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Zhang B, Zhu Y, Zhang Z, Wu F, Ma X, Sheng W, Dai R, Guo Z, Yan W, Hao L, Huang G, Ma D, Hao B, Ma J. SMC3 contributes to heart development by regulating super-enhancer associated genes. Exp Mol Med 2024:10.1038/s12276-024-01293-0. [PMID: 39085358 DOI: 10.1038/s12276-024-01293-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/23/2024] [Accepted: 05/21/2024] [Indexed: 08/02/2024] Open
Abstract
Abnormal cardiac development has been observed in individuals with Cornelia de Lange syndrome (CdLS) due to mutations in genes encoding members of the cohesin complex. However, the precise role of cohesin in heart development remains elusive. In this study, we aimed to elucidate the indispensable role of SMC3, a component of the cohesin complex, in cardiac development and its underlying mechanism. Our investigation revealed that CdLS patients with SMC3 mutations have high rates of congenital heart disease (CHD). We utilized heart-specific Smc3-knockout (SMC3-cKO) mice, which exhibit varying degrees of outflow tract (OFT) abnormalities, to further explore this relationship. Additionally, we identified 16 rare SMC3 variants with potential pathogenicity in individuals with isolated CHD. By employing single-nucleus RNA sequencing and chromosome conformation capture high-throughput genome-wide translocation sequencing, we revealed that Smc3 deletion downregulates the expression of key genes, including Ets2, in OFT cardiac muscle cells by specifically decreasing interactions between super-enhancers (SEs) and promoters. Notably, Ets2-SE-null mice also exhibit delayed OFT development in the heart. Our research revealed a novel role for SMC3 in heart development via the regulation of SE-associated genes, suggesting its potential relevance as a CHD-related gene and providing crucial insights into the molecular basis of cardiac development.
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Affiliation(s)
- Bowen Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Yongchang Zhu
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, China
| | - Zhen Zhang
- Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Feizhen Wu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Xiaojing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Wei Sheng
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Ranran Dai
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong, 510080, China
| | - Zhenglong Guo
- Henan Medical Genetics Institute, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, People's Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, China
| | - Weili Yan
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Lili Hao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Guoying Huang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
| | - Bingtao Hao
- Department of Immunology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- Henan Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, Henan, 450000, China.
| | - Jing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences; ENT Institute, Department of Facial Plastic and Reconstructive Surgery, Eye & ENT Hospital; Institute of Medical Genetics & Genomics; Key Laboratory of Birth Defects, Children's Hospital; Medical Science Data Center at Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China.
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2
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Liu H, Tsai H, Yang M, Li G, Bian Q, Ding G, Wu D, Dai J. Three-dimensional genome structure and function. MedComm (Beijing) 2023; 4:e326. [PMID: 37426677 PMCID: PMC10329473 DOI: 10.1002/mco2.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/31/2023] [Accepted: 06/09/2023] [Indexed: 07/11/2023] Open
Abstract
Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.
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Affiliation(s)
- Hao Liu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Hsiangyu Tsai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Maoquan Yang
- School of Clinical MedicineWeifang Medical UniversityWeifangChina
| | - Guozhi Li
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Qian Bian
- Shanghai Institute of Precision MedicineShanghaiChina
| | - Gang Ding
- School of StomatologyWeifang Medical UniversityWeifangChina
| | - Dandan Wu
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
| | - Jiewen Dai
- Department of Oral and Cranio‐Maxillofacial SurgeryShanghai Ninth People's Hospital, Shanghai Jiao Tong University School of MedicineCollege of Stomatology, Shanghai Jiao Tong UniversityNational Center for StomatologyNational Clinical Research Center for Oral DiseasesShanghai Key Laboratory of StomatologyShanghaiChina
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Kiefer L, Chiosso A, Langen J, Buckley A, Gaudin S, Rajkumar SM, Servito GIF, Cha ES, Vijay A, Yeung A, Horta A, Mui MH, Canzio D. WAPL functions as a rheostat of Protocadherin isoform diversity that controls neural wiring. Science 2023; 380:eadf8440. [PMID: 37347873 DOI: 10.1126/science.adf8440] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/07/2023] [Indexed: 06/24/2023]
Abstract
Neural type-specific expression of clustered Protocadherin (Pcdh) proteins is essential for the establishment of connectivity patterns during brain development. In mammals, deterministic expression of the same Pcdh isoform promotes minimal overlap of tiled projections of serotonergic neuron axons throughout the brain, while stochastic expression of Pcdh genes allows for convergence of tightly packed, overlapping olfactory sensory neuron axons into targeted structures. How can the same gene locus generate opposite transcriptional programs that orchestrate distinct spatial arrangements of axonal patterns? Here, we reveal that cell type-specific Pcdh expression and axonal behavior depend on the activity of cohesin and its unloader, WAPL (wings apart-like protein homolog). While cohesin erases genomic-distance biases in Pcdh choice, WAPL functions as a rheostat of cohesin processivity that determines Pcdh isoform diversity.
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Affiliation(s)
- Lea Kiefer
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anna Chiosso
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jennifer Langen
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alex Buckley
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Simon Gaudin
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Ecole Normale Superieure de Lyon, 69432 Lyon, France
| | - Sandy M Rajkumar
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Gabrielle Isabelle F Servito
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth S Cha
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Akshara Vijay
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Albert Yeung
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Adan Horta
- Pura Vida Investments, New York, NY 10106, USA
| | - Michael H Mui
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniele Canzio
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA
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4
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Shi M, Liang Y, Xie B, Wei X, Zheng H, Gui C, Huang R, Fan X, Li C, Wei X, Ma Y, Chen S, Chen Y, Gui B. Case report: A novel heterozygous synonymous variant in deep exon region of NIPBL gene generating a non-canonical splice donor in a patient with cornelia de lange syndrome. Front Genet 2022; 13:1056127. [PMID: 36506332 PMCID: PMC9726764 DOI: 10.3389/fgene.2022.1056127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is an autosomal dominant or X-linked genetic disease with significant genetic heterogeneity. Variants of the NIPBL gene are responsible for CdLS in 60% of patients. Herein, we report the case of a patient with CdLS showing distinctive facial features, microcephaly, developmental delay, and growth retardation. Whole exome sequencing was performed for the patient, and a novel de novo heterozygous synonymous variant was identified in the deep region of exon 40 in the NIPBL gene (NM_133433.4: c. 6819G > T, p. Gly2273 = ). The clinical significance of the variant was uncertain according to the ACMG/AMP guidelines; however, based on in silico analysis, it was predicted to alter mRNA splicing. To validate the prediction, a reverse transcriptase-polymerase chain reaction was conducted. The variant activated a cryptic splice donor, generating a short transcript of NIPBL. A loss of 137 bp at the 3' end of NIPBL exon 40 was detected, which potentially altered the open reading frame by inserting multiple premature termination codons. Quantitative real-time PCR analysis showed that the ratio of the transcription level of the full-length transcript to that of the altered short transcript in the patient was 5:1, instead of 1:1. These findings may explain the relatively mild phenotype of the patient, regardless of the loss of function of the truncated protein due to a frameshift in the mRNA. To the best of our knowledge, this study is the first to report a synonymous variant in the deep exon regions of the NIPBL gene responsible for CdLS. The identified variant expands the mutational spectrum of the NIPBL gene. Furthermore, synonymous variations may be pathogenic, which should not be ignored in the clinical and genetic diagnosis of the disease.
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Affiliation(s)
- Meizhen Shi
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yuying Liang
- Department of Pediatrics, The Traditional Chinese Medicine Hospital of YuLin, Yulin, China
| | - Bobo Xie
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xianda Wei
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Haiyang Zheng
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chunrong Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Rong Huang
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xin Fan
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chuan Li
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaojiao Wei
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yunting Ma
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shaoke Chen
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
| | - Yujun Chen
- The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
| | - Baoheng Gui
- Center for Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,The Guangxi Health Commission Key Laboratory of Medical Genetics and Genomics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China,*Correspondence: Shaoke Chen, ; Yujun Chen, ; Baoheng Gui,
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HDACs and the epigenetic plasticity of cancer cells: Target the complexity. Pharmacol Ther 2022; 238:108190. [PMID: 35430294 DOI: 10.1016/j.pharmthera.2022.108190] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/11/2022]
Abstract
Cancer cells must adapt to the hostile conditions of the microenvironment in terms of nutrition, space, and immune system attack. Mutations of DNA are the drivers of the tumorigenic process, but mutations must be able to hijack cellular functions to sustain the spread of mutant genomes. Transcriptional control is a key function in this context and is controlled by the rearrangement of the epigenome. Unlike genomic mutations, the epigenome of cancer cells can in principle be reversed. The discovery of the first epigenetic drugs triggered a contaminating enthusiasm. Unfortunately, the complexity of the epigenetic machinery has frustrated this enthusiasm. To develop efficient patient-oriented epigenetic therapies, we need to better understand the nature of this complexity. In this review, we will discuss recent advances in understanding the contribution of HDACs to the maintenance of the transformed state and the rational for their selective targeting.
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Pileggi S, La Vecchia M, Colombo EA, Fontana L, Colapietro P, Rovina D, Morotti A, Tabano S, Porta G, Alcalay M, Gervasini C, Miozzo M, Sirchia SM. Cohesin Mutations Induce Chromatin Conformation Perturbation of the H19/ IGF2 Imprinted Region and Gene Expression Dysregulation in Cornelia de Lange Syndrome Cell Lines. Biomolecules 2021; 11:1622. [PMID: 34827619 PMCID: PMC8615450 DOI: 10.3390/biom11111622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
Traditionally, Cornelia de Lange Syndrome (CdLS) is considered a cohesinopathy caused by constitutive mutations in cohesin complex genes. Cohesin is a major regulator of chromatin architecture, including the formation of chromatin loops at the imprinted IGF2/H19 domain. We used 3C analysis on lymphoblastoid cells from CdLS patients carrying mutations in NIPBL and SMC1A genes to explore 3D chromatin structure of the IGF2/H19 locus and evaluate the influence of cohesin alterations in chromatin architecture. We also assessed quantitative expression of imprinted loci and WNT pathway genes, together with DMR methylation status of the imprinted genes. A general impairment of chromatin architecture and the emergence of new interactions were found. Moreover, imprinting alterations also involved the expression and methylation levels of imprinted genes, suggesting an association among cohesin genetic defects, chromatin architecture impairment, and imprinting network alteration. The WNT pathway resulted dysregulated: canonical WNT, cell cycle, and WNT signal negative regulation were the most significantly affected subpathways. Among the deregulated pathway nodes, the key node of the frizzled receptors was repressed. Our study provides new evidence that mutations in genes of the cohesin complex have effects on the chromatin architecture and epigenetic stability of genes commonly regulated by high order chromatin structure.
