p63 consensus DNA-binding site: identification, analysis and application into a p63MH algorithm

Abstract

p53 and p63 belong to a family of sequence-specific transcription factors regulating key cellular processes. Differential composition of the p53 and p63 DNA-binding sites may contribute to distinct functions of these protein homologues. We used SELEX (systematic evolution of ligands by exponential enrichment) methodology to identify nucleic acid ligands for p63. We found that p63 bound preferentially to DNA fragments conforming to the 20 bp sequence 5 0 -RRRC(A/G)(A/T)GYYYRRRC(A/T) (C/T)GYYY-3 0 . Relative to the p53 consensus, the p63 consensus DNA-binding site (DBS) was more degenerate, particularly at positions 10 and 11, and was enriched for A/G at position 5 and C/T at position 16 of the consensus. The differences in DNA-binding site preferences between p63 and p53 influenced their ability to activate transcription from select response elements (REs) in cells. A computer algorithm, p63MH, was developed to find candidate p63-binding motifs on input sequences. We identified genes responsive to p63 regulation that contain functional p63 REs. Our results suggest that the sequence composition of REs could be one contributing factor to target gene discrimination between p63 and p53.

Differential regulation of the p73 cistrome by mammalian target of rapamycin reveals transcriptional programs of mesenchymal differentiation and tumorigenesis

“…S2E, p73 shares certain degenerate motif elements with p63 compared with p53. These degenerate elements are thought to decrease selectivity of binding, leading to a larger pool of potential binding sites (8). Consistent with these data, p73 binds ∼4,000 genes, compared with ∼3,000 for p63 and ∼1,500 for p53 (3,5).…”

“…Treatment with rapamycin did not significantly alter this motif (Fig. S2E), which is nearly identical to the p53 and p63 response elements (2,8). However, as indicated by the arrows in Fig.…”

Mechanisms of regulatory diversity within the p53 transcriptional network

“…For example, DNp63a, the p63 isoform predominantly expressed in epidermis, could bind with high affinity to some, but not all, p53REs, and thus exert dominant-negative effects in a gene-specific manner. In fact, it is well established that DNp63a is required for proliferation and survival of keratinocytes, and these effects are due at least in part to attenuation of p53 activity (Westfall et al, 2003;Truong et al, 2006;Perez et al, 2007). Similarly, DNp73 may repress p53 function in sympathetic neurons, as deduced from the loss of these cells in p73 À/À null mice (Yang et al, 2000;Moll and Slade, 2004).…”

Smad4-Irf6 genetic interaction and TGFβ-mediated IRF6 signaling cascade are crucial for palatal fusion in mice

“…The recognition sequences searched for SMAD binding were 5Ј-GTCT-3Ј, 5Ј-AGAC-3Ј and 5Ј-GTCTAGAC-3Ј (Denissova et al, 2000;Zawel et al, 1998) and for MEF2 family member binding was 5Ј-YTAWWWWTAR-3Ј (Black and Olson, 1998). In addition, we evaluated the following potential p63 recognition sites: the canonical p53 family 20-base recognition sequence formed from duplicates of the half-site recognition sequence 5Ј-RRRCWWGYYY-3Ј separated by any combination of 0 to 13 bases (Cai et al, 2012;el-Deiry et al, 1992) and the p63-preferential recognition sequence 5Ј-RRRCRWGYYYRRRC WYGYYY-3Ј (Perez et al, 2007). To account for the possibility of degenerate p53 family member-binding sites, we used the p53scan and p63scan algorithms with default options , which allow the consensus half-site to vary slightly in composition.…”