BMC Genomics 2007, 8:139 http://www.biomedcentral.com/1471-2164/8/139 possibility of p53 apoptotic control in immune cells through localized secreted factors. The transcription factor cp2-like 4 gene, a Rattus norvegicus grainyhead family homolog, is homologous to the grhl3 mouse and human family members. In Drosophila, the grainyhead gene product participates in wnt-frizzled sign- aling in the establishment of wing planar polarity [64] and in cuticle barrier formation and function [65]. The lat- ter function is conserved in mammals, where grainyhead homologs are involved in epidermal stratification and wound repair [66]. The importance of the grhl3 transcrip- tion factor during development is underscored in the grhl3-null mouse, in which neural tube defects are preva- lent [67,68]. Absence of the p53-tfcp2l4 network in p53- mice may represent a potential mechanism through which a proportion of these mice are born with neural tube defects. The role of grhl3 in ectodermal differentia- tion and specification into epidermal tissue and also within epidermal wound healing is strikingly similar to the demonstrated involvement of the p53 family member p63 in these events [69]. Since p63 has an overlapping transcriptional program with p53 [58], investigation into joint regulation of tfcp2l4 is warranted as a possible com- mon juncture of in vivo redundant transcriptional control in development. Other transcriptional targets of p53 found in our study may play roles within the differentiating PC12 cell or developing organism. The nme1/nm23 gene is a positive regulator of neuronal differentiation through regulation of Rb2/p130 expression [70]. The Kctd (potassium chan- nel tetramerization domain containing) family, of which FLJ12242 is a member, is involved in the left-right symme- try of developing zebrafish brain [71]. We found FLJ12242 to be the most highly expressed p53-regulated gene in NGF-mediated differentiation. Txnl2 is involved in P19 cardiac cell differentiation [72], while BRK promotes ente- rocyte differentiation [73]. The Sdk2 neuronal adhesion molecule is involved in synaptic connectivity [74]. Dusp5 is a negative regulator of ERK signaling [75], thus regulat- ing MAPK signal propagation. The Lect1/Chm1 gene, an anti-angiogenic factor in differentiating cartilage [76] and a bone remodeling factor [77], may be involved in bone development. Furthermore, the additional unannotated p53-regulated targets described here such as FLJ32743, LOC366671 and LOC362557 may be important in yet unknown developmental, differentiation or signaling processes. Data from previous studies have reported a number of p53 regulated genes that do not completely correspond to expression changes observed in PC12 differentiation. This observation suggests that p53 transcriptional regulation in response to diverse stimuli shows similar gene expres- sion but also some level of stimulus specificity. For exam- ple, our data show an overlap of p53 occupancy at some genomic loci irrespective of the p53-activating stimulus when compared to results from a recent chromatin immu- noprecipitation/paired-end ditag (ChIP PET) screen for p53 genomic occupancy in human colorectal cells treated with 5-fluorouracil, [5] and another study identifying p53-regulated genes through microarray analysis from irradiated wild-type and p53-null animals [54]. We con- firmed the findings of p53 occupancy at the Snk/Plk2 [54], MDMX, Nck2, Dyrk3, p21Waf1/Cip1, MDM2 and cyclin G1 [5] regulatory regions but we observe p53-dependent expression changes only in the p21Waf1/Cip1, MDM2 and cyclin G1 targets with NGF treatment. Regulation of Snk/ Plk2, MDMX, Nck2 and Dyrk3 may not completely depend upon p53 promoter binding alone but also on availability of other transcriptional cofactors. Since these targets were previously identified as p53-regulated, by extension, the genes we report as shmt1, rnf10, hmmr, trim34, znf609 and ovary-specific MOB-like protein may also be regulated under other p53-activating conditions. Along with the NGF- dependent regulation of p53 gene targets described in our study as wnt7b, pkcbpb15 and lect, we believe that the p53- occupied targets shmt1, rnf10, hmmr, trim34, znf609 and ovary-specific MOB-like protein may provide additional examples of stimulus-dependent p53 transcriptional tar- gets. Interestingly, we did not find enrichment of p53- occupied loci in NGF-differentiated PC12 cells for media- tors of apoptosis or DNA repair [see Additional file 2] probably because these recognized functions of p53 are not involved in NGF differentiation. For instance, we did not observe DNA repair genes, MLH1 and PMS2, found in a recent p53-binding genomic study through serial analy- sis of binding elements (SABE) in p53-expressing Jurkat cells and verified in cisplatin challenged fibroblasts [78]. In addition, computational approaches combining ChIP, DNA microarray with p53 sequence binding matrices have derived genomic maps of candidate p53 binding sites that reveal p53 regulation of a proapoptotic gene, BCL-G/BCL2L14 [79], various coding and non-coding genes [4] and regulation of micro-RNAs [80]. By compar- ison, we show that NGF-directed p53 transcription in neu- ronal cells regulated several genes unique to differentiation and different from transcriptional targets previously identified in other p53 genome-wide studies. NGF receptor-mediated induction of p53 activity through TrkA [39,44] may represent a useful therapeutic avenue for development of non-genotoxic chemotherapeutics [29]. While activation of the p53 protein in response to NGF treatment within PC12 cells has recently been described [44], it is less clear what particular signaling proteins are responsible for the marked increase in p53 protein stability and transactivational selectivity. Changes in p53 activity are related, directly or indirectly, to TrkA Page 12 of 17 (page number not for citation purposes)