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Affiliation(s)
- Silvana Pileggi
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Marta La Vecchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Elisa Adele Colombo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Laura Fontana
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Patrizia Colapietro
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
| | - Davide Rovina
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Annamaria Morotti
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Silvia Tabano
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
- Laboratory of Medical Genetics, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giovanni Porta
- Centro di Medicina Genomica, Department of Medicine and Surgery, Università degli Studi dell’Insubria, 21100 Varese, Italy;
| | - Myriam Alcalay
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Monica Miozzo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Silvia Maria Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
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7
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Mio C, Passon N, Fogolari F, Cesario C, Novelli A, Pittini C, Damante G. A novel de novo HDAC8 missense mutation causing Cornelia de Lange syndrome. Mol Genet Genomic Med 2021; 9:e1612. [PMID: 34342180 PMCID: PMC8457687 DOI: 10.1002/mgg3.1612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/21/2022] Open
Abstract
Background Cornelia de Lange syndrome (CdLS) is a rare and clinically variable syndrome characterized by growth impairment, multi‐organ anomalies, and a typical set of facial dysmorphisms. Here we describe a 2‐year‐old female child harboring a novel de novo missense variant in HDAC8, whose phenotypical score, according to the recent consensus on CdLS clinical diagnostic criteria, allowed the diagnosis of a non‐classic CdLS. Methods Clinical exome sequencing was performed on the trio, identifying a de novo heterozygous variant in HDAC8 (NM_018486; c. 356C>G p.Thr119Arg). Molecular modeling was performed to evaluate putative functional consequence of the HDAC8 protein. Results The variant HDAC8 c.356C>G is classified as pathogenic following the ACMG (American College of Medical Genetics and Genomics)/AMP (Association for Molecular Pathology) guidelines. By molecular modeling, we confirmed the deleterious effect of this variant, since the amino acid change compromises the conformational flexibility of the HDAC8 loop required for optimal catalytic function. Conclusion We described a novel Thr119Arg mutation in HDAC8 in a patient displaying the major phenotypic traits of the CdLS. Our results suggest that a modest change outside an active site is capable of triggering global structural changes that propagate through the protein scaffold to the catalytic site, creating de facto haploinsufficiency.
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Affiliation(s)
- Catia Mio
- Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Nadia Passon
- Institute of Medical Genetics, Academic Hospital of Udine, Udine, Italy
| | - Federico Fogolari
- Department of Mathematics, Computer Sciences and Physics (DMIF), University of Udine, Udine, Italy
| | - Claudia Cesario
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children Hospital, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, IRCCS Bambino Gesù Children Hospital, Rome, Italy
| | - Carla Pittini
- Maternal and Child Health Department, Academic Hospital of Udine, Udine, Italy
| | - Giuseppe Damante
- Department of Medicine (DAME), University of Udine, Udine, Italy.,Institute of Medical Genetics, Academic Hospital of Udine, Udine, Italy
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8
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Garcia P, Fernandez-Hernandez R, Cuadrado A, Coca I, Gomez A, Maqueda M, Latorre-Pellicer A, Puisac B, Ramos FJ, Sandoval J, Esteller M, Mosquera JL, Rodriguez J, Pié J, Losada A, Queralt E. Disruption of NIPBL/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome. Nat Commun 2021; 12:4551. [PMID: 34315879 PMCID: PMC8316422 DOI: 10.1038/s41467-021-24808-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/05/2021] [Indexed: 12/31/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, NIPBL/Scc2, were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanisms driving CdLS phenotypes are not understood. In addition to its canonical role in sister chromatid cohesion, cohesin is implicated in the spatial organization of the genome. Here, we investigate the transcriptome of CdLS patient-derived primary fibroblasts and observe the downregulation of genes involved in development and system skeletal organization, providing a link to the developmental alterations and limb abnormalities characteristic of CdLS patients. Genome-wide distribution studies demonstrate a global reduction of NIPBL at the NIPBL-associated high GC content regions in CdLS-derived cells. In addition, cohesin accumulates at NIPBL-occupied sites at CpG islands potentially due to reduced cohesin translocation along chromosomes, and fewer cohesin peaks colocalize with CTCF.
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Affiliation(s)
- Patricia Garcia
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.
| | - Rita Fernandez-Hernandez
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ignacio Coca
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Grup de Recerca de Reumatologia, Parc Científic de Barcelona, Barcelona, Spain
| | - Maria Maqueda
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Feliciano J Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit (UByMP) and Epigenomics Core Facility, Health Research Institute La Fe (IISLaFe), Valencia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Jairo Rodriguez
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - J Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ethel Queralt
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.
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9
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Abstract
Cohesin helps mediate sister chromatid cohesion, chromosome condensation, DNA repair, and transcription regulation. We exploited proximity-dependent labeling to define the in vivo interactions of cohesin domains with DNA or with other cohesin domains that lie within the same or in different cohesin complexes. Our results suggest that both cohesin's head and hinge domains are proximal to DNA, and cohesin structure is dynamic with differential folding of its coiled coil regions to generate butterfly confirmations. This method also reveals that cohesins form ordered clusters on and off DNA. The levels of cohesin clusters and their distribution on chromosomes are cell cycle-regulated. Cohesin clustering is likely necessary for cohesion maintenance because clustering and maintenance uniquely require the same subset of cohesin domains and the auxiliary cohesin factor Pds5p. These conclusions provide important new mechanistic and biological insights into the architecture of the cohesin complex, cohesin-cohesin interactions, and cohesin's tethering and loop-extruding activities.
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Affiliation(s)
- Siheng Xiang
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Douglas Koshland
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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10
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Li R, Tian B, Liang H, Chen M, Yang H, Wang L, Pan H, Zhu H. A Chinese Case of Cornelia de Lange Syndrome Caused by a Pathogenic Variant in SMC3 and a Literature Review. Front Endocrinol (Lausanne) 2021; 12:604500. [PMID: 34659104 PMCID: PMC8515141 DOI: 10.3389/fendo.2021.604500] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Cornelia de Lange syndrome (CdLS) is a rare congenital developmental disorder, and cases caused by variants in SMC3 are infrequent. This article describes a case of CdLS related to a pathogenic variant in SMC3 and performs a literature review. METHODS We collected clinical data and biological samples from a 12-year-old boy with "short stature for 11 years". Gene variants in the proband were detected by whole-exome sequencing, and the variants in his parents were verified by Sanger sequencing. All SMC3-related CdLS patients from the PubMed and Web of Science databases were collected and summarized using the available data. RESULTS A pathogenic variant in SMC3 in the proband, c.1942A>G, was identified. Neither of his parents carried the same variant. Twenty-eight patients were diagnosed with CdLS with variants in SMC3, including the cases in this study and those reported in the literature, where half of the variant types were missense, followed by 32% (9/28) with a deletion and 11% (3/28) with a duplication. All patients showed symptoms of verbal development delay and intellectual disability to different degrees, and 90% patients had long eyelashes while 89% patients had arched eyebrows. CONCLUSION This study summarized different gene variants in SMC3 and the frequencies of the various clinical manifestations according to the reported literature. For CdLS caused by SMC3 variants, short stature and facial dysmorphic features are the two most important clinical clues. Definite diagnosis of this rare disease may be challenging clinically; thus, it is significant to use molecular diagnosis.
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Affiliation(s)
- Ran Li
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Bowen Tian
- Department of Internal Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hanting Liang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Meiping Chen
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hongbo Yang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linjie Wang
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Hui Pan
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Huijuan Zhu
- Key Laboratory of Endocrinology of National Health Commission, Department of Endocrinology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Huijuan Zhu,
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11
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Liu C, Li X, Cui J, Dong R, Lv Y, Wang D, Zhang H, Li X, Li Z, Ma J, Liu Y, Gai Z. Analysis of clinical and genetic characteristics in 10 Chinese individuals with Cornelia de Lange syndrome and literature review. Mol Genet Genomic Med 2020; 8:e1471. [PMID: 32856424 PMCID: PMC7549606 DOI: 10.1002/mgg3.1471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 01/03/2023] Open
Abstract
Background Cornelia de Lange syndrome (CdLS) is a rare congenital developmental disorder with variable multisystem involvement and genetic heterogeneity. We aimed to analyze the clinical and genetic characteristics of Chinese individuals with CdLS. Methods We collected data regarding the neonatal period, maternal status, clinical manifestation, including facial dimorphisms and development, and follow‐up treatment for individuals diagnosed with CdLS. In individuals with suspected CdLS, high‐throughput sequencing, Sanger sequencing, and real‐time qualitative PCR were used to verify the diagnosis. Results Variants, including six that were novel, were concentrated in the NIPBL (70%), HDAC8 (20%), and SMC3 (10%) genes. We found two nonsense, three splicing, and two deletion variants in NIPBL; a missense variant and an absence variant in HDAC8; and a missense variant in SMC3. Eleven cardinal features of CdLS were present in more than 80% of Chinese individuals. Compared with non‐Chinese individuals of diverse ancestry, there were significant differences in the clinical characteristics of eight of these features. Conclusion Six novel pathological variants were identified; thus, the study expanded the gene variant spectrum. Furthermore, most cardinal features of CdLS found in Chinese individuals were also found in individuals from other countries. However, there were significant differences in eight clinical features.
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Affiliation(s)
- Chen Liu
- Department of Neonatology, Pediatric Research Institute, Qilu Children's Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Neonatology, Pediatric Research Institute, Jinan Children's Hospital, Jinan, China
| | - Xiaoying Li
- Department of Neonatology, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Jing Cui
- Department of Neonatology, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Rui Dong
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Yvqiang Lv
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Dong Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Haiyan Zhang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Xiaomei Li
- Department of Neonatology, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Zilong Li
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Jian Ma
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan, China
| | - Zhongtao Gai
- Department of Neonatology, Pediatric Research Institute, Qilu Children's Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Neonatology, Pediatric Research Institute, Jinan Children's Hospital, Jinan, China
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12
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Pan H, Jin M, Ghadiyaram A, Kaur P, Miller HE, Ta HM, Liu M, Fan Y, Mahn C, Gorthi A, You C, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Cohesin SA1 and SA2 are RNA binding proteins that localize to RNA containing regions on DNA. Nucleic Acids Res 2020; 48:5639-5655. [PMID: 32352519 PMCID: PMC7261166 DOI: 10.1093/nar/gkaa284] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/28/2020] [Accepted: 04/28/2020] [Indexed: 12/16/2022] Open
Abstract
Cohesin SA1 (STAG1) and SA2 (STAG2) are key components of the cohesin complex. Previous studies have highlighted the unique contributions by SA1 and SA2 to 3D chromatin organization, DNA replication fork progression, and DNA double-strand break (DSB) repair. Recently, we discovered that cohesin SA1 and SA2 are DNA binding proteins. Given the recently discovered link between SA2 and RNA-mediated biological pathways, we investigated whether or not SA1 and SA2 directly bind to RNA using a combination of bulk biochemical assays and single-molecule techniques, including atomic force microscopy (AFM) and the DNA tightrope assay. We discovered that both SA1 and SA2 bind to various RNA containing substrates, including ssRNA, dsRNA, RNA:DNA hybrids, and R-loops. Importantly, both SA1 and SA2 localize to regions on dsDNA that contain RNA. We directly compared the SA1/SA2 binding and R-loops sites extracted from Chromatin Immunoprecipitation sequencing (ChIP-seq) and DNA-RNA Immunoprecipitation sequencing (DRIP-Seq) data sets, respectively. This analysis revealed that SA1 and SA2 binding sites overlap significantly with R-loops. The majority of R-loop-localized SA1 and SA2 are also sites where other subunits of the cohesin complex bind. These results provide a new direction for future investigation of the diverse biological functions of SA1 and SA2.
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Affiliation(s)
- Hai Pan
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Miao Jin
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ashwin Ghadiyaram
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
| | - Henry E Miller
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, TX 78229, USA
| | - Hai Minh Ta
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ming Liu
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Yanlin Fan
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Chelsea Mahn
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Aparna Gorthi
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, TX 78229, USA
| | - Changjiang You
- Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany
| | - Robert Riehn
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Institute, University of Texas Health at San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, TX 78229, USA
| | - Yizhi Jane Tao
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695, USA
- Toxiology Program, North Carolina State University, Raleigh, NC 27695, USA
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13
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Krab LC, Marcos-Alcalde I, Assaf M, Balasubramanian M, Andersen JB, Bisgaard AM, Fitzpatrick DR, Gudmundsson S, Huisman SA, Kalayci T, Maas SM, Martinez F, McKee S, Menke LA, Mulder PA, Murch OD, Parker M, Pie J, Ramos FJ, Rieubland C, Rosenfeld Mokry JA, Scarano E, Shinawi M, Gómez-Puertas P, Tümer Z, Hennekam RC. Delineation of phenotypes and genotypes related to cohesin structural protein RAD21. Hum Genet 2020; 139:575-592. [PMID: 32193685 PMCID: PMC7170815 DOI: 10.1007/s00439-020-02138-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/10/2020] [Indexed: 01/23/2023]
Abstract
RAD21 encodes a key component of the cohesin complex, and variants in RAD21 have been associated with Cornelia de Lange Syndrome (CdLS). Limited information on phenotypes attributable to RAD21 variants and genotype–phenotype relationships is currently published. We gathered a series of 49 individuals from 33 families with RAD21 alterations [24 different intragenic sequence variants (2 recurrent), 7 unique microdeletions], including 24 hitherto unpublished cases. We evaluated consequences of 12 intragenic variants by protein modelling and molecular dynamic studies. Full clinical information was available for 29 individuals. Their phenotype is an attenuated CdLS phenotype compared to that caused by variants in NIPBL or SMC1A for facial morphology, limb anomalies, and especially for cognition and behavior. In the 20 individuals with limited clinical information, additional phenotypes include Mungan syndrome (in patients with biallelic variants) and holoprosencephaly, with or without CdLS characteristics. We describe several additional cases with phenotypes including sclerocornea, in which involvement of the RAD21 variant is uncertain. Variants were frequently familial, and genotype–phenotype analyses demonstrated striking interfamilial and intrafamilial variability. Careful phenotyping is essential in interpreting consequences of RAD21 variants, and protein modeling and dynamics can be helpful in determining pathogenicity. The current study should be helpful when counseling families with a RAD21 variation.
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Affiliation(s)
- Lianne C Krab
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands. .,Cordaan, Outpatient Clinic for ID Medicine, Klinkerweg 75, 1033 PK, Amsterdam, The Netherlands. .,Odion, Outpatient Clinic for ID Medicine, Purmerend, The Netherlands.
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain.,School of Experimental Sciences-IIB, Universidad Francisco de Vitoria, UFV, Pozuelo de Alarcón, Spain
| | - Melissa Assaf
- Banner Childrens Specialists Neurology Clinic, Glendale, AZ, USA
| | - Meena Balasubramanian
- Clinical Genetics Service, Sheffield Children's Hospital, Academic Unit for Child Health, University of Sheffield, Sheffield, UK
| | - Janne Bayer Andersen
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Gl. Landevej 7, 2600, Glostrup, Denmark
| | - Anne-Marie Bisgaard
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | | | - Sanna Gudmundsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sylvia A Huisman
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Prinsenstichting, Purmerend, The Netherlands
| | - Tugba Kalayci
- Division of Medical Genetics, Department of Internal Medicine, Istanbul University, Istanbul, Turkey
| | - Saskia M Maas
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.,Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Francisco Martinez
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Leonie A Menke
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Paul A Mulder
- Autism Team Northern-Netherlands, Jonx Department of Youth Mental Health and Autism, Lentis Psychiatric Institute, Groningen, The Netherlands
| | - Oliver D Murch
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Michael Parker
- Clinical Genetic Service, Northern General Hospital, Sheffield, UK
| | - Juan Pie
- Unit of Clinical Genetics Unit, Service of Pediatrics, University Hospital "Lozano Blesa", University of Zaragoza School of Medicine, Saragossa, Spain
| | - Feliciano J Ramos
- Unit of Clinical Genetics Unit and Functional Genomics, Department of Pharmacology and Physiology, University of Zaragoza School of Medicine, Saragossa, Spain
| | - Claudine Rieubland
- Department of Pediatrics, Division of Human Genetics, Inselspital, University of Bern, Bern, Switzerland
| | - Jill A Rosenfeld Mokry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Baylor Genetics Laboratories, Houston, TX, USA
| | - Emanuela Scarano
- Rare Disease Unit, Department of Pediatrics, St. Orsola Hospital, Bologna, Italy
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), Madrid, Spain
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Gl. Landevej 7, 2600, Glostrup, Denmark. .,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
| | - Raoul C Hennekam
- Department of Pediatrics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
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14
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Latorre-Pellicer A, Ascaso Á, Trujillano L, Gil-Salvador M, Arnedo M, Lucia-Campos C, Antoñanzas-Pérez R, Marcos-Alcalde I, Parenti I, Bueno-Lozano G, Musio A, Puisac B, Kaiser FJ, Ramos FJ, Gómez-Puertas P, Pié J. Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes. Int J Mol Sci 2020; 21:ijms21031042. [PMID: 32033219 PMCID: PMC7038094 DOI: 10.3390/ijms21031042] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/01/2020] [Accepted: 02/02/2020] [Indexed: 12/19/2022] Open
Abstract
Characteristic or classic phenotype of Cornelia de Lange syndrome (CdLS) is associated with a recognisable facial pattern. However, the heterogeneity in causal genes and the presence of overlapping syndromes have made it increasingly difficult to diagnose only by clinical features. DeepGestalt technology, and its app Face2Gene, is having a growing impact on the diagnosis and management of genetic diseases by analysing the features of affected individuals. Here, we performed a phenotypic study on a cohort of 49 individuals harbouring causative variants in known CdLS genes in order to evaluate Face2Gene utility and sensitivity in the clinical diagnosis of CdLS. Based on the profile images of patients, a diagnosis of CdLS was within the top five predicted syndromes for 97.9% of our cases and even listed as first prediction for 83.7%. The age of patients did not seem to affect the prediction accuracy, whereas our results indicate a correlation between the clinical score and affected genes. Furthermore, each gene presents a different pattern recognition that may be used to develop new neural networks with the goal of separating different genetic subtypes in CdLS. Overall, we conclude that computer-assisted image analysis based on deep learning could support the clinical diagnosis of CdLS.
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Affiliation(s)
- Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Ángela Ascaso
- Department of Paediatrics, Hospital Clínico Universitario “Lozano Blesa”, E-50009 Zaragoza, Spain; (Á.A.); (L.T.)
| | - Laura Trujillano
- Department of Paediatrics, Hospital Clínico Universitario “Lozano Blesa”, E-50009 Zaragoza, Spain; (Á.A.); (L.T.)
| | - Marta Gil-Salvador
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Maria Arnedo
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Cristina Lucia-Campos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Rebeca Antoñanzas-Pérez
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Iñigo Marcos-Alcalde
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), E-28049 Madrid, Spain;
- Bioscience Research Institute, School of Experimental Sciences, Universidad Francisco de Vitoria, UFV, E-28223 Pozuelo de Alarcón, Spain
| | - Ilaria Parenti
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany; (I.P.); (F.J.K.)
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | - Gloria Bueno-Lozano
- Department of Paediatrics, Hospital Clínico Universitario “Lozano Blesa”, E-50009 Zaragoza, Spain; (Á.A.); (L.T.)
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, I-56124 Pisa, Italy;
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
| | - Frank J. Kaiser
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, 23562 Lübeck, Germany; (I.P.); (F.J.K.)
- Institute for Human Genetics, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany
| | - Feliciano J. Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
- Department of Paediatrics, Hospital Clínico Universitario “Lozano Blesa”, E-50009 Zaragoza, Spain; (Á.A.); (L.T.)
| | - Paulino Gómez-Puertas
- Molecular Modelling Group, Centro de Biología Molecular Severo Ochoa, CBMSO (CSIC-UAM), E-28049 Madrid, Spain;
- Correspondence: (J.P.); (P.G.-P.); Tel.: +34-976-761677 (J.P.); +34-91-1964663 (P.G.-P.)
| | - Juan Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, CIBERER-GCV02 and ISS-Aragon, E-50009 Zaragoza, Spain; (A.L.-P.); (M.G.-S.); (M.A.); (C.L.-C.); (R.A.-P.); (B.P.); (F.J.R.)
- Correspondence: (J.P.); (P.G.-P.); Tel.: +34-976-761677 (J.P.); +34-91-1964663 (P.G.-P.)
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15
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Birot A, Tormos-Pérez M, Vaur S, Feytout A, Jaegy J, Alonso Gil D, Vazquez S, Ekwall K, Javerzat JP. The CDK Pef1 and protein phosphatase 4 oppose each other for regulating cohesin binding to fission yeast chromosomes. eLife 2020; 9:e50556. [PMID: 31895039 PMCID: PMC6954021 DOI: 10.7554/elife.50556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/02/2020] [Indexed: 12/19/2022] Open
Abstract
Cohesin has essential roles in chromosome structure, segregation and repair. Cohesin binding to chromosomes is catalyzed by the cohesin loader, Mis4 in fission yeast. How cells fine tune cohesin deposition is largely unknown. Here, we provide evidence that Mis4 activity is regulated by phosphorylation of its cohesin substrate. A genetic screen for negative regulators of Mis4 yielded a CDK called Pef1, whose closest human homologue is CDK5. Inhibition of Pef1 kinase activity rescued cohesin loader deficiencies. In an otherwise wild-type background, Pef1 ablation stimulated cohesin binding to its regular sites along chromosomes while ablating Protein Phosphatase 4 had the opposite effect. Pef1 and PP4 control the phosphorylation state of the cohesin kleisin Rad21. The CDK phosphorylates Rad21 on Threonine 262. Pef1 ablation, non-phosphorylatable Rad21-T262 or mutations within a Rad21 binding domain of Mis4 alleviated the effect of PP4 deficiency. Such a CDK/PP4-based regulation of cohesin loader activity could provide an efficient mechanism for translating cellular cues into a fast and accurate cohesin response.
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Affiliation(s)
- Adrien Birot
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Marta Tormos-Pérez
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Sabine Vaur
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Amélie Feytout
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Julien Jaegy
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Dácil Alonso Gil
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Stéphanie Vazquez
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
| | - Karl Ekwall
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Jean-Paul Javerzat
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de BordeauxBordeauxFrance
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16
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Avagliano L, Parenti I, Grazioli P, Di Fede E, Parodi C, Mariani M, Kaiser FJ, Selicorni A, Gervasini C, Massa V. Chromatinopathies: A focus on Cornelia de Lange syndrome. Clin Genet 2020; 97:3-11. [PMID: 31721174 DOI: 10.1111/cge.13674] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 01/01/2023]
Abstract
In recent years, many genes have been associated with chromatinopathies classified as "Cornelia de Lange Syndrome-like." It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that "CdLS-like syndromes" are part of a larger "rare disease family" sharing multiple clinical features and common disrupted molecular pathways.
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Affiliation(s)
- Laura Avagliano
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Ilaria Parenti
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Paolo Grazioli
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Elisabetta Di Fede
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Chiara Parodi
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | | | - Frank J Kaiser
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, Lübeck, Germany
- DZHK e.V. (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Lübeck, Germany
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | | | - Cristina Gervasini
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Valentina Massa
- Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
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17
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Panousis NI, Bertsias GK, Ongen H, Gergianaki I, Tektonidou MG, Trachana M, Romano-Palumbo L, Bielser D, Howald C, Pamfil C, Fanouriakis A, Kosmara D, Repa A, Sidiropoulos P, Dermitzakis ET, Boumpas DT. Combined genetic and transcriptome analysis of patients with SLE: distinct, targetable signatures for susceptibility and severity. Ann Rheum Dis 2019; 78:1079-1089. [PMID: 31167757 PMCID: PMC6691930 DOI: 10.1136/annrheumdis-2018-214379] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 12/21/2022]
Abstract
Objectives Systemic lupus erythematosus (SLE) diagnosis and treatment remain empirical and the molecular basis for its heterogeneity elusive. We explored the genomic basis for disease susceptibility and severity. Methods mRNA sequencing and genotyping in blood from 142 patients with SLE and 58 healthy volunteers. Abundances of cell types were assessed by CIBERSORT and cell-specific effects by interaction terms in linear models. Differentially expressed genes (DEGs) were used to train classifiers (linear discriminant analysis) of SLE versus healthy individuals in 80% of the dataset and were validated in the remaining 20% running 1000 iterations. Transcriptome/genotypes were integrated by expression-quantitative trail loci (eQTL) analysis; tissue-specific genetic causality was assessed by regulatory trait concordance (RTC). Results SLE has a ‘susceptibility signature’ present in patients in clinical remission, an ‘activity signature’ linked to genes that regulate immune cell metabolism, protein synthesis and proliferation, and a ‘severity signature’ best illustrated in active nephritis, enriched in druggable granulocyte and plasmablast/plasma–cell pathways. Patients with SLE have also perturbed mRNA splicing enriched in immune system and interferon signalling genes. A novel transcriptome index distinguished active versus inactive disease—but not low disease activity—and correlated with disease severity. DEGs discriminate SLE versus healthy individuals with median sensitivity 86% and specificity 92% suggesting a potential use in diagnostics. Combined eQTL analysis from the Genotype Tissue Expression (GTEx) project and SLE-associated genetic polymorphisms demonstrates that susceptibility variants may regulate gene expression in the blood but also in other tissues. Conclusion Specific gene networks confer susceptibility to SLE, activity and severity, and may facilitate personalised care.
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Affiliation(s)
- Nikolaos I Panousis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iG3), University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - George K Bertsias
- Department of Rheumatology, Clinical Immunology and Allergy, University of Crete, Medical School, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iG3), University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Irini Gergianaki
- Department of Rheumatology, Clinical Immunology and Allergy, University of Crete, Medical School, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Maria G Tektonidou
- Department of Propaedeutic Internal Medicine, National and Kapodistrian University of Athens, Medical School, Athens, Greece.,Joint Academic Rheumatology Program, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Maria Trachana
- First Department of Pediatrics, Pediatric Immunology and Rheumatology Referral Center, Hippokration General Hospital, Aristotle University, Thessaloniki, Greece
| | - Luciana Romano-Palumbo
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Deborah Bielser
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Cedric Howald
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iG3), University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Cristina Pamfil
- Department of Rheumatology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Antonis Fanouriakis
- 4th Department of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Despoina Kosmara
- Department of Rheumatology, Clinical Immunology and Allergy, University of Crete, Medical School, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Argyro Repa
- Department of Rheumatology, Clinical Immunology and Allergy, University of Crete, Medical School, Heraklion, Greece
| | - Prodromos Sidiropoulos
- Department of Rheumatology, Clinical Immunology and Allergy, University of Crete, Medical School, Heraklion, Greece.,Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland .,Institute of Genetics and Genomics in Geneva (iG3), University of Geneva Medical School, Geneva, Switzerland.,Swiss Institute of Bioinformatics, Geneva, Switzerland.,Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece
| | - Dimitrios T Boumpas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas (FORTH), Heraklion, Greece .,Joint Academic Rheumatology Program, National and Kapodistrian University of Athens, Medical School, Athens, Greece.,4th Department of Medicine, Attikon University Hospital, National and Kapodistrian University of Athens, Medical School, Athens, Greece.,Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece.,Medical school, University of Cyprus, Nicosia, Cyprus
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18
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Perez S, Gevor M, Davidovich A, Kaspi A, Yamin K, Domovich T, Meirson T, Matityahu A, Brody Y, Stemmer SM, El-Osta A, Haviv I, Onn I, Gal-Tanamy M. Dysregulation of the cohesin subunit RAD21 by Hepatitis C virus mediates host-virus interactions. Nucleic Acids Res 2019; 47:2455-2471. [PMID: 30698808 PMCID: PMC6412124 DOI: 10.1093/nar/gkz052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 12/30/2018] [Accepted: 01/24/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection is the leading cause of chronic hepatitis, which often results in liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC). HCV possesses an RNA genome and its replication is confined to the cytoplasm. Yet, infection with HCV leads to global changes in gene expression, and chromosomal instability (CIN) in the host cell. The mechanisms by which the cytoplasmic virus affects these nuclear processes are elusive. Here, we show that HCV modulates the function of the Structural Maintenance of Chromosome (SMC) protein complex, cohesin, which tethers remote regions of chromatin. We demonstrate that infection of hepatoma cells with HCV leads to up regulation of the expression of the RAD21 cohesin subunit and changes cohesin residency on the chromatin. These changes regulate the expression of genes associated with virus-induced pathways. Furthermore, siRNA downregulation of viral-induced RAD21 reduces HCV infection. During mitosis, HCV infection induces hypercondensation of chromosomes and the appearance of multi-centrosomes. We provide evidence that the underlying mechanism involves the viral NS3/4 protease and the cohesin regulator, WAPL. Altogether, our results provide the first evidence that HCV induces changes in gene expression and chromosome structure of infected cells by modulating cohesin.
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Affiliation(s)
- Shira Perez
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Gevor
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ateret Davidovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
| | - Katreena Yamin
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tom Domovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tomer Meirson
- Cell Migration and Invasion Laboratory, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yehuda Brody
- The Broad institute of Harvard and MIT, Cambridge, MA, USA
| | - Salomon M Stemmer
- Davidoff Center, Rabin Medical Center, Beilinson Campus, Petach Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Izhak Haviv
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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19
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Cukrov D, Newman TAC, Leask M, Leeke B, Sarogni P, Patimo A, Kline AD, Krantz ID, Horsfield JA, Musio A. Antioxidant treatment ameliorates phenotypic features of SMC1A-mutated Cornelia de Lange syndrome in vitro and in vivo. Hum Mol Genet 2019; 27:3002-3011. [PMID: 29860495 DOI: 10.1093/hmg/ddy203] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/17/2018] [Indexed: 12/30/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare disease characterized by cognitive impairment, multisystemic alterations and premature aging. Furthermore, CdLS cells display gene expression dysregulation and genomic instability. Here, we demonstrated that treatment with antioxidant drugs, such as ascorbic acid and riboceine, reduced the level of genomic instability and extended the in vitro lifespan of CdLS cell lines. We also found that antioxidant treatment partially rescued the phenotype of a zebrafish model of CdLS. Gene expression profiling showed that antioxidant drugs caused dysregulation of gene transcription; notably, a number of genes coding for the zinc finger (ZNF)-containing Krueppel-associated box (KRAB) protein domain (KRAB-ZNF) were found to be downregulated. Taken together, these data suggest that antioxidant drugs have the potential to ameliorate the developmental phenotype of CdLS.
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Affiliation(s)
- Dubravka Cukrov
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Trent A C Newman
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Megan Leask
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Bryony Leeke
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Patrizia Sarogni
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Alessandra Patimo
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Ian D Krantz
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Julia A Horsfield
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
- The Maurice Wilkins Centre for Molecular Biodiscovery, c/o The University of Auckland, Private Bag, Auckland, New Zealand
| | - Antonio Musio
- Institute for Genetic and Biomedical Research, National Research Council, Pisa, Italy
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20
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Scarano E, Tassone M, Graziano C, Gibertoni D, Tamburrino F, Perri A, Gnazzo M, Severi G, Lepri F, Mazzanti L. Novel Mutations and Unreported Clinical Features in KBG Syndrome. Mol Syndromol 2019; 10:130-138. [PMID: 31191201 DOI: 10.1159/000496172] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/03/2018] [Indexed: 01/06/2023] Open
Abstract
KBG syndrome is an autosomal dominant disorder caused by pathogenic variants within ANKRD11 or deletions of 16q24.3 which include ANKRD11. It is characterized by distinctive facial features, developmental delay, short stature, and skeletal anomalies. We report 12 unrelated patients where a clinical diagnosis of KBG was suspected and confirmed by targeted analyses. Nine patients showed a point mutation in ANKRD11 (none of which were previously reported) and 3 carried a 16q24.3 deletion. All patients presented with typical facial features and macrodontia. Skeletal abnormalities were constant, and the majority of patients showed joint stiffness. Three patients required growth hormone treatment with a significant increase of height velocity. Brain malformations were identified in 8 patients. All patients showed behavioral abnormalities and most had developmental delay. Two patients had hematological abnormalities. We emphasize that genetic analysis of ANKRD11 can easily reach a detection rate higher than 50% thanks to clinical phenotyping, although it is known that a subset of ANKRD11-mutated patients show very mild features and will be more easily identified through the implementation of gene panels or exome sequencing. Joint stiffness was reported previously in few patients, but it seems to be a common feature and can be helpful for the diagnosis. Hematological abnormalities could be present and warrant a specific follow-up.
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Affiliation(s)
- Emanuela Scarano
- Rare Disease Unit, Department of Pediatrics, St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Martina Tassone
- Rare Disease Unit, Department of Pediatrics, St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Claudio Graziano
- Unit of Medical Genetics, Department of Medical and Surgical Sciences, University Alma Mater Studiorum, St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Dino Gibertoni
- Unit of Hygiene and Medical Statistics, Department of Biomedical and Neuromotor Sciences, University Alma Mater Studiorum, Bologna, Italy
| | - Federica Tamburrino
- Rare Disease Unit, Department of Pediatrics, St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Annamaria Perri
- Rare Disease Unit, Department of Pediatrics, St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Maria Gnazzo
- Laboratory of Medical Genetics, Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy
| | - Giulia Severi
- Unit of Medical Genetics, Department of Medical and Surgical Sciences, University Alma Mater Studiorum, St. Orsola-Malpighi Hospital, Bologna, Italy
| | - Francesca Lepri
- Laboratory of Medical Genetics, Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy
| | - Laura Mazzanti
- Rare Disease Unit, Department of Pediatrics, St. Orsola-Malpighi Hospital, Bologna, Italy
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21
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Vermunt MW, Zhang D, Blobel GA. The interdependence of gene-regulatory elements and the 3D genome. J Cell Biol 2018; 218:12-26. [PMID: 30442643 PMCID: PMC6314554 DOI: 10.1083/jcb.201809040] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 01/12/2023] Open
Abstract
Vermunt et al. discuss the relationship between gene-regulatory elements and nuclear architectural features in transcription. Imaging studies, high-resolution chromatin conformation maps, and genome-wide occupancy data of architectural proteins have revealed that genome topology is tightly intertwined with gene expression. Cross-talk between gene-regulatory elements is often organized within insulated neighborhoods, and regulatory cues that induce transcriptional changes can reshape chromatin folding patterns and gene positioning within the nucleus. The cause–consequence relationship of genome architecture and gene expression is intricate, and its molecular mechanisms are under intense investigation. Here, we review the interdependency of transcription and genome organization with emphasis on enhancer–promoter contacts in gene regulation.
