Journal
NUCLEIC ACIDS RESEARCH
Volume 46, Issue 22, Pages 11883-11897Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gky1057
Keywords
-
Categories
Funding
- National Institutes of Health [GM120625]
- Science Engineering and Research Board, Department of Science and Technology, Government of India [SR/S2/JCB-47/2009]
Ask authors/readers for more resources
Spatial and temporal expression of genes is essential formaintaining phenotype integrity. Transcription factors (TFs) modulate expression patterns by binding to specific DNA sequences in the genome. Along with the core binding motif, the flanking sequence context can play a role in DNA-TF recognition. Here, we employ high-throughput in vitro and in silico analyses to understand the influence of sequences flanking the cognate sites in binding of three most prevalent eukaryotic TF families (zinc finger, homeodomain and bZIP). In vitro binding preferences of each TF toward the entire DNA sequence space were correlated with a wide range of DNA structural parameters, including DNA flexibility. Results demonstrate that conformational plasticity of flanking regions modulates binding affinity of certain TF families. DNA duplex stability and minor groove width also play an important role in DNA-TF recognition but differ in how exactly they influence the binding in each specific case. Our analyses further reveal that the structural features of preferred flanking sequences are not universal, as similar DNA-binding folds can employ distinct DNA recognition modes.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available