BMC Genomics 2006, 7:42 http://www.biomedcentral.com/1471-2164/7/42 FNiogrutrheer2n blotting Northern blotting. Northern blots showing differential expression of TFF3 (A), SPINK1 (B), and GIMAP8 (C). mRNA levels were normalised to that of GAPDH (D). moter regions of the genes more highly expressed in sus- ceptible animals. The sequence logo for these motifs is shown in Figure 3. MAST analysis indicated that despite individual motifs not being significant, the combination of motifs identified in promoter regions of both groups were unique to the group in which they were discovered as they were not significantly associated with the oppos- ing group or with all the genes on the array by Fisher's exact test (Table 4). A separate MAST analysis indicated that the motifs identified in this study were also not sig- nificantly associated (P > 0.05) with genes previously reported to be differentially expressed in sheep exposed to gastrointestinal nematodes [25] (data not shown). In order to identify which transcription factors could bind to the motifs, each motif was compared to the transcrip- tion factor binding sites in the TRANSFAC database [33]. Each motif was shuffled 1,000 times and the comparison process repeated in order to establish its significance. Fig- ure 3 lists the significant motifs discovered along with their best TRANSFAC hits. The full list of identified motifs and their TRANSFAC hits are available in Additional files 1 and 2. The two significant motifs found in the promoter regions of the genes more highly expressed in susceptible animals give B cell lineage specific activator protein (BSAP) and Peroxisome proliferative activated receptor gamma (PPARG) as their best hit. BSAP, also known as PAX5 is a transcription factor required for B cell develop- ment [34], however, it should be noted that the P value of this hit is not significant and so this motif may be bound by a transcription factor not represented in the TRANSFAC dataset. Interestingly, five of the six genes associated with the GO term "response to biotic stimulus" have this motif in their promoter regions, indicating this motif may be involved in the regulation of this response. Peroxisome proliferative activated receptor gamma (PPARG) is a lig- and activated transcription factor which has an important role in adipocyte differentiation [35]. PPARG is known to have anti-inflammatory effects and to play an important role in the maintenance of mucosal integrity in the intes- tine [36]. This transcription factor may therefore play a role in co-ordinately regulating genes more highly expressed in the intestine of the susceptible animals. Discussion This study identified a number of genes differentially expressed between lines of lambs differing genetically in their ability to become resistant to gastrointestinal nema- todes. These genes were differentially expressed in the absence of nematode challenge and so represent basal expression differences between the selection lines. It is noteworthy that significant differences were observed in naïve animals as much previous work has shown that ani- mals differing in host resistance primarily differ in the rapidity and strength of their acquired immune response rather than differing in their innate immunity [3,5,6]. To our knowledge this is the first report of constitutive differ- ences in gene expression in naïve sheep differing in their genetic ability to respond to host infection. Gene Ontology terms associated with the genes more highly expressed in susceptible animals included "response to stimulus", "response to stress", "defence response" and "response to pests, pathogens and para- sites". This implies that the gastrointestinal tract of the susceptible animals is responding to stress even in the absence of nematode challenge. This is evidenced by the elevated expression of seven genes that are induced in response to stimulus, HLA-A, MSH6, GPX2, IFI35, UBD, SERPING1 and TFF3. HLA-A encodes an MHC class I heavy chain molecule that, in conjunction with B2M, presents endogenously derived peptides to CD8+ cytotoxic T cells. HLA-A has broad tissue expression and has been shown to be induced by a number of cytokines, in response to infection and in patients with the inflamma- tory bowel syndrome Crohn's disease [37-39]. MSH6 encodes a MutS homologue protein which, in complex with MSH2, forms the MutSα heterodimer, while MSH2 in complex with MSH3 forms the MutSβ heterodimer. Both these complexes are involved in mismatch repair and repair mutagen-induced lesions in DNA as well as errors in DNA replication [40]. MutSα repairs both DNA mismatches and short 1–2 bp insertions or deletions Page 5 of 12 (page number not for citation purposes)