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Affiliation(s)
- Marit W Vermunt
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Di Zhang
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gerd A Blobel
- Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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22
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Abstract
Protein assemblies consisting of structural maintenance of chromosomes (SMC) and kleisin subunits are essential for the process of chromosome segregation across all domains of life. Prokaryotic condensin belonging to this class of protein complexes is composed of a homodimer of SMC that associates with a kleisin protein subunit called ScpA. While limited structural data exist for the proteins that comprise the (SMC)-kleisin complex, the complete structure of the entire complex remains unknown. Using an integrative approach combining both crystallographic data and coevolutionary information, we predict an atomic-scale structure of the whole condensin complex, which our results indicate being composed of a single ring. Coupling coevolutionary information with molecular-dynamics simulations, we study the interaction surfaces between the subunits and examine the plausibility of alternative stoichiometries of the complex. Our analysis also reveals several additional configurational states of the condensin hinge domain and the SMC-kleisin interaction domains, which are likely involved with the functional opening and closing of the condensin ring. This study provides the foundation for future investigations of the structure-function relationship of the various SMC-kleisin protein complexes at atomic resolution.
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23
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Kline AD, Moss JF, Selicorni A, Bisgaard AM, Deardorff MA, Gillett PM, Ishman SL, Kerr LM, Levin AV, Mulder PA, Ramos FJ, Wierzba J, Ajmone PF, Axtell D, Blagowidow N, Cereda A, Costantino A, Cormier-Daire V, FitzPatrick D, Grados M, Groves L, Guthrie W, Huisman S, Kaiser FJ, Koekkoek G, Levis M, Mariani M, McCleery JP, Menke LA, Metrena A, O'Connor J, Oliver C, Pie J, Piening S, Potter CJ, Quaglio AL, Redeker E, Richman D, Rigamonti C, Shi A, Tümer Z, Van Balkom IDC, Hennekam RC. Diagnosis and management of Cornelia de Lange syndrome: first international consensus statement. Nat Rev Genet 2018; 19:649-666. [PMID: 29995837 PMCID: PMC7136165 DOI: 10.1038/s41576-018-0031-0] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cornelia de Lange syndrome (CdLS) is an archetypical genetic syndrome that is characterized by intellectual disability, well-defined facial features, upper limb anomalies and atypical growth, among numerous other signs and symptoms. It is caused by variants in any one of seven genes, all of which have a structural or regulatory function in the cohesin complex. Although recent advances in next-generation sequencing have improved molecular diagnostics, marked heterogeneity exists in clinical and molecular diagnostic approaches and care practices worldwide. Here, we outline a series of recommendations that document the consensus of a group of international experts on clinical diagnostic criteria, both for classic CdLS and non-classic CdLS phenotypes, molecular investigations, long-term management and care planning.
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Affiliation(s)
- Antonie D Kline
- Harvey Institute of Human Genetics, Greater Baltimore Medical Centre, Baltimore, MD, USA
| | - Joanna F Moss
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - Angelo Selicorni
- Department of Paediatrics, Presidio S. Femro, ASST Lariana, Como, Italy
| | - Anne-Marie Bisgaard
- Kennedy Centre, Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Glostrup, Denmark
| | - Matthew A Deardorff
- Division of Human Genetics, Children's Hospital of Philadelphia, and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Peter M Gillett
- GI Department, Royal Hospital for Sick Children, Edinburgh, Scotland, UK
| | - Stacey L Ishman
- Departments of Otolaryngology and Pulmonary Medicine, Cincinnati Children's Hospital Medical Centre, University of Cincinnati, Cincinnati, OH, USA
| | - Lynne M Kerr
- Division of Pediatric Neurology, Department of Paediatrics, University of Utah Medical Centre, Salt Lake City, UT, USA
| | - Alex V Levin
- Paediatric Ophthalmology and Ocular Genetics, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA, USA
| | - Paul A Mulder
- Jonx Department of Youth Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
| | - Feliciano J Ramos
- Unit of Clinical Genetics, Paediatrics, University Clinic Hospital 'Lozano Blesa' CIBERER-GCV02 and ISS-Aragón, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, Zaragoza, Spain
| | - Jolanta Wierzba
- Department of Paediatrics, Haematology and Oncology, Department of General Nursery, Medical University of Gdansk, Gdansk, Poland
| | - Paola Francesca Ajmone
- Child and Adolescent Neuropsychiatric Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - David Axtell
- CdLS Foundation UK and Ireland, The Tower, North Stifford, Grays, Essex, UK
| | - Natalie Blagowidow
- Harvey Institute of Human Genetics, Greater Baltimore Medical Center, Baltimore, MD, USA
| | - Anna Cereda
- Department of Paediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Antonella Costantino
- Child and Adolescent Neuropsychiatric Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valerie Cormier-Daire
- Department of Genetics, INSERM UMR1163, Université Paris Descartes-Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, Paris, France
| | - David FitzPatrick
- Human Genetics Unit, Medical and Developmental Genetics, University of Edinburgh Western General Hospital, Edinburgh, Scotland, UK
| | - Marco Grados
- Division of Child and Adolescent Psychiatry, John Hopkins University School of Medicine, Baltimore, MD, USA
| | - Laura Groves
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - Whitney Guthrie
- Centre for Autism Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sylvia Huisman
- Department of Paediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - Frank J Kaiser
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | | | - Mary Levis
- Wicomico County Board of Education, Salisbury, MD, USA
| | - Milena Mariani
- Clinical Paediatric Genetics Unit, Paediatrics Clinics, MBBM Foundation, S. Gerardo Hospital, Monza, Italy
| | - Joseph P McCleery
- Centre for Autism Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Leonie A Menke
- Department of Paediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | | | - Julia O'Connor
- Kennedy Krieger Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chris Oliver
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, UK
| | - Juan Pie
- Unit of Clinical Genetics, Paediatrics, University Clinic Hospital 'Lozano Blesa' CIBERER-GCV02 and ISS-Aragón, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, Zaragoza, Spain
| | - Sigrid Piening
- Jonx Department of Youth Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
| | - Carol J Potter
- Department of Gastroenterology, Nationwide Children's, Columbus, OH, USA
| | - Ana L Quaglio
- Genética Médica, Hospital del Este, Eva Perón, Tucumán, Argentina
| | - Egbert Redeker
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | - David Richman
- Department of Educational Psychology and Leadership, Texas Tech University, Lubbock, TX, USA
| | - Claudia Rigamonti
- Child and Adolescent Neuropsychiatric Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angell Shi
- The Sidney Kimmel Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| | - Zeynep Tümer
- Kennedy Centre, Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Glostrup, Denmark
| | - Ingrid D C Van Balkom
- Jonx Department of Youth Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Rob Giel Research Centre, Department of Psychiatry, University Medical Centre Groningen, Groningen, Netherlands
| | - Raoul C Hennekam
- Department of Paediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, Netherlands.
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24
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BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange-like syndrome. Nat Genet 2018; 50:329-332. [PMID: 29379197 DOI: 10.1038/s41588-018-0042-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 12/29/2017] [Indexed: 11/08/2022]
Abstract
We found that the clinical phenotype associated with BRD4 haploinsufficiency overlapped with that of Cornelia de Lange syndrome (CdLS), which is most often caused by mutation of NIPBL. More typical CdLS was observed with a de novo BRD4 missense variant, which retained the ability to coimmunoprecipitate with NIPBL, but bound poorly to acetylated histones. BRD4 and NIPBL displayed correlated binding at super-enhancers and appeared to co-regulate developmental gene expression.
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25
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Countryman P, Fan Y, Gorthi A, Pan H, Strickland E, Kaur P, Wang X, Lin J, Lei X, White C, You C, Wirth N, Tessmer I, Piehler J, Riehn R, Bishop AJR, Tao YJ, Wang H. Cohesin SA2 is a sequence-independent DNA-binding protein that recognizes DNA replication and repair intermediates. J Biol Chem 2018; 293:1054-1069. [PMID: 29175904 PMCID: PMC5777247 DOI: 10.1074/jbc.m117.806406] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/22/2017] [Indexed: 11/06/2022] Open
Abstract
Proper chromosome alignment and segregation during mitosis depend on cohesion between sister chromatids, mediated by the cohesin protein complex, which also plays crucial roles in diverse genome maintenance pathways. Current models attribute DNA binding by cohesin to entrapment of dsDNA by the cohesin ring subunits (SMC1, SMC3, and RAD21 in humans). However, the biophysical properties and activities of the fourth core cohesin subunit SA2 (STAG2) are largely unknown. Here, using single-molecule atomic force and fluorescence microscopy imaging as well as fluorescence anisotropy measurements, we established that SA2 binds to both dsDNA and ssDNA, albeit with a higher binding affinity for ssDNA. We observed that SA2 can switch between the 1D diffusing (search) mode on dsDNA and stable binding (recognition) mode at ssDNA gaps. Although SA2 does not specifically bind to centromeric or telomeric sequences, it does recognize DNA structures often associated with DNA replication and double-strand break repair, such as a double-stranded end, single-stranded overhang, flap, fork, and ssDNA gap. SA2 loss leads to a defect in homologous recombination-mediated DNA double-strand break repair. These results suggest that SA2 functions at intermediate DNA structures during DNA transactions in genome maintenance pathways. These findings have important implications for understanding the function of cohesin in these pathways.
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Affiliation(s)
| | - Yanlin Fan
- the Department of BioSciences, Rice University, Houston, Texas 77251
| | - Aparna Gorthi
- the Greehey Children's Cancer Research Institute and
- Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, Texas 78229
| | | | | | | | | | - Jiangguo Lin
- From the Physics Department
- the Institute of Biomechanics, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaoying Lei
- the Department of BioSciences, Rice University, Houston, Texas 77251
- the School of Public Health, Shandong University, Jinan 250012, China
| | | | - Changjiang You
- the Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany, and
| | - Nicolas Wirth
- the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- the Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080 Würzburg, Germany
| | - Jacob Piehler
- the Division of Biophysics, Universität Osnabrück, Barbarstrasse 11, 49076 Osnabrück, Germany, and
| | | | - Alexander J R Bishop
- the Greehey Children's Cancer Research Institute and
- Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, Texas 78229
| | - Yizhi Jane Tao
- the Department of BioSciences, Rice University, Houston, Texas 77251
| | - Hong Wang
- From the Physics Department,
- Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
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26
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Banerji R, Skibbens RV, Iovine MK. Cohesin mediates Esco2-dependent transcriptional regulation in a zebrafish regenerating fin model of Roberts Syndrome. Biol Open 2017; 6:1802-1813. [PMID: 29084713 PMCID: PMC5769645 DOI: 10.1242/bio.026013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Robert syndrome (RBS) and Cornelia de Lange syndrome (CdLS) are human developmental disorders characterized by craniofacial deformities, limb malformation and mental retardation. These birth defects are collectively termed cohesinopathies as both arise from mutations in cohesion genes. CdLS arises due to autosomal dominant mutations or haploinsufficiencies in cohesin subunits (SMC1A, SMC3 and RAD21) or cohesin auxiliary factors (NIPBL and HDAC8) that result in transcriptional dysregulation of developmental programs. RBS arises due to autosomal recessive mutations in cohesin auxiliary factor ESCO2, the gene that encodes an N-acetyltransferase which targets the SMC3 subunit of the cohesin complex. The mechanism that underlies RBS, however, remains unknown. A popular model states that RBS arises due to mitotic failure and loss of progenitor stem cells through apoptosis. Previous findings in the zebrafish regenerating fin, however, suggest that Esco2-knockdown results in transcription dysregulation, independent of apoptosis, similar to that observed in CdLS patients. Previously, we used the clinically relevant CX43 to demonstrate a transcriptional role for Esco2. CX43 is a gap junction gene conserved among all vertebrates that is required for direct cell-cell communication between adjacent cells such that cx43 mutations result in oculodentodigital dysplasia. Here, we show that morpholino-mediated knockdown of smc3 reduces cx43 expression and perturbs zebrafish bone and tissue regeneration similar to those previously reported for esco2 knockdown. Also similar to Esco2-dependent phenotypes, Smc3-dependent bone and tissue regeneration defects are rescued by transgenic Cx43 overexpression, suggesting that Smc3 and Esco2 cooperatively act to regulate cx43 transcription. In support of this model, chromatin immunoprecipitation assays reveal that Smc3 binds to a discrete region of the cx43 promoter, suggesting that Esco2 exerts transcriptional regulation of cx43 through modification of Smc3 bound to the cx43 promoter. These findings have the potential to unify RBS and CdLS as transcription-based mechanisms.
