Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits

Daniel Wong, Ana Teixeira, Spyros Oikonomopoulos, Peter Humburg, Imtiaz N. Lone, David Saliba, Trevor Siggers, Martha Bulyk, Dimitar Angelov, Stefan Dimitrov, Irina A. Udalova, Jiannis Ragoussis

Research output: Contribution to journalArticle

85 Citations (Scopus)

Abstract

Background: Genetic studies have provided ample evidence of the influence of non-coding DNA polymorphisms on trait variance, particularly those occurring within transcription factor binding sites. Protein binding microarrays and other platforms that can map these sites with great precision have enhanced our understanding of how a single nucleotide polymorphism can alter binding potential within an in vitro setting, allowing for greater predictive capability of its effect on a transcription factor binding site.Results: We have used protein binding microarrays and electrophoretic mobility shift assay-sequencing (EMSA-Seq), a deep sequencing based method we developed to analyze nine distinct human NF-κB dimers. This family of transcription factors is one of the most extensively studied, but our understanding of its DNA binding preferences has been limited to the originally described consensus motif, GGRRNNYYCC. We highlight differences between NF-κB family members and also put under the spotlight non-canonical motifs that have so far received little attention. We utilize our data to interpret the binding of transcription factors between individuals across 1,405 genomic regions laden with single nucleotide polymorphisms. We also associated binding correlations made using our data with risk alleles of disease and demonstrate its utility as a tool for functional studies of single nucleotide polymorphisms in regulatory regions.Conclusions: NF-κB dimers bind specifically to non-canonical motifs and these can be found within genomic regions in which a canonical motif is not evident. Binding affinity data generated with these different motifs can be used in conjunction with data from chromatin immunoprecipitation-sequencing (ChIP-Seq) to enable allele-specific analyses of expression and transcription factor-DNA interactions on a genome-wide scale.

Original languageEnglish
Article numberr70
JournalGenome Biology
Volume12
Issue number7
DOIs
Publication statusPublished - 19 Jul 2011
Externally publishedYes

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polymorphism
Transcription Factors
transcription factors
single nucleotide polymorphism
Single Nucleotide Polymorphism
Protein Array Analysis
DNA
protein binding
genomics
allele
Protein Binding
binding sites
Alleles
protein
Binding Sites
alleles
High-Throughput Nucleotide Sequencing
Chromatin Immunoprecipitation
Nucleic Acid Regulatory Sequences
Electrophoretic Mobility Shift Assay

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Wong, D., Teixeira, A., Oikonomopoulos, S., Humburg, P., Lone, I. N., Saliba, D., ... Ragoussis, J. (2011). Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. Genome Biology, 12(7), [r70]. https://doi.org/10.1186/gb-2011-12-7-r70

Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. / Wong, Daniel; Teixeira, Ana; Oikonomopoulos, Spyros; Humburg, Peter; Lone, Imtiaz N.; Saliba, David; Siggers, Trevor; Bulyk, Martha; Angelov, Dimitar; Dimitrov, Stefan; Udalova, Irina A.; Ragoussis, Jiannis.

In: Genome Biology, Vol. 12, No. 7, r70, 19.07.2011.

Research output: Contribution to journalArticle

Wong, D, Teixeira, A, Oikonomopoulos, S, Humburg, P, Lone, IN, Saliba, D, Siggers, T, Bulyk, M, Angelov, D, Dimitrov, S, Udalova, IA & Ragoussis, J 2011, 'Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits', Genome Biology, vol. 12, no. 7, r70. https://doi.org/10.1186/gb-2011-12-7-r70
Wong, Daniel ; Teixeira, Ana ; Oikonomopoulos, Spyros ; Humburg, Peter ; Lone, Imtiaz N. ; Saliba, David ; Siggers, Trevor ; Bulyk, Martha ; Angelov, Dimitar ; Dimitrov, Stefan ; Udalova, Irina A. ; Ragoussis, Jiannis. / Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits. In: Genome Biology. 2011 ; Vol. 12, No. 7.
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