Positive and negative design for nonconsensus protein-DNA binding affinity in the vicinity of functional binding sites.

ABSTRACT: Recent experiments provide an unprecedented view of protein-DNA binding in yeast and human genomes at single-nucleotide resolution. These measurements, performed over large cell populations, show quite generally that sequence-specific transcription regulators with well-defined protein-DNA consensus motifs bind only a fraction among all consensus motifs present in the genome. Alternatively, proteins in vivo often bind DNA regions lacking known consensus sequences. The rules determining whether a consensus motif is functional remain incompletely understood. Here we predict that genomic background surrounding specific protein-DNA binding motifs statistically modulates the binding of sequence-specific transcription regulators to these motifs. In particular, we show that nonconsensus protein-DN

SUBMITTER: Afek A 

PROVIDER: S-EPMC3822674 | biostudies-literature | 2013 Oct

REPOSITORIES: biostudies-literature