Cis regulatory module discovery in immune cell development

Transcriptional regulatory mechanisms are mediated by a set of transcription factors (TFs), which bind to a specific region (motifs or transcription factor binding sites, TFBS), on the target gene(s) leading to gene expression. Eukaryotic regulatory motifs, referred to as cis regulatory modules (CRMs), tend to co-occur near the regulated gene's transcription start site and provide the building blocks to transcriptional regulatory networks that model the relevant TF-TFBS interactions. Here, we study IL-12 stimulated transcriptional regulators in STAT4 mediated T helper 1 (Th1) cell development by focusing on the identification of TFBS and CRMs using a set of Stat4 ChIP-on-chip target genes. A region containing 2000 bases of Mus musculus sequences with the Stat4 binding site, derived from the ChIP-on-chip data, has been characterized for enrichment of other motifs and, thus CRMs. We find two such motifs, (NF-κB and PPARγ/RXR) being enriched in the Stat4 binding sequences compared to neighboring background sequences and sets of random sequences of equal size. Furthermore, these predicted CRMs were observed to be associated with biologically relevant target genes in the ChIP-on-chip data set by meaningful gene ontology annotations. These analyses will lead to a better understanding of transcriptional regulatory networks in IL-12 stimulated Stat4 mediated Th1 cell differentiation.