairment, and limb malformations. Mutations in three genes (NIPBL, SMC1A, and SMC3) of the cohesin complex and its regulators have been found in affected patients. Here, we present clinical and molecular characterization of 30 unrelated patients with CdLS. Eleven patients had mutations in NIPBL (37%) and three patients had mutations in SMC1A (10%), giving an overall rate of mutations of 47%. Several patients shared the same mutation in NIPBL (p.R827GfsX2) but had variable phenotypes, indicating the influence of modifiers in CdLS. Patients with NIPBL mutations had a more severe phenotype than those with mutations in SMC1A or those without identified mutations. However, a high incidence of palate defects was noted in patients with SMC1A mutations. In addition, we observed a similar phenotype in both male and female patients with SMC1A mutations. Finally, we report the first patient with an SMC1A mutation and the Sandifer complex.
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Affiliation(s)
- Juan Pié
- Laboratory of Clinical Genetics and Functional Genomics, Department of Pharmacology, Medical School, University of Zaragoza, Zaragoza, Spain.
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45
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Mannini L, Menga S, Musio A. The expanding universe of cohesin functions: a new genome stability caretaker involved in human disease and cancer. Hum Mutat 2010; 31:623-30. [PMID: 20513141 DOI: 10.1002/humu.21252] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cohesin is responsible for sister chromatid cohesion, ensuring the correct chromosome segregation. Beyond this role, cohesin and regulatory cohesin genes seem to play a role in preserving genome stability and gene transcription regulation. DNA damage is thought to be a major culprit for many human diseases, including cancer. Our present knowledge of the molecular basis underlying genome instability is extremely limited. Mutations in cohesin genes cause human diseases such as Cornelia de Lange syndrome and Roberts syndrome/SC phocomelia, and all the cell lines derived from affected patients show genome instability. Cohesin mutations have also been identified in colorectal cancer. Here, we will discuss the human disorders caused by alterations of cohesin function, with emphasis on the emerging role of cohesin as a genome stability caretaker.
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Affiliation(s)
- Linda Mannini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa, Italy
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Multiple organ system defects and transcriptional dysregulation in the Nipbl(+/-) mouse, a model of Cornelia de Lange Syndrome. PLoS Genet 2009; 5:e1000650. [PMID: 19763162 PMCID: PMC2730539 DOI: 10.1371/journal.pgen.1000650] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 08/16/2009] [Indexed: 12/22/2022] Open
Abstract
Cornelia de Lange Syndrome (CdLS) is a multi-organ system birth defects disorder linked, in at least half of cases, to heterozygous mutations in the NIPBL gene. In animals and fungi, orthologs of NIPBL regulate cohesin, a complex of proteins that is essential for chromosome cohesion and is also implicated in DNA repair and transcriptional regulation. Mice heterozygous for a gene-trap mutation in Nipbl were produced and exhibited defects characteristic of CdLS, including small size, craniofacial anomalies, microbrachycephaly, heart defects, hearing abnormalities, delayed bone maturation, reduced body fat, behavioral disturbances, and high mortality (75–80%) during the first weeks of life. These phenotypes arose despite a decrease in Nipbl transcript levels of only ∼30%, implying extreme sensitivity of development to small changes in Nipbl activity. Gene expression profiling demonstrated that Nipbl deficiency leads to modest but significant transcriptional dysregulation of many genes. Expression changes at the protocadherin beta (Pcdhb) locus, as well as at other loci, support the view that NIPBL influences long-range chromosomal regulatory interactions. In addition, evidence is presented that reduced expression of genes involved in adipogenic differentiation may underlie the low amounts of body fat observed both in Nipbl+/− mice and in individuals with CdLS. Cornelia de Lange Syndrome (CdLS) is a genetic disease marked by growth retardation, cognitive and neurological problems, and structural defects in many organ systems. The majority of CdLS cases are due to mutation of one copy of the Nipped B-like (NIPBL) gene, the product of which regulates a complex of chromosomal proteins called cohesin. How reduction of NIPBL function gives rise to pervasive developmental defects in CdLS is not understood, so a model of CdLS was developed by generating mice that carry one null allele of Nipbl. Developmental defects in these mice show remarkable similarity to those observed in individuals with CdLS, including small stature, craniofacial abnormalities, reduced body fat, behavioral disturbances, and high perinatal mortality. Molecular analysis of tissues and cells from Nipbl mutant mice provide the first evidence that the major role of Nipbl in the etiology of CdLS is to exert modest, but significant, effects on the expression of diverse sets of genes, some of which are located in characteristic arrangements along the DNA. Among affected genes is a set involved in the development of adipocytes, the cells that make and accumulate body fat, potentially explaining reductions in body fat accumulation commonly observed in individuals with CdLS.
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Abstract
In interphase, chromosomes are associated with proteins and RNAs that participate in many processes, such as DNA replication, transcription, recombination and repair of DNA damage. These components (for example, cohesin) might have to be removed during mitosis, as they might become obstacles that inhibit chromosome segregation or reduce its fidelity. Such a clearing mechanism that operates along mitotic chromosomes might require proteins that are implicated in chromosome segregation. I propose that condensin and DNA topoisomerase II (TOP2), as well as separase, help to clear the way for mitosis.
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Affiliation(s)
- Mitsuhiro Yanagida
- Mitsuhiro Yanagida is at the CREST Research Program, Japan Science Technology Corporation, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
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Revenkova E, Focarelli ML, Susani L, Paulis M, Bassi MT, Mannini L, Frattini A, Delia D, Krantz I, Vezzoni P, Jessberger R, Musio A. Cornelia de Lange syndrome mutations in SMC1A or SMC3 affect binding to DNA. Hum Mol Genet 2009; 18:418-27. [PMID: 18996922 PMCID: PMC2722190 DOI: 10.1093/hmg/ddn369] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 11/04/2008] [Indexed: 01/09/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a clinically heterogeneous developmental disorder characterized by facial dysmorphia, upper limb malformations, growth and cognitive retardation. Mutations in the sister chromatid cohesion factor genes NIPBL, SMC1A and SMC3 are present in approximately 65% of CdLS patients. In addition to their canonical roles in chromosome segregation, the cohesin proteins are involved in other biological processes such as regulation of gene expression, DNA repair and maintenance of genome stability. To gain insights into the molecular basis of CdLS, we analyzed the affinity of mutated SMC1A and SMC3 hinge domains for DNA. Mutated hinge dimers bind DNA with higher affinity than wild-type proteins. SMC1A- and SMC3-mutated CdLS cell lines display genomic instability and sensitivity to ionizing radiation and interstrand crosslinking agents. We propose that SMC1A and SMC3 CdLS mutations affect the dynamic association between SMC proteins and DNA, providing new clues to the underlying molecular cause of CdLS.
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Affiliation(s)
- Ekaterina Revenkova
- Department of Gene and Cell Medicine, Mount Sinai School of Medicine, New York, USA
| | - Maria Luisa Focarelli
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | - Lucia Susani
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | - Marianna Paulis
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | - Maria Teresa Bassi
- Laboratory of Molecular Biology, E. Medea Scientific Institute, Bosisio Parini (LC), Italy
| | - Linda Mannini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Annalisa Frattini
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | | | - Ian Krantz
- Division of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia, The University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Paolo Vezzoni
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Segrate (MI), Italy
- Istituto Clinico Humanitas, Rozzano (MI), Italy
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Dresden University of Technology, Dresden, Germany
| | - Antonio Musio
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche, Pisa, Italy
- Istituto Toscano Tumori, Florence, Italy
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