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Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding.

Siggers T, Chang AB, Teixeira A, Wong D, Williams KJ, Ahmed B, Ragoussis J, Udalova IA, Smale ST, Bulyk ML.

Nat Immunol. 2011 Nov 20;13(1):95-102. doi: 10.1038/ni.2151.


Characterizing the DNA binding site specificity of NF-κB with protein-binding microarrays (PBMs).

Siggers T, Gilmore TD, Barron B, Penvose A.

Methods Mol Biol. 2015;1280:609-30. doi: 10.1007/978-1-4939-2422-6_36.


Crystal structure of a free kappaB DNA: insights into DNA recognition by transcription factor NF-kappaB.

Huang DB, Phelps CB, Fusco AJ, Ghosh G.

J Mol Biol. 2005 Feb 11;346(1):147-60. Epub 2004 Dec 13.


A roadmap of constitutive NF-κB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses.

de Oliveira KA, Kaergel E, Heinig M, Fontaine JF, Patone G, Muro EM, Mathas S, Hummel M, Andrade-Navarro MA, Hübner N, Scheidereit C.

Genome Med. 2016 Mar 17;8(1):28. doi: 10.1186/s13073-016-0280-5.


The transcriptional specificity of NF-κB dimers is coded within the κB DNA response elements.

Wang VY, Huang W, Asagiri M, Spann N, Hoffmann A, Glass C, Ghosh G.

Cell Rep. 2012 Oct 25;2(4):824-39. doi: 10.1016/j.celrep.2012.08.042. Epub 2012 Oct 11.


Dimer-specific regulatory mechanisms within the NF-κB family of transcription factors.

Smale ST.

Immunol Rev. 2012 Mar;246(1):193-204. doi: 10.1111/j.1600-065X.2011.01091.x. Review.


One nucleotide in a kappaB site can determine cofactor specificity for NF-kappaB dimers.

Leung TH, Hoffmann A, Baltimore D.

Cell. 2004 Aug 20;118(4):453-64.


The CpG Dinucleotide Adjacent to a κB Site Affects NF-κB Function through Its Methylation.

Wang T, Li J, Ding K, Zhang L, Che Q, Sun X, Dai Y, Sun W, Bao M, Wang X, Yang L, Li Z.

Int J Mol Sci. 2017 Mar 1;18(3). pii: E528. doi: 10.3390/ijms18030528.


A biophysical characterisation of factors controlling dimerisation and selectivity in the NF-kappaB and NFAT families.

de Lumley M, Hart DJ, Cooper MA, Symeonides S, Blackburn JM.

J Mol Biol. 2004 Jun 18;339(5):1059-75.


Assessing sites of NF-κB DNA binding using chromatin immunoprecipitation.

Colleran A, Collins PE, Carmody RJ.

Methods Mol Biol. 2015;1280:47-59. doi: 10.1007/978-1-4939-2422-6_4.


Detection of a ternary complex of NF-kappaB and IkappaBalpha with DNA provides insights into how IkappaBalpha removes NF-kappaB from transcription sites.

Sue SC, Alverdi V, Komives EA, Dyson HJ.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1367-72. doi: 10.1073/pnas.1014323108. Epub 2011 Jan 10.


Characterization of the human intestinal CD98 promoter and its regulation by interferon-gamma.

Yan Y, Dalmasso G, Sitaraman S, Merlin D.

Am J Physiol Gastrointest Liver Physiol. 2007 Feb;292(2):G535-45. Epub 2006 Oct 5.


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

Wong D, Teixeira A, Oikonomopoulos S, Humburg P, Lone IN, Saliba D, Siggers T, Bulyk M, Angelov D, Dimitrov S, Udalova IA, Ragoussis J.

Genome Biol. 2011 Jul 29;12(7):R70. doi: 10.1186/gb-2011-12-7-r70.


Genome-wide analysis of gene expression in T cells to identify targets of the NF-kappa B transcription factor c-Rel.

Bunting K, Rao S, Hardy K, Woltring D, Denyer GS, Wang J, Gerondakis S, Shannon MF.

J Immunol. 2007 Jun 1;178(11):7097-109.


An optimized extended DNA kappa B site that enhances plasmid DNA nuclear import and gene expression.

Gonçalves C, Ardourel MY, Decoville M, Breuzard G, Midoux P, Hartmann B, Pichon C.

J Gene Med. 2009 May;11(5):401-11. doi: 10.1002/jgm.1312.


Genomic analysis reveals a novel nuclear factor-κB (NF-κB)-binding site in Alu-repetitive elements.

Antonaki A, Demetriades C, Polyzos A, Banos A, Vatsellas G, Lavigne MD, Apostolou E, Mantouvalou E, Papadopoulou D, Mosialos G, Thanos D.

J Biol Chem. 2011 Nov 4;286(44):38768-82. doi: 10.1074/jbc.M111.234161. Epub 2011 Sep 5.


A c-Rel subdomain responsible for enhanced DNA-binding affinity and selective gene activation.

Sanjabi S, Williams KJ, Saccani S, Zhou L, Hoffmann A, Ghosh G, Gerondakis S, Natoli G, Smale ST.

Genes Dev. 2005 Sep 15;19(18):2138-51.


Involvement of 5'-flanking kappaB-like sites within bcl-x gene in silica-induced Bcl-x expression.

Chen F, Demers LM, Vallyathan V, Lu Y, Castranova V, Shi X.

J Biol Chem. 1999 Dec 10;274(50):35591-5.

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