Many genes are spaced closely, allowing coordination without explicit control through
shared regulatory elements and molecular interactions. We study the dynamics of a …

Closely spaced promoters in tandem formation are abundant in bacteria. We investigated
the evolutionary conservation, biological functions, and the RNA and single-cell protein …

What are the forces that shape the structure of prokaryotic genomes: the order of genes, their
proximity, and their orientation? Coregulation and coordinated horizontal gene transfer are …

Through combinatorial regulation, regulators partner with each other to control common
targets and this allows a small number of regulators to govern many targets. One interesting …

Coordination of transcription in bacteria occurs at supra-operonic scales, but the extent,
specificity, and mechanisms of such regulation are poorly understood. Here, we tackle this …

Following recent discoveries of colocalization of downstream-regulating genes in living
cells, the impact of the spatial distance between such genes on the kinetics of gene product …

Coregulation of the expression of groups of genes has been extensively demonstrated
empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use …

Transcription initiation starts with unwinding of promoter DNA by RNA polymerase (RNAP)
to form a catalytically competent RNAP-promoter complex (RPo). Despite extensive study …

Chromosomes in the eukaryotic nucleus are highly compacted, with a crowded polymer
organization of fractal dimension three. However, for many functional processes, including …

The ability to construct synthetic gene networks enables experimental investigations of
deliberately simplified systems that can be compared to qualitative and quantitative …