Microarray gene expression profiling and correlation with morphological changes during mouse colonic development

Several genes such as Cdx2 and HoxD ase known to be expressed ditterentially during colonic developmem; however, mechanisms regulating remodeling of colon after early organogenesis are poorly understood. In order to study changes in gene expression during this remodeling, we compared RNA kvels usmg eDNA microarrays made from a set ot 20,114 cDNA clones (Research Genetics and National Institute of Aging) containing approximately" 14,723 different murine genes. We made eDNA probes from total RNA that had been twice amplified. RNA samples were obtained from embryonic colons of CD-1 and C57BU6j inbred mice at six dflterent embryonic stages between 13.5 and 18.5 days. Comrol probe was prepared from Wtmle 17.5 day" embryos. Ten [housand eighty nine genes exhibited consistent patterns of expression intensity in [hree rephcations using two sets of probes made from each embrymxic stage of colon in both strains Gene expression in the six embryonic stages clustered into two main groups (13.5 to 155 day versus 16.5 to 18.5 day) according to hierarchical chistering. These clusters corresponded to major changes in morphological remodeling, as determined by light and electron microscopy. We observed, for instance, that tf~e colon developed a central lumen and stromal invagination by day 16.5. Most of the genes (91.8% (CD-1) and 93.6% (C57BU6J)) did not show sigmficant changes in expression during this period However, 530 (5.3%) genes in both strains exhibited at least two-fold diflerences in expression leveI. By a pair-wlse comparison of expression levels of these genes between 13.5 and 18.5 days, we identified ibur difterent expression patterns (figure) A complete characterizatmn, atong with validation of selected genes by RT-PCR and in situ hybridization, will be presented.