Your browser doesn't support javascript.
loading
Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation.
Khamis, Hadeel; Rudnizky, Sergei; Melamed, Philippa; Kaplan, Ariel.
Affiliation
  • Khamis H; Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Rudnizky S; Faculty of Physics, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Melamed P; Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
  • Kaplan A; Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel.
Nucleic Acids Res ; 49(19): 10975-10987, 2021 11 08.
Article in En | MEDLINE | ID: mdl-34606618
ABSTRACT
The interaction of transcription factors with their response elements in DNA is emerging as a highly complex process, whose characterization requires measuring the full distribution of binding and dissociation times in a well-controlled assay. Here, we present a single-molecule assay that exploits the thermal fluctuations of a DNA hairpin to detect the association and dissociation of individual, unlabeled transcription factors. We demonstrate this new approach by following the binding of Egr1 to its consensus motif and the three binding sites found in the promoter of the Lhb gene, and find that both association and dissociation are modulated by the 9 bp core motif and the sequences around it. In addition, CpG methylation modulates the dissociation kinetics in a sequence and position-dependent manner, which can both stabilize or destabilize the complex. Together, our findings show how variations in sequence and methylation patterns synergistically extend the spectrum of a protein's binding properties, and demonstrate how the proposed approach can provide new insights on the function of transcription factors.
Subject(s)

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: DNA / DNA Methylation / Response Elements / Luteinizing Hormone, beta Subunit / Early Growth Response Protein 1 Limits: Humans Language: En Journal: Nucleic Acids Res Year: 2021 Document type: Article Affiliation country: Israel

Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: DNA / DNA Methylation / Response Elements / Luteinizing Hormone, beta Subunit / Early Growth Response Protein 1 Limits: Humans Language: En Journal: Nucleic Acids Res Year: 2021 Document type: Article Affiliation country: Israel
...