• Open Access

Quantitative assessment of higher-order chromatin structure of the INK4/ARF locus in human senescent cells

Authors

  • Akiyuki Hirosue,

    1. Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Global Center of Excellence ‘Cell Fate Regulation Research and Education Unit’, Kumamoto University, Kumamoto 860-0811, Japan
    2. Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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  • Ko Ishihara,

    1. Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto 860-0811, Japan
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  • Kazuaki Tokunaga,

    1. Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Global Center of Excellence ‘Cell Fate Regulation Research and Education Unit’, Kumamoto University, Kumamoto 860-0811, Japan
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  • Takehisa Watanabe,

    1. Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Global Center of Excellence ‘Cell Fate Regulation Research and Education Unit’, Kumamoto University, Kumamoto 860-0811, Japan
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  • Noriko Saitoh,

    1. Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Global Center of Excellence ‘Cell Fate Regulation Research and Education Unit’, Kumamoto University, Kumamoto 860-0811, Japan
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  • Masafumi Nakamoto,

    1. Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Global Center of Excellence ‘Cell Fate Regulation Research and Education Unit’, Kumamoto University, Kumamoto 860-0811, Japan
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  • Tamir Chandra,

    1. Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
    2. Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
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  • Masashi Narita,

    1. Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge CB2 0RE, UK
    2. Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK
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  • Masanori Shinohara,

    1. Department of Oral and Maxillofacial Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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  • Mitsuyoshi Nakao

    1. Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Global Center of Excellence ‘Cell Fate Regulation Research and Education Unit’, Kumamoto University, Kumamoto 860-0811, Japan
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Mitsuyoshi Nakao, Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811,Japan. Tel: +81 96 373 6800; fax: +81 96 373 6804; e-mail: mnakao@gpo.kumamoto-u.ac.jp

Summary

Somatic cells can be reset to oncogene-induced senescent (OIS) cells or induced pluripotent stem (iPS) cells by expressing specified factors. The INK4/ARF locus encodes p15INK4b, ARF, and p16INK4a genes in human chromosome 9p21, the products of which are known as common key reprogramming regulators. Compared with growing fibroblasts, the CCCTC-binding factor CTCF is remarkably up-regulated in iPS cells with silencing of the three genes in the locus and is reversely down-regulated in OIS cells with high expression of p15INK4b and p16INK4a genes. There are at least three CTCF-enriched sites in the INK4/ARF locus, which possess chromatin loop-forming activities. These CTCF-enriched sites and the p16INK4a promoter associate to form compact chromatin loops in growing fibroblasts, while CTCF depletion disrupts the loop structure. Interestingly, the loose chromatin structure is found in OIS cells. In addition, the INK4/ARF locus has an intermediate type of chromatin compaction in iPS cells. These results suggest that senescent cells have distinct higher-order chromatin signature in the INK4/ARF locus.

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