The homeobox transcription factor Pdx-1 is necessary for pancreas organogenesis and beta cell function, however, most Pdx-1-regulated genes are unknown. To further the understanding of Pdx-1 in beta cell biology, we have characterized its genomic targets in NIT-1 cells, a mouse insulinoma cell line. To identify novel targets, we developed a microarray that includes traditional promoters as well as non-coding conserved elements, micro-RNAs, and elements identified through an unbiased approach

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... med serial analysis of chromatin occupancy. In total, 583 new Pdx-1 target genes were identified, many of which contribute to energy sensing and insulin release in pancreatic beta cells. By analyzing 31 of the protein-coding Pdx-1 target genes, we show that 29 are expressed in beta cells and, of these, 68% are down-or up-regulated in cells expressing a dominant negative mutant of Pdx-1. We additionