Transcriptomic analysis on the promoter regions discover gene networks involving mastitis in cattle

Abstract

Mastitis is one of the costliest diseases in dairy farms caused by infection of different<br>microorganisms such as Escherichia coli, Streptococcus uberis and Staphylococcus aureus.<br>Promoters play an essential role in controlling gene expression and understanding the mechanisms<br>of transcriptional regulation involved in physiological and immunological processes involved in<br>infections. Exploiting regulatory elements such as transcription factor binding sites (TFBSs<br>modules) on the promoter region could reveal co-regulated genes allowing to create regulatory <br>models and to execute a cross-sectional analysis on several databases. In this study, the promoter<br>regions of 11 genes associated with contagious mastitis including CCL4, CXCL8, STAT3, IKBKB,<br>MAPK14, NFKBIA, NFKB1, TNF, IL18, IL6, and HCK were investigated to predict the activating<br>regulatory modules on promoters and also to discover the key related transcription factors. By<br>exploring the promoter regions, 228 genes were discovered comprising the same transcription<br>factors modules. Thirty six out of 228 genes were validated using five microarray datasets. The<br>promoter research of these genes revealed that as many as 7 down-regulated and 12 up-regulated<br>genes are predictable in the network. The genes whose functions were associated with the initial<br>gene list (11 genes), were identified by DAVID queries with TFBSs models. This implies that the<br>approach provides a clear image on the underlying regulatory mechanism of gene expression profile<br>and also offers a novel approach in designing gene networks in cattle.