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The HMGB chromatin protein Nhp6A can bypass obstacles when traveling on DNA.
Kamagata, Kiyoto; Ouchi, Kana; Tan, Cheng; Mano, Eriko; Mandali, Sridhar; Wu, Yining; Takada, Shoji; Takahashi, Satoshi; Johnson, Reid C.
Afiliación
  • Kamagata K; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
  • Ouchi K; Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
  • Tan C; Department of Chemistry, Faculty of Science, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
  • Mano E; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
  • Mandali S; Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
  • Wu Y; Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
  • Takada S; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
  • Takahashi S; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1737 USA.
  • Johnson RC; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan.
Nucleic Acids Res ; 48(19): 10820-10831, 2020 11 04.
Article en En | MEDLINE | ID: mdl-32997109
ABSTRACT
DNA binding proteins rapidly locate their specific DNA targets through a combination of 3D and 1D diffusion mechanisms, with the 1D search involving bidirectional sliding along DNA. However, even in nucleosome-free regions, chromosomes are highly decorated with associated proteins that may block sliding. Here we investigate the ability of the abundant chromatin-associated HMGB protein Nhp6A from Saccharomyces cerevisiae to travel along DNA in the presence of other architectural DNA binding proteins using single-molecule fluorescence microscopy. We observed that 1D diffusion by Nhp6A molecules is retarded by increasing densities of the bacterial proteins Fis and HU and by Nhp6A, indicating these structurally diverse proteins impede Nhp6A mobility on DNA. However, the average travel distances were larger than the average distances between neighboring proteins, implying Nhp6A is able to bypass each of these obstacles. Together with molecular dynamics simulations, our analyses suggest two binding modes mobile molecules that can bypass barriers as they seek out DNA targets, and near stationary molecules that are associated with neighboring proteins or preferred DNA structures. The ability of mobile Nhp6A molecules to bypass different obstacles on DNA suggests they do not block 1D searches by other DNA binding proteins.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: ADN / Proteínas de Saccharomyces cerevisiae / Proteínas HMGN Idioma: En Revista: Nucleic Acids Res Año: 2020 Tipo del documento: Article País de afiliación: Japón

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: ADN / Proteínas de Saccharomyces cerevisiae / Proteínas HMGN Idioma: En Revista: Nucleic Acids Res Año: 2020 Tipo del documento: Article País de afiliación: Japón