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Liu J, Zhang Z, Bando M, Itoh T, Deardorff MA, Li JR, Clark D, Kaur M, Tatsuro K, Kline AD, Chang C, Vega H, Jackson LG, Spinner NB, Shirahige K, Krantz ID. Genome-wide DNA methylation analysis in cohesin mutant human cell lines. Nucleic Acids Res 2010; 38:5657-71. [PMID: 20448023 PMCID: PMC2943628 DOI: 10.1093/nar/gkq346] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Revised: 04/19/2010] [Accepted: 04/21/2010] [Indexed: 12/17/2022] Open
Abstract
The cohesin complex has recently been shown to be a key regulator of eukaryotic gene expression, although the mechanisms by which it exerts its effects are poorly understood. We have undertaken a genome-wide analysis of DNA methylation in cohesin-deficient cell lines from probands with Cornelia de Lange syndrome (CdLS). Heterozygous mutations in NIPBL, SMC1A and SMC3 genes account for ∼65% of individuals with CdLS. SMC1A and SMC3 are subunits of the cohesin complex that controls sister chromatid cohesion, whereas NIPBL facilitates cohesin loading and unloading. We have examined the methylation status of 27 578 CpG dinucleotides in 72 CdLS and control samples. We have documented the DNA methylation pattern in human lymphoblastoid cell lines (LCLs) as well as identified specific differential DNA methylation in CdLS. Subgroups of CdLS probands and controls can be classified using selected CpG loci. The X chromosome was also found to have a unique DNA methylation pattern in CdLS. Cohesin preferentially binds to hypo-methylated DNA in control LCLs, whereas the differential DNA methylation alters cohesin binding in CdLS. Our results suggest that in addition to DNA methylation multiple mechanisms may be involved in transcriptional regulation in human cells and in the resultant gene misexpression in CdLS.
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Affiliation(s)
- Jinglan Liu
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Masashige Bando
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Takehiko Itoh
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew A. Deardorff
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Jennifer R. Li
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Dinah Clark
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Maninder Kaur
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Kondo Tatsuro
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Antonie D. Kline
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Celia Chang
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Hugo Vega
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Laird G. Jackson
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Nancy B. Spinner
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Katsuhiko Shirahige
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
| | - Ian D. Krantz
- Division of Human Genetics, Abramson Research Institute, Center for Biomedical Informatics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA, Laboratory of Chromosome Structure and Function, Department of Biological Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, B2C 4259, Nagatsuta, Midori-ku, Yokohama City, Kanagawa 226-8501, Japan, The University of Pennsylvania School of Medicine, PA 19104, USA, Division of Developmental Disability, Misakaenosono Mutsumi Developmental, Medical, and Welfare Center, Konagai-cho Maki 570-1, Isahaya, 859-0169, Japan, Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD 21204, Genomic and Microarray Facility, the Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA, Department of Genetics and Genomics Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA and Department of Obstetrics and Gynecology, Drexel University School of Medicine, Philadelphia, PA 19104, USA
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