Interaction of the Chromatin Remodeling Protein hINO80 with DNA

• Published in: PloS one 2016-07, Vol.11 (7), p.e0159370-e0159370
• Main Authors: Mendiratta, Shweta, Bhatia, Shipra, Jain, Shruti, Kaur, Taniya, Brahmachari, Vani
• Format: Article
• Language: English
• Subjects: Ambedkar, Bhimra Ramji (1891-1956); Analysis; Animals; Base Sequence; Binding; Binding Sites; Biology and Life Sciences; Biomedical research; Cell division; Cell Nucleus - chemistry; Cell Nucleus - metabolism; Chromatin; Chromatin - chemistry; Chromatin - metabolism; Chromatin Assembly and Disassembly; Chromatin remodeling; Cloning, Molecular; Deoxyribonucleic acid; DNA; DNA - metabolism; DNA binding; DNA Helicases - antagonists & inhibitors; DNA Helicases - genetics; DNA Helicases - metabolism; DNA repair; Drosophila; Drosophila melanogaster; Drosophila Proteins - genetics; Drosophila Proteins - metabolism; Escherichia coli - genetics; Escherichia coli - metabolism; Gene Expression; Gene regulation; Genomes; HEK293 Cells; Histones - genetics; Histones - metabolism; Humans; Insects; Polycomb group proteins; Protein Binding; Protein Interaction Domains and Motifs; Proteins; Recombinant Fusion Proteins - genetics; Recombinant Fusion Proteins - metabolism; Reporter gene; Research and Analysis Methods; RNA, Small Interfering - genetics; RNA, Small Interfering - metabolism; SELEX Aptamer Technique; Stem cells; Transcription Factors - genetics; Transcription Factors - metabolism; YY1 Transcription Factor - genetics; YY1 Transcription Factor - metabolism
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0159370

The presence of a highly conserved DNA binding domain in INO80 subfamily predicted that INO80 directly interacts with DNA and we demonstrated its DNA binding activity in vitro. Here we report the consensus motif recognized by the DBINO domain identified by SELEX method and demonstrate the specific interaction of INO80 with the consensus motif. We show that INO80 significantly down regulates the reporter gene expression through its binding motif, and the repression is dependent on the presence of INO80 but not YY1 in the cell. The interaction is lost if specific residues within the consensus motif are altered. We identify a large number of potential target sites of INO80 in the human genome through in silico analysis that can grouped into three classes; sites that contain the recognition sequence for INO80 and YY1, only YY1 and only INO80. We demonstrate the binding of INO80 to a representative set of sites in HEK cells and the correlated repressive histone modifications around the binding motif. In the light of the role of INO80 in homeotic gene regulation in Drosophila as an Enhancer of trithorax and polycomb protein (ETP) that can modify the effect of both repressive complexes like polycomb as well as the activating complex like trithorax, it remains to be seen if INO80 can act as a recruiter of chromatin modifying complexes.