DNA methylation in mouse A-repeats in DNA methyltransferase-knockout ES cells and in normal cells determined by bisulfite genomic sequencing |
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| Institution: | 1. Neuroimmunology Unit, Department of Neuroscience, Hospital Alemán, Buenos Aires, Argentina;2. Internal Medicine Department, Hospital Alemán, Buenos Aires, Argentina;3. Centro de esclerosis múltiple de Buenos Aires, Buenos Aires, Argentina;4. Neurology Department, Sanatorio Güemes, Buenos Aires, Argentina;5. Neuroimmunology Section, Neurology Department, Hospital de Clínicas “José de San Martín”, University of Buenos Aires, Buenos Aires, Argentina;6. Servicio de Neurología, Hospital Universitario de CEMIC, Buenos Aires, Argentina;1. UT Southwestern Medical Center, Department of Neurology & Neurotherapeutics Neuroinnovation Program, Multiple Sclerosis & Neuroimmunology Imaging Program, Dallas, Texas, U.S.A;2. University of Texas at Dallas, Department of Computer Science, Dallas, Texas, U.S.A;3. UT Southwestern Medical Center, Department of Radiology, Dallas, Texas, U.S.A;4. University of Calgary, Cumming School of Medicine, Calgary, Alberta, Canada;5. Mayo Clinic, Rochester, Minnesota, U.S.A;1. Department of Neurology, Centro Hospitalar Universitário de São João, Porto, Portugal;2. Department of Clinical Neurosciences and Mental Health, Faculdade de Medicina da Universidade do Porto, Porto, Portugal;3. Department of Medicine, Queen Elizabeth Hospital, Hong Kong SAR, China;4. Department of Neurology, Research Institute and Hospital of National Cancer Center, Goyang, Republic of Korea;5. Neurological Institute, Cleveland Clinic Abu Dhabi, United Arab Emirates;6. Walton Center NHS Foundation Trust, Liverpool, United Kingdom;7. Service de Neurologie, Hôpital Pierre Zobda-Quitman, Fort-de-France, Martinique;8. NeuroCure Clinical Research, Berlin, Germany;9. Department of Neurology, Charité - Universitätsmedizin Berlin, Germany;10. Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, Germany;11. Max-Delbrück-Center for Molecular Medicine, Berlin, Germany;12. Department of Neurology, Tohoku Medical and Pharmaceutical University, Sendai, Japan;13. Department of Neurology, National Neuroscience Institute, Singapore;14. Department of Neurology and Clinical Investigation Center, Strasbourg University Hospital, Strasbourg, France;15. Siriraj Neuroimmunology Center, Siriraj Hospital, Mahidol University,Thailand;p. Department of Neurology, National Neuroscience Institute, Singapore;q. Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China;r. Walton Center NHS Foundation Trust, Liverpool, United Kingdom;s. Nuffield Department of Clinical Neurosciences, Oxford University Hospitals, Oxford, United Kingdom;t. Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States;u. Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States;v. Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China;w. Experimental and Clinical Research Center, Charité - Universitätsmedizin Berlin, Germany;x. Max-Delbrück-Center for Molecular Medicine, Berlin, Germany;y. Neurobiology, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark;z. Department of Neurology, Slagelse Hospital, Institute of Regional Health Research, Slagelse, Denmark;11. Service de Neurologie, Hôpital Pierre Zobda-Quitman, Fort-de-France, Martinique;22. Siriraj Neuroimmunology Center, Siriraj Hospital, Mahidol University, Thailand;33. Bumrungrad International Hospital, Thailand;44. Departments of Laboratory Medicine and Pathology and Neurology and the Center for MS and Autoimmune Neurology, Mayo Clinic, Rochester, MN, United States;55. Department of Medicine, Pamela Youde Nethersole Eastern Hospital, Hong Kong;66. Department of Neurology and Clinical Investigation Center, Strasbourg University Hospital, Strasbourg, France;77. Department of Pharmacology, Experimental Neuropathology Group, University of Oxford, Mansfield Road OX1 3QT, United Kingdom;88. Department of Neurology, National Neuroscience Institute, Singapore;99. Department of Neurology, Tohoku University Graduate School of Medicine, Sendai, Japan;1010. Center for Advanced Neurological Research, Nitte University, Mangalore, India;1111. Department of Neurology, Research Institute and Hospital of National Cancer Center, Goyang, Republic of Korea;1212. Nuffield Department of Clinical Neurosciences, West Wing, John Radcliffe Hospital, Oxford University Hospitals, Oxford OX3 9DU, United Kingdom |
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| Abstract: | Mouse ES cells with a null mutation of the known DNA methyltransferase retain some residual DNA methylation and can methylate foreign sequences de novo. We have used bisulfite genomic sequencing to examine the sequence specificity and distributions of methylation of a hypermethylated CG island sequence, mouse A-repeats. There were 13 CG dinucleotides in the region examined, 12 of which were methylated to variable extents in all DNAs. We found that: (1) there is considerable residual DNA methylation in ES cells lacking the known DNA methyltransferase (29% of normal methylation in the complete knockout ES DNA); (2) this other activity methylates at exactly the same CG sites as the major methyltransferase; and (3) differences in the distribution of methylated sites between A-repeats in these DNAs are consistent with this other activity methylating in a random de novo fashion. Also, the lack of any methylation in non-CG sites argues that, in other studies where non-CG methylation sites have been found by bisulfite sequencing, detection of such sites of non-CG methylation is not an inherent artifact in this methodology. |
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