Using synthetic bacterial enhancers to reveal a looping-based mechanism for quenching-like repression

Michal Brunwasser-Meirom, Yaroslav Pollak, Sarah Goldberg, Lior Levy, Orna Atar and Roee Amit ()
Additional contact information
Michal Brunwasser-Meirom: Technion—Israel Institute of Technology
Yaroslav Pollak: Russell Berrie Nanotechnology Institute, Technion—Israel Institute of Technology
Sarah Goldberg: Technion—Israel Institute of Technology
Lior Levy: Technion—Israel Institute of Technology
Orna Atar: Technion—Israel Institute of Technology
Roee Amit: Technion—Israel Institute of Technology

Nature Communications, 2016, vol. 7, issue 1, 1-12

Abstract: Abstract We explore a model for ‘quenching-like’ repression by studying synthetic bacterial enhancers, each characterized by a different binding site architecture. To do so, we take a three-pronged approach: first, we compute the probability that a protein-bound dsDNA molecule will loop. Second, we use hundreds of synthetic enhancers to test the model’s predictions in bacteria. Finally, we verify the mechanism bioinformatically in native genomes. Here we show that excluded volume effects generated by DNA-bound proteins can generate substantial quenching. Moreover, the type and extent of the regulatory effect depend strongly on the relative arrangement of the binding sites. The implications of these results are that enhancers should be insensitive to 10–11 bp insertions or deletions (INDELs) and sensitive to 5–6 bp INDELs. We test this prediction on 61 σ54-regulated qrr genes from the Vibrio genus and confirm the tolerance of these enhancers’ sequences to the DNA’s helical repeat.

Date: 2016
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/ncomms10407 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms10407

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/ncomms10407

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().