Identification of cis -regulatory elements in the upstream regions of zebrafish runx3 through in silico analysis: implications for function

Abstract

RUNX3 encodes a member of the runt domain family of transcription factors. In mammals this family includes three genes (RUNX1-3) and their protein products function as context-dependent transcription factors, either transcriptional activators or repressors, during developmental processes such as hematopoiesis, neurogenesis, and osteogenesis; all are proto-oncogenes or tumour suppressors. All three genes were shown to be transcribed from two promoters, giving rise to protein products bearing either the P1 or the P2 N-termini, translated respectively from transcripts originating from the distal (P1)- or the proximal (P2)-promoters. Understanding their differential regulation and interaction may help explain how RUNX factors contribute to such different and often opposing biological processes. In this study, we have identified putative molecular players affecting zebrafish runx3 transcription by using a computational approach to search for cis-regulatory transcription factor binding sites (TFBSs) in the runx3 promoter regions of zebrafish (Danio rerio) and fugu (Takifugu rubripes). From the data obtained it was possible to identify the sites most likely involved in regulating expression of runx3 in zebrafish. Our comparative approach reduced substantially the number of putative TFBSs in the runx3 promoter regions; reassuringly, published TFs identified as transcriptional regulators of Runx3 are confirmed by our in silico analysis. Our data now provides the basis for focused in vitro and/or in vivo experimental tests of the transcriptional regulatory activities of strong candidate regulators of zebrafish runx3. RUNX3 encodes a member of the runt domain family of transcription factors. In mammals this family includes three genes (RUNX1-3) and their protein products function as context-dependent transcription factors, either transcriptional activators or repressors, during developmental processes such as hematopoiesis, neurogenesis, and osteogenesis; all are proto-oncogenes or tumour suppressors. All three genes were shown to be transcribed from two promoters, giving rise to protein products bearing either the P1 or the P2 N-termini, translated respectively from transcripts originating from the distal (P1)- or the proximal (P2)-promoters. Understanding their differential regulation and interaction may help explain how RUNX factors contribute to such different and often opposing biological processes. In this study, we have identified putative molecular players affecting zebrafish runx3 transcription by using a computational approach to search for cis-regulatory transcription factor binding sites (TFBSs) in the runx3 promoter regions of zebrafish (Danio rerio) and fugu (Takifugu rubripes). From the data obtained it was possible to identify the sites most likely involved in regulating expression of runx3 in zebrafish. Our comparative approach reduced substantially the number of putative TFBSs in the runx3 promoter regions; reassuringly, published TFs identified as transcriptional regulators of Runx3 are confirmed by our in silico analysis. Our data now provides the basis for focused in vitro and/or in vivo experimental tests of the transcriptional regulatory activities of strong candidate regulators of zebrafish runx3.