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

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 sen

SUBMITTER: Brunwasser-Meirom M 

PROVIDER: S-EPMC4740811 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature