Protein-mediated looping of DNA under tension requires supercoiling

• Type of Material: Article
• Authors: Yan Yan, Emory University; Fenfei Leng, Florida International University; Laura Finzi, Emory University; David Dunlap, Emory University
• Language: English
• Date: 2018-03-16
• Publisher: Oxford University Press (OUP): Policy C - Option B
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2018.
• License: Creative Commons Attribution-NonCommercial 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1093/nar/gky021
• Title of Journal or Parent Work: Nucleic Acids Research
• ISSN: 0305-1048
• Volume: 46
• Issue: 5
• Start Page: 2370
• End Page: 2379
• Grant/Funding Information: National Institutes of Health [GM084070, 1R15GM109254]. Funding for open access charge: National Institutes of Health [GM084070].
• Keywords: FORCE; BACTERIAL CHROMOSOME; TRANSCRIPTION; TETHERED-PARTICLE MOTION; MOLECULE; Life Sciences & Biomedicine; CHROMATIN; ESCHERICHIA-COLI; Biochemistry & Molecular Biology; Science & Technology; LAC REPRESSOR; HU PROTEIN; BINDING
• Research Categories: Chemistry, Biochemistry; Physics, Molecular

Abstract

Protein-mediated DNA looping is ubiquitous in chromatin organization and gene regulation, but to what extent supercoiling or nucleoid associated proteins promote looping is poorly understood. Using the lac repressor (LacI), a paradigmatic loop-mediating protein, we measured LacI-induced looping as a function of either supercoiling or the concentration of the HU protein, an abundant nucleoid protein in Escherichia coli. Negative supercoiling to physiological levels with magnetic tweezers easily drove the looping probability from 0 to 100% in single DNA molecules under slight tension that likely exists in vivo. In contrast, even saturating (micromolar) concentrations of HU could not raise the looping probability above 30% in similarly stretched DNA or 80% in DNA without tension. Negative supercoiling is required to induce significant looping of DNA under any appreciable tension.