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Affiliation(s)
- Rajeswari Banerji
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Robert V Skibbens
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - M Kathryn Iovine
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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27
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Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, Walther N, Koch B, Kueblbeck M, Ellenberg J, Zuber J, Fraser P, Peters JM. Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins. EMBO J 2017; 36:3573-3599. [PMID: 29217591 PMCID: PMC5730888 DOI: 10.15252/embj.201798004] [Citation(s) in RCA: 471] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 01/05/2023] Open
Abstract
Mammalian genomes are spatially organized into compartments, topologically associating domains (TADs), and loops to facilitate gene regulation and other chromosomal functions. How compartments, TADs, and loops are generated is unknown. It has been proposed that cohesin forms TADs and loops by extruding chromatin loops until it encounters CTCF, but direct evidence for this hypothesis is missing. Here, we show that cohesin suppresses compartments but is required for TADs and loops, that CTCF defines their boundaries, and that the cohesin unloading factor WAPL and its PDS5 binding partners control the length of loops. In the absence of WAPL and PDS5 proteins, cohesin forms extended loops, presumably by passing CTCF sites, accumulates in axial chromosomal positions (vermicelli), and condenses chromosomes. Unexpectedly, PDS5 proteins are also required for boundary function. These results show that cohesin has an essential genome-wide function in mediating long-range chromatin interactions and support the hypothesis that cohesin creates these by loop extrusion, until it is delayed by CTCF in a manner dependent on PDS5 proteins, or until it is released from DNA by WAPL.
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Affiliation(s)
- Gordana Wutz
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Csilla Várnai
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Kota Nagasaka
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - David A Cisneros
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Roman R Stocsits
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Stefan Schoenfelder
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Gregor Jessberger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Matthias Muhar
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - M Julius Hossain
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nike Walther
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Birgit Koch
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Moritz Kueblbeck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jan Ellenberg
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
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28
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Vial Y, Lachenaud J, Verloes A, Besnard M, Fenneteau O, Lainey E, Marceau-Renaut A, Preudhomme C, Baruchel A, Cavé H, Drunat S. Down syndrome-like acute megakaryoblastic leukemia in a patient with Cornelia de Lange syndrome. Haematologica 2017; 103:e274-e276. [PMID: 29217785 DOI: 10.3324/haematol.2017.178590] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Yoann Vial
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, France.,Université Paris Diderot, Paris Sorbonne Cité, France.,INSERM UMR 1131, Institut Universitaire d'Hématologie, Paris, France
| | - Julie Lachenaud
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Service d'Hématologie Pédiatrique, France
| | - Alain Verloes
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, France.,Université Paris Diderot, Paris Sorbonne Cité, France.,INSERM UMR 1141, Hôpital Robert Debré, Paris, France
| | - Marianne Besnard
- Centre Hospitalier de Polynésie Française (CHPF), Service de Réanimation néonatale et Néonatologie, Papeete, Tahiti
| | - Odile Fenneteau
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Service d'Hématologie Biologique, France
| | - Elodie Lainey
- Université Paris Diderot, Paris Sorbonne Cité, France.,INSERM UMR 1131, Institut Universitaire d'Hématologie, Paris, France.,Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Service d'Hématologie Biologique, France
| | | | - Claude Preudhomme
- CHU Lille, Laboratoire d'hématologie, France.,INSERM, UMR-S 1172, France
| | - André Baruchel
- Université Paris Diderot, Paris Sorbonne Cité, France.,Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Service d'Hématologie Pédiatrique, France
| | - Hélène Cavé
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, France.,Université Paris Diderot, Paris Sorbonne Cité, France.,INSERM UMR 1131, Institut Universitaire d'Hématologie, Paris, France
| | - Séverine Drunat
- Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Robert Debré, Département de Génétique, France .,INSERM UMR 1141, Hôpital Robert Debré, Paris, France
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29
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Functional analysis of the cfdp1 gene in zebrafish provides evidence for its crucial role in craniofacial development and osteogenesis. Exp Cell Res 2017; 361:236-245. [PMID: 29107067 DOI: 10.1016/j.yexcr.2017.10.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/17/2017] [Accepted: 10/23/2017] [Indexed: 11/20/2022]
Abstract
The CFDP1 proteins have been linked to craniofacial development and osteogenesis in vertebrates, though specific human syndromes have not yet been identified. Alterations of craniofacial development represent the main cause of infant disability and mortality in humans. For this reason, it is crucial to understand the cellular functions and mechanism of action of the CFDP1 protein in model vertebrate organisms. Using a combination of genomic, molecular and cell biology approaches, we have performed a functional analysis of the cfdp1 gene and its encoded protein, zCFDP1, in the zebrafish model system. We found that zCFDP1 is present in the zygote, is rapidly produced after MTZ transition and is highly abundant in the head structures. Depletion of zCFDP1, induced by an ATG-blocking morpholino, produces considerable defects in craniofacial structures and bone mineralization. Together, our results show that zCFDP1 is an essential protein required for proper development and provide the first experimental evidence showing that in vertebrates it actively participates to the morphogenesis of craniofacial territories.
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30
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Fazio G, Bettini LR, Rigamonti S, Meta D, Biondi A, Cazzaniga G, Selicorni A, Massa V. Impairment of Retinoic Acid Signaling in Cornelia de Lange Syndrome Fibroblasts. Birth Defects Res 2017; 109:1268-1276. [PMID: 28752682 DOI: 10.1002/bdr2.1070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 05/12/2017] [Accepted: 05/24/2017] [Indexed: 12/16/2023]
Abstract
BACKGROUND Cornelia de Lange syndrome (CdLS) is a rare genetic disorder affecting the neurodevelopment, gastrointestinal, musculoskeletal systems. CdLS is caused by mutations within NIPBL, SMC1A, SMC3, RAD21, and HDAC8 genes. These genes codify for the "cohesin complex" playing a role in chromatid adhesion, DNA repair and gene expression regulation. The aim of this study was to investigate retinoic acid (RA) signaling pathway, a master developmental regulator, in CdLS cells. METHODS Skin biopsies from CdLS patients and healthy controls were cultured and derived primary fibroblast cells were treated with RA or dimethyl sulfoxide (vehicle). After RA treatment, cells were harvested and RNA was isolated for quantitative real-time polymerase chain reaction experiments. RESULTS We analyzed several components of RA metabolism in a human cell line of kidney fibroblasts (293T), in addition to fibroblasts collected from both NIPBL-mutated patients and healthy donors, with or without RA treatment. In all cases, ADH and RALDH1 gene expression was not affected by RA treatment, while CRABP1 was induced. CRABP2 was dramatically upregulated upon RA treatment in healthy donors but not in CdLS patients cells. CONCLUSION We investigated if CdLS alterations are associated to perturbation of RA signaling. Cells derived from CdLS patients do not respond to RA signaling as efficiently as healthy controls. RA pathway alterations suggest a possible underlying mechanism for several cellular and developmental abnormalities associated with cohesin function. Birth Defects Research 109:1268-1276, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Grazia Fazio
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Laura Rachele Bettini
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Silvia Rigamonti
- Università degli Studi di Milano, Dipartimento di Scienze della Salute, Milan, Italy
| | - Dorela Meta
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
- Istituto Auxologico Italiano, Cusano Milanino, Italy
| | - Andrea Biondi
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca M. Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Angelo Selicorni
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
- Department of Pediatrics, Presidio S. Fermo, ASST Lariana, Como, Italy
| | - Valentina Massa
- Università degli Studi di Milano, Dipartimento di Scienze della Salute, Milan, Italy
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31
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Schalbetter SA, Goloborodko A, Fudenberg G, Belton JM, Miles C, Yu M, Dekker J, Mirny L, Baxter J. SMC complexes differentially compact mitotic chromosomes according to genomic context. Nat Cell Biol 2017; 19:1071-1080. [PMID: 28825700 PMCID: PMC5640152 DOI: 10.1038/ncb3594] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/19/2017] [Indexed: 12/26/2022]
Abstract
Structural maintenance of chromosomes (SMC) protein complexes are key determinants of chromosome conformation. Using Hi-C and polymer modelling, we study how cohesin and condensin, two deeply conserved SMC complexes, organize chromosomes in the budding yeast Saccharomyces cerevisiae. The canonical role of cohesin is to co-align sister chromatids, while condensin generally compacts mitotic chromosomes. We find strikingly different roles for the two complexes in budding yeast mitosis. First, cohesin is responsible for compacting mitotic chromosome arms, independently of sister chromatid cohesion. Polymer simulations demonstrate that this role can be fully accounted for through cis-looping of chromatin. Second, condensin is generally dispensable for compaction along chromosome arms. Instead, it plays a targeted role compacting the rDNA proximal regions and promoting resolution of peri-centromeric regions. Our results argue that the conserved mechanism of SMC complexes is to form chromatin loops and that distinct SMC-dependent looping activities are selectively deployed to appropriately compact chromosomes.
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MESH Headings
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Chromatin/chemistry
- Chromatin/genetics
- Chromatin/metabolism
- Chromatin Assembly and Disassembly
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Chromosome Structures
- Chromosomes, Fungal/chemistry
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/metabolism
- Computer Simulation
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Mitosis
- Models, Genetic
- Models, Molecular
- Multiprotein Complexes/genetics
- Multiprotein Complexes/metabolism
- Nucleic Acid Conformation
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/growth & development
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Structure-Activity Relationship
- Cohesins
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Affiliation(s)
| | - Anton Goloborodko
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Geoffrey Fudenberg
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jon-Matthew Belton
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Catrina Miles
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Miao Yu
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Job Dekker
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Leonid Mirny
- Institute for Medical Engineering and Sciences, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jonathan Baxter
- Genome Damage and Stability Centre, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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32
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Abstract
How eukaryotic chromosomes fold inside the nucleus is an age-old question that remains unanswered today. Early biochemical and microscopic studies revealed the existence of chromatin domains and loops as a pervasive feature of interphase chromosomes, but the biological implications of such organizational features were obscure. Genome-wide analysis of pair-wise chromatin interactions using chromatin conformation capture (3C)-based techniques has shed new light on the organization of chromosomes in interphase nuclei. Particularly, the finding of cell-type invariant, evolutionarily conserved topologically associating domains (TADs) in a broad spectrum of cell types has provided a new molecular framework for the study of animal development and human diseases. Here, we review recent progress in characterization of such chromatin domains and delineation of mechanisms of their formation in animal cells.
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Affiliation(s)
- Jesse R Dixon
- Peptide Biology Lab and the Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - David U Gorkin
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA; University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, and Moores Cancer Center, 9500 Gilman Drive, La Jolla, CA 92093-0653, USA.
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33
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Rohban S, Cerutti A, Morelli MJ, d'Adda di Fagagna F, Campaner S. The cohesin complex prevents Myc-induced replication stress. Cell Death Dis 2017; 8:e2956. [PMID: 28749464 PMCID: PMC5550886 DOI: 10.1038/cddis.2017.345] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 06/20/2017] [Accepted: 06/21/2017] [Indexed: 11/25/2022]
Abstract
The cohesin complex is mutated in cancer and in a number of rare syndromes collectively known as Cohesinopathies. In the latter case, cohesin deficiencies have been linked to transcriptional alterations affecting Myc and its target genes. Here, we set out to understand to what extent the role of cohesins in controlling cell cycle is dependent on Myc expression and activity. Inactivation of the cohesin complex by silencing the RAD21 subunit led to cell cycle arrest due to both transcriptional impairment of Myc target genes and alterations of replication forks, which were fewer and preferentially unidirectional. Ectopic activation of Myc in RAD21 depleted cells rescued Myc-dependent transcription and promoted S-phase entry but failed to sustain S-phase progression due to a strong replicative stress response, which was associated to a robust DNA damage response, DNA damage checkpoint activation and synthetic lethality. Thus, the cohesin complex is dispensable for Myc-dependent transcription but essential to prevent Myc-induced replicative stress. This suggests the presence of a feed-forward regulatory loop where cohesins by regulating Myc level control S-phase entry and prevent replicative stress.
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Affiliation(s)
- Sara Rohban
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Aurora Cerutti
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, CNR – Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy
- Istituto di Genetica Molecolare, CNR – Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Stefano Campaner
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139 Milan, Italy
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34
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Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome. Genetics 2017; 207:139-151. [PMID: 28679547 DOI: 10.1534/genetics.117.202291] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 12/25/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While its precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Cohesin is associated with the boundaries of chromosome domains and with enhancer and promoter regions connecting the three-dimensional genome organization with transcriptional regulation. Here, we show that connected gene communities, structures emerging from the interactions of noncoding regulatory elements and genes in the three-dimensional chromosomal space, provide a molecular explanation for the pathoetiology of CdLS associated with mutations in the cohesin-loading factor NIPBL and the cohesin subunit SMC1A NIPBL and cohesin are important constituents of connected gene communities that are centrally positioned at noncoding regulatory elements. Accordingly, genes deregulated in CdLS are positioned within reach of NIPBL- and cohesin-occupied regions through promoter-promoter interactions. Our findings suggest a dynamic model where NIPBL loads cohesin to connect genes in communities, offering an explanation for the gene expression deregulation in the CdLS.
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35
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Marcos-Alcalde Í, Mendieta-Moreno JI, Puisac B, Gil-Rodríguez MC, Hernández-Marcos M, Soler-Polo D, Ramos FJ, Ortega J, Pié J, Mendieta J, Gómez-Puertas P. Two-step ATP-driven opening of cohesin head. Sci Rep 2017; 7:3266. [PMID: 28607419 PMCID: PMC5468275 DOI: 10.1038/s41598-017-03118-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/24/2017] [Indexed: 02/07/2023] Open
Abstract
The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the "head" structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.
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Affiliation(s)
| | - Jesús I Mendieta-Moreno
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Beatriz Puisac
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - María Concepción Gil-Rodríguez
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - María Hernández-Marcos
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - Diego Soler-Polo
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Feliciano J Ramos
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Pié
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología y Departamento de Pediatría, Hospital Clínico Universitario "Lozano Blesa", Facultad de Medicina, Universidad de Zaragoza, ISS-Aragon and CIBERER-GCV02, 50009, Zaragoza, Spain
| | - Jesús Mendieta
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), 28049, Madrid, Spain
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Departamento de Biotecnología, Universidad Francisco de Vitoria, Pozuelo de Alarcón, 28223, Madrid, Spain
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Abstract
Folding of mammalian genomes into spatial domains is thought to depend on cohesin and CTCF proteins. Busslinger et al. (2017) reveal that transcription moves cohesin along DNA to CTCF-binding sites, providing insights into how cohesin and CTCF mediate chromosomal interactions by formation of chromatin loops.
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Affiliation(s)
- Judita Richterova
- Department of Genetics, Faculty of Life Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215 Bratislava, Slovakia
| | - Barbora Huraiova
- Department of Genetics, Faculty of Life Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215 Bratislava, Slovakia
| | - Juraj Gregan
- Department of Genetics, Faculty of Life Sciences, Comenius University in Bratislava, Ilkovicova 6, 84215 Bratislava, Slovakia; Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr.Bohr-Gasse 9, 1030 Vienna, Austria.
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Birot A, Eguienta K, Vazquez S, Claverol S, Bonneu M, Ekwall K, Javerzat JP, Vaur S. A second Wpl1 anti-cohesion pathway requires dephosphorylation of fission yeast kleisin Rad21 by PP4. EMBO J 2017; 36:1364-1378. [PMID: 28438891 PMCID: PMC5430217 DOI: 10.15252/embj.201696050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 03/10/2017] [Accepted: 03/27/2017] [Indexed: 01/06/2023] Open
Abstract
Cohesin mediates sister chromatid cohesion which is essential for chromosome segregation and repair. Sister chromatid cohesion requires an acetyl-transferase (Eso1 in fission yeast) counteracting Wpl1, promoting cohesin release from DNA We report here that Wpl1 anti-cohesion function includes an additional mechanism. A genetic screen uncovered that Protein Phosphatase 4 (PP4) mutants allowed cell survival in the complete absence of Eso1. PP4 co-immunoprecipitated Wpl1 and cohesin and Wpl1 triggered Rad21 de-phosphorylation in a PP4-dependent manner. Relevant residues were identified and mapped within the central domain of Rad21. Phospho-mimicking alleles dampened Wpl1 anti-cohesion activity, while alanine mutants were neutral indicating that Rad21 phosphorylation would shelter cohesin from Wpl1 unless erased by PP4. Experiments in post-replicative cells lacking Eso1 revealed two cohesin populations. Type 1 was released from DNA by Wpl1 in a PP4-independent manner. Type 2 cohesin, however, remained DNA-bound and lost its cohesiveness in a manner depending on Wpl1- and PP4-mediated Rad21 de-phosphorylation. These results reveal that Wpl1 antagonizes sister chromatid cohesion by a novel pathway regulated by the phosphorylation status of the cohesin kleisin subunit.
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Affiliation(s)
- Adrien Birot
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
| | - Karen Eguienta
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
| | - Stéphanie Vazquez
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
| | - Stéphane Claverol
- Centre Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Marc Bonneu
- Centre Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Karl Ekwall
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jean-Paul Javerzat
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
| | - Sabine Vaur
- Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS - Université de Bordeaux, Bordeaux, France
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38
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Messina G, Atterrato MT, Prozzillo Y, Piacentini L, Losada A, Dimitri P. The human Cranio Facial Development Protein 1 (Cfdp1) gene encodes a protein required for the maintenance of higher-order chromatin organization. Sci Rep 2017; 7:45022. [PMID: 28367969 PMCID: PMC5377257 DOI: 10.1038/srep45022] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/20/2017] [Indexed: 12/26/2022] Open
Abstract
The human Cranio Facial Development Protein 1 (Cfdp1) gene maps to chromosome 16q22.2-q22.3 and encodes the CFDP1 protein, which belongs to the evolutionarily conserved Bucentaur (BCNT) family. Craniofacial malformations are developmental disorders of particular biomedical and clinical interest, because they represent the main cause of infant mortality and disability in humans, thus it is important to understand the cellular functions and mechanism of action of the CFDP1 protein. We have carried out a multi-disciplinary study, combining cell biology, reverse genetics and biochemistry, to provide the first in vivo characterization of CFDP1 protein functions in human cells. We show that CFDP1 binds to chromatin and interacts with subunits of the SRCAP chromatin remodeling complex. An RNAi-mediated depletion of CFDP1 in HeLa cells affects chromosome organization, SMC2 condensin recruitment and cell cycle progression. Our findings provide new insight into the chromatin functions and mechanisms of the CFDP1 protein and contribute to our understanding of the link between epigenetic regulation and the onset of human complex developmental disorders.
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Affiliation(s)
- Giovanni Messina
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Maria Teresa Atterrato
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Yuri Prozzillo
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | - Lucia Piacentini
- Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
| | | | - Patrizio Dimitri
- Istituto Pasteur Italia-Fondazione Cenci Bolognetti and Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Italy.,Dipartimento di Biologia e Biotecnologie "Charles Darwin" Sapienza Università di Roma, Roma, Italy
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39
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Minina EA, Reza SH, Gutierrez-Beltran E, Elander PH, Bozhkov PV, Moschou PN. The Arabidopsis homolog of Scc4/MAU2 is essential for embryogenesis. J Cell Sci 2017; 130:1051-1063. [PMID: 28137757 DOI: 10.1242/jcs.196865] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/25/2017] [Indexed: 01/25/2023] Open
Abstract
Factors regulating dynamics of chromatin structure have direct impact on expression of genetic information. Cohesin is a multi-subunit protein complex that is crucial for pairing sister chromatids during cell division, DNA repair and regulation of gene transcription and silencing. In non-plant species, cohesin is loaded on chromatin by the Scc2-Scc4 complex (also known as the NIBPL-MAU2 complex). Here, we identify the Arabidopsis homolog of Scc4, which we denote Arabidopsis thaliana (At)SCC4, and show that it forms a functional complex with AtSCC2, the homolog of Scc2. We demonstrate that AtSCC2 and AtSCC4 act in the same pathway, and that both proteins are indispensable for cell fate determination during early stages of embryo development. Mutant embryos lacking either of these proteins develop only up to the globular stage, and show the suspensor overproliferation phenotype preceded by ectopic auxin maxima distribution. We further establish a new assay to reveal the AtSCC4-dependent dynamics of cohesin loading on chromatin in vivo Our findings define the Scc2-Scc4 complex as an evolutionary conserved machinery controlling cohesin loading and chromatin structure maintenance, and provide new insight into the plant-specific role of this complex in controlling cell fate during embryogenesis.
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Affiliation(s)
- Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, Uppsala SE-75007, Sweden
| | - Salim Hossain Reza
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, Uppsala SE-75007, Sweden
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, Uppsala SE-75007, Sweden
| | - Emilio Gutierrez-Beltran
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, Uppsala SE-75007, Sweden
| | - Pernilla H Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, Uppsala SE-75007, Sweden
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7015, Uppsala SE-75007, Sweden
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, PO Box 7080, Uppsala SE-75007, Sweden
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40
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Schenkel LC, Kernohan KD, McBride A, Reina D, Hodge A, Ainsworth PJ, Rodenhiser DI, Pare G, Bérubé NG, Skinner C, Boycott KM, Schwartz C, Sadikovic B. Identification of epigenetic signature associated with alpha thalassemia/mental retardation X-linked syndrome. Epigenetics Chromatin 2017; 10:10. [PMID: 28293299 PMCID: PMC5345252 DOI: 10.1186/s13072-017-0118-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Alpha thalassemia/mental retardation X-linked syndrome (ATR-X) is caused by a mutation at the chromatin regulator gene ATRX. The mechanisms involved in the ATR-X pathology are not completely understood, but may involve epigenetic modifications. ATRX has been linked to the regulation of histone H3 and DNA methylation, while mutations in the ATRX gene may lead to the downstream epigenetic and transcriptional effects. Elucidating the underlying epigenetic mechanisms altered in ATR-X will provide a better understanding about the pathobiology of this disease, as well as provide novel diagnostic biomarkers. RESULTS We performed genome-wide DNA methylation assessment of the peripheral blood samples from 18 patients with ATR-X and compared it to 210 controls. We demonstrated the evidence of a unique and highly specific DNA methylation "epi-signature" in the peripheral blood of ATRX patients, which was corroborated by targeted bisulfite sequencing experiments. Although genomically represented, differentially methylated regions showed evidence of preferential clustering in pericentromeric and telometric chromosomal regions, areas where ATRX has multiple functions related to maintenance of heterochromatin and genomic integrity. CONCLUSION Most significant methylation changes in the 14 genomic loci provide a unique epigenetic signature for this syndrome that may be used as a highly sensitive and specific diagnostic biomarker to support the diagnosis of ATR-X, particularly in patients with phenotypic complexity and in patients with ATRX gene sequence variants of unknown significance.
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Affiliation(s)
- Laila C Schenkel
- Department of Pathology and Lab Medicine, Western University, London, ON Canada
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON Canada
| | - Arran McBride
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON Canada
| | - Ditta Reina
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada.,Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON Canada
| | - Amanda Hodge
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada.,Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON Canada
| | - Peter J Ainsworth
- Department of Pathology and Lab Medicine, Western University, London, ON Canada.,Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Center, 800 Commissioner's Road E, B10-104, London, ON N6A 5W9 Canada.,Department of Paediatrics, Western University, London, ON Canada.,Department of Biochemistry, Western University, London, ON Canada.,Department of Oncology, Western University, London, ON Canada.,Children's Health Research Institute, London, ON Canada
| | - David I Rodenhiser
- Department of Paediatrics, Western University, London, ON Canada.,Department of Biochemistry, Western University, London, ON Canada.,Department of Oncology, Western University, London, ON Canada.,Children's Health Research Institute, London, ON Canada
| | - Guillaume Pare
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON Canada.,Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, ON Canada
| | - Nathalie G Bérubé
- Department of Paediatrics, Western University, London, ON Canada.,Department of Biochemistry, Western University, London, ON Canada.,Department of Oncology, Western University, London, ON Canada.,Children's Health Research Institute, London, ON Canada
| | - Cindy Skinner
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC USA
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON Canada
| | - Charles Schwartz
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC USA
| | - Bekim Sadikovic
- Department of Pathology and Lab Medicine, Western University, London, ON Canada.,Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Center, 800 Commissioner's Road E, B10-104, London, ON N6A 5W9 Canada.,Children's Health Research Institute, London, ON Canada
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41
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Zhang N, Pati D. Biology and insights into the role of cohesin protease separase in human malignancies. Biol Rev Camb Philos Soc 2017; 92:2070-2083. [PMID: 28177203 DOI: 10.1111/brv.12321] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/05/2017] [Accepted: 01/12/2017] [Indexed: 12/11/2022]
Abstract
Separase, an enzyme that resolves sister chromatid cohesion during the metaphase-to-anaphase transition, plays a pivotal role in chromosomal segregation and cell division. Separase protein, encoded by the extra spindle pole bodies like 1 (ESPL1) gene, is overexpressed in numerous human cancers including breast, bone, brain, and prostate. Separase is oncogenic, and its overexpression is sufficient to induce mammary tumours in mice. Either acute or chronic overexpression of separase in mouse mammary glands leads to aneuploidy and tumorigenesis, and inhibition of separase enzymatic activity decreases the growth of human breast tumour xenografts in mice. This review focuses on the biology of and insights into the molecular mechanisms of separase as an oncogene, and its significance and implications for human cancers.
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Affiliation(s)
- Nenggang Zhang
- Departments of Pediatrics and Molecular and Cellular Biology, Texas Children's Cancer Center, Baylor College of Medicine, 1102 Bates St., FC1220, Houston, TX 77030, U.S.A
| | - Debananda Pati
- Departments of Pediatrics and Molecular and Cellular Biology, Texas Children's Cancer Center, Baylor College of Medicine, 1102 Bates St., FC1220, Houston, TX 77030, U.S.A
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42
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Hopfner KP. Invited review: Architectures and mechanisms of ATP binding cassette proteins. Biopolymers 2017; 105:492-504. [PMID: 27037766 DOI: 10.1002/bip.22843] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/24/2016] [Accepted: 03/28/2016] [Indexed: 12/29/2022]
Abstract
ATP binding cassette (ABC) ATPases form chemo-mechanical engines and switches that function in a broad range of biological processes. Most prominently, a very large family of integral membrane NTPases-ABC transporters-catalyzes the import or export of a diverse molecules across membranes. ABC proteins are also important components of the chromosome segregation, recombination, and DNA repair machineries and regulate or catalyze critical steps of ribosomal protein synthesis. Recent structural and mechanistic studies draw interesting architectural and mechanistic parallels between diverse ABC proteins. Here, I review this state of our understanding how NTP-dependent conformational changes of ABC proteins drive diverse biological processes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 492-504, 2016.
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Affiliation(s)
- Karl-Peter Hopfner
- Department Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.,Center for Integrated Protein Science Munich, Ludwigs-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
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43
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Meulenbelt IM, Bhutani N, den Hollander W, Gay S, Oppermann U, Reynard LN, Skelton AJ, Young DA, Beier F, Loughlin J. The first international workshop on the epigenetics of osteoarthritis. Connect Tissue Res 2017; 58:37-48. [PMID: 27028588 DOI: 10.3109/03008207.2016.1168409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Osteoarthritis (OA) is a major clinical problem across the world, in part due to the lack of disease-modifying drugs resulting, to a significant degree, from our incomplete understanding of the underlying molecular mechanisms of the disease. Emerging evidence points to a role of epigenetics in the pathogenesis of OA, but research in this area is still in its early stages. In order to summarize current knowledge and to facilitate the potential coordination of future research activities, the first international workshop on the epigenetics of OA was held in Amsterdam in October 2015. Recent findings on DNA methylation and hydroxymethylation, histone modifications, noncoding RNAs, and other epigenetic mechanisms were presented and discussed. The workshop demonstrated the advantage of bringing together those working in this nascent field and highlights from the event are summarized in this report in the form of summaries from invited speakers and organizers.
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Affiliation(s)
- Ingrid M Meulenbelt
- a Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology , Leiden University Medical Center , Leiden , The Netherlands
| | - Nidhi Bhutani
- b Department of Orthopaedic Surgery , Stanford University School of Medicine , Stanford , CA , USA
| | - Wouter den Hollander
- a Department of Medical Statistics and Bioinformatics, Section of Molecular Epidemiology , Leiden University Medical Center , Leiden , The Netherlands
| | - Steffen Gay
- c Department of Rheumatology , Center of Experimental Rheumatology, University Hospital Zurich , Zurich , Switzerland
| | - Udo Oppermann
- d Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics , Rheumatology and Musculoskeletal Sciences, University of Oxford , Oxford , UK.,e Structural Genomics Consortium , University of Oxford , Oxford , UK
| | - Louise N Reynard
- f Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University , Newcastle-upon-Tyne , UK
| | - Andrew J Skelton
- f Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University , Newcastle-upon-Tyne , UK.,g Faculty of Medical Sciences, Bioinformatics Support Unit , Newcastle University , Newcastle-upon-Tyne , UK
| | - David A Young
- f Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University , Newcastle-upon-Tyne , UK
| | - Frank Beier
- h Department of Physiology and Pharmacology , Schulich School of Medicine and Dentistry, University of Western Ontario , London , ON , Canada
| | - John Loughlin
- f Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University , Newcastle-upon-Tyne , UK
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Grant MG, Patterson VL, Grimes DT, Burdine RD. Modeling Syndromic Congenital Heart Defects in Zebrafish. Curr Top Dev Biol 2017; 124:1-40. [DOI: 10.1016/bs.ctdb.2016.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
Genetic variation associated with disease often appears in non-coding parts of the genome. Understanding the mechanisms by which this phenomenon leads to disease is necessary to translate results from genetic association studies to the clinic. Assigning function to this type of variation is notoriously difficult because the human genome harbours a complex regulatory landscape with a dizzying array of transcriptional regulatory sequences, such as enhancers that have unpredictable, promiscuous and context-dependent behaviour. In this Review, we discuss how technological advances have provided increasingly detailed information on genome folding; for example, genome folding forms loops that bring enhancers and target genes into close proximity. We also now know that enhancers function within topologically associated domains, which are structural and functional units of chromosomes. Studying disease-associated mutations and chromosomal rearrangements in the context of the 3D genome will enable the identification of dysregulated target genes and aid the progression from descriptive genetic association results to discovering molecular mechanisms underlying disease.
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Murtha M, Esteller M. Extraordinary Cancer Epigenomics: Thinking Outside the Classical Coding and Promoter Box. Trends Cancer 2016; 2:572-584. [DOI: 10.1016/j.trecan.2016.08.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 12/23/2022]
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Ntziachristos P, Abdel-Wahab O, Aifantis I. Emerging concepts of epigenetic dysregulation in hematological malignancies. Nat Immunol 2016; 17:1016-24. [PMID: 27478938 PMCID: PMC5134743 DOI: 10.1038/ni.3517] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
The past decade brought a revolution in understanding of the structure, topology and disease-inducing lesions of RNA and DNA, fueled by unprecedented progress in next-generation sequencing. This technological revolution has also affected understanding of the epigenome and has provided unique opportunities for the analysis of DNA and histone modifications, as well as the first map of the non-protein-coding genome and three-dimensional (3D) chromosomal interactions. Overall, these advances have facilitated studies that combine genetic, transcriptomics and epigenomics data to address a wide range of issues ranging from understanding the role of the epigenome in development to targeting the transcription of noncoding genes in human cancer. Here we describe recent insights into epigenetic dysregulation characteristic of the malignant differentiation of blood stem cells based on studies of alterations that affect epigenetic complexes, enhancers, chromatin, long noncoding RNAs (lncRNAs), RNA splicing, nuclear topology and the 3D conformation of chromatin.
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Affiliation(s)
- Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Iannis Aifantis
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, New York, USA
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Gligoris T, Löwe J. Structural Insights into Ring Formation of Cohesin and Related Smc Complexes. Trends Cell Biol 2016; 26:680-693. [PMID: 27134029 PMCID: PMC4989898 DOI: 10.1016/j.tcb.2016.04.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 12/14/2022]
Abstract
Cohesin facilitates sister chromatid cohesion through the formation of a large ring structure that encircles DNA. Its function relies on two structural maintenance of chromosomes (Smc) proteins, which are found in almost all organisms tested, from bacteria to humans. In accordance with their ubiquity, Smc complexes, such as cohesin, condensin, Smc5-6, and the dosage compensation complex, affect almost all processes of DNA homeostasis. Although their precise molecular mechanism remains enigmatic, here we provide an overview of the architecture of eukaryotic Smc complexes with a particular focus on cohesin, which has seen the most progress recently. Given the evident conservation of many structural features between Smc complexes, it is expected that architecture and topology will have a significant role when deciphering their precise molecular mechanisms.
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Affiliation(s)
- Thomas Gligoris
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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Messina G, Atterrato MT, Dimitri P. When chromatin organisation floats astray: theSrcapgene and Floating–Harbor syndrome. J Med Genet 2016; 53:793-797. [DOI: 10.1136/jmedgenet-2016-103842] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 02/29/2016] [Accepted: 03/29/2016] [Indexed: 01/19/2023]
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