Abstract
DEAF1 is a transcriptional regulator associated with autoimmune and neurological disorders and is known to bind TTCG motifs. To further ascertain preferred DEAF1 DNA ligands, we screened a random oligonucleotide library containing an “anchored” CpG motif. We identified a binding consensus that generally conformed to a repeated TTCGGG motif, with the two invariant CpG dinucleotides separated by 6–11 nucleotides. Alteration of the consensus surrounding the dual CpG dinucleotides, or cytosine methylation of a single CpG half-site, eliminated DEAF1 binding. A sequence within the Htr1a promoter that resembles the binding consensus but contains a single CpG motif was confirmed to have low affinity binding with DEAF1. A DEAF1 binding consensus was identified in the EIF4G3 promoter and ChIP assay showed endogenous DEAF1 was bound to the region. We conclude that DEAF1 preferentially binds variably spaced and unmethylated CpG-containing half-sites when they occur within an appropriate consensus.
Highlights
Deformed Epidermal Autoregulatory Factor 1 (DEAF1) is a transcription factor that binds to TTCG half-sites through a centralized DNA binding SAND (Sp-100, AIRE, NucP41/75 and DEAF1) domain [1,2,3]
MEME analysis indicated that 43 of the 58 identified binding sequences utilized the anchor CpG dinucleotide as one of two CpG dinucleotides found in the DEAF1 binding motif
Based on the half-site consensus analysis of this sequence, the 2nd and 3rd TTCG half-sites have a CpG spacing of 6 nucleotides, while the 1st and 3rd TTCG motifs have a CpG spacing of 10 nucleotides, suggesting either spacing could contribute to binding
Summary
Deformed Epidermal Autoregulatory Factor 1 (DEAF1) is a transcription factor that binds to TTCG half-sites through a centralized DNA binding SAND (Sp-100, AIRE, NucP41/75 and DEAF1) domain [1,2,3]. The SAND domain contains a positively charged region encompassing a conserved KDWK motif [3]. An adjacent zinc finger domain and nuclear localization signal are necessary for DEAF1-DNA interactions [4]. DEAF1 displays dual activity, repressing its own promoter activity while activating other promoters such as Eif4g3 [3, 5, 6]. PLOS ONE | DOI:10.1371/journal.pone.0115908 December 22, 2014
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