Identification of a module of HAP transcription factors for seed development in rice

Heme activator protein (HAP) is a CCAAT box-binding factor family conserved in all higher eukaryotes. HAP transcription factors (TFs) consist of three subunits: HAP2, HAP3, and HAP5. Using recent rice genome information, we identified 11 HAP2 genes, 11 HAP3 genes, and 12 HAP5 genes. A HAP2 and five HAP5 genes were acknowledged more in this study than in the previous studies. Due to the functional association of HAP subunits, we carried out clustering analysis for expression patterns of all HAP members using anatomical meta-expression data of 983 rice Affymetrix arrays collected from the public database. Subsequently, we identified HAP members with endosperm and seed-preferred expression and focused on nine HAP family members associated with this expression pattern. We confirmed their expression patterns by RT-PCR analyses. The nine members were OsHAP2G, OsHAP2I, OsHAP3D, OsHAP3K, and five HAP5 genes (LOC_Os05g23910, LOC_Os10g11580, LOC_Os01g24460, LOC_Os01g01290, and LOC_Os01g39850). Promoter analyses using GUS activity again demonstrated that OsHAP3K is preferentially expressed in the aleurone layer of the seed and the LOC_Os05g23910 gene-encoding HAP5 showed endosperm-preferred expression. Network analysis using RiceNet suggests a functional gene network mediated by four rice HAP genes, further helping in the prediction of the biological function of OsHAP2G and OsHAP5 (LOC_Os10g11580). Our data provide new insight into HAP family-mediated regulatory pathways for endosperm or seed development in rice.