DNA Architecture and Transcriptional Regulation Exploring DNA's Mechanical Code

Abstract

DNA architecture plays a key role in determining spatial and temporal patterns of gene expression. This architecture encompasses both the nucleotide sequence (i.e., the information content) and the physical state of the DNA such as its spatial organization and mechanical properties. We explore transcriptional regulation by DNA looping in the lac operon, where transcriptional control is realized by the simultaneous binding of Lac repressor to two binding sites separated by hundreds of base pairs on the DNA. We develop a statistical mechanical model to quantify repression and the in vivo energy cost of different DNA conformations in bacteria.Based on the falsifiable predictions generated by this model we construct a library of promoters in which their DNA architecture is varied systematically. Properties such as the length of the intervening DNA and its sequence-dependent flexibility are controlled and their resulting effect on the gene expression level and its noise are quantified at the single cell level. The goal of this work is to make a systematic and thorough comparison of theory and experiment in a parameter-free setting which strictly tests our understanding of the relation between DNA architecture and the level of gene expression.