Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context
| Autor: | Sergei Rudnizky, Amit Meller, Philippa Melamed, Allison H. Squires, Omri Malik, Ariel Kaplan, Hadeel Khamis |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Optical Tweezers Transcription Genetic Base pair Biology Substrate Specificity 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine Structural Biology Genetics Transcriptional regulation Humans Protein Interaction Domains and Motifs Binding site Promoter Regions Genetic Transcription factor Gene 030304 developmental biology Early Growth Response Protein 1 Regulation of gene expression Zinc finger 0303 health sciences Binding Sites Base Sequence Promoter DNA Single Molecule Imaging Cell biology DNA binding site Kinetics 030104 developmental biology chemistry Gene Expression Regulation Biophysics Nucleic Acid Conformation Thermodynamics 030217 neurology & neurosurgery hormones hormone substitutes and hormone antagonists Protein Binding |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 |
| Popis: | Most functional transcription factor (TF) binding sites deviate from their “consensus” recognition motif, although their sites and flanking sequences are often conserved across species. Here, we used single-molecule DNA unzipping with optical tweezers to study how Egr-1, a TF harbouring 3 zinc fingers (ZF1,ZF2 and ZF3), is modulated by the sequence and context of its functional sites in the Lhb gene promoter. We find that both the core 9 base pairs bound to Egr-1 in each of the sites, and the base pairs flanking them, modulate the affinity and structure of the protein-DNA complex. The effect of the flanking sequences is asymmetric, with a stronger effect for the sequence flanking ZF3. Characterization of the dissociation time of Egr-1 revealed that a local, mechanical perturbation of the interactions of ZF3 destabilizes the complex more effectively than a perturbation of the ZF1 interactions. Our results reveal a novel role for ZF3 in the interaction of Egr-1 with other proteins and the DNA, providing insight on the regulation of Lhb and other genes by Egr-1. Moreover, our findings reveal the potential of small changes in DNA sequence to alter transcriptional regulation, and may shed light on the organization of regulatory elements at promoters. |
| Databáze: | OpenAIRE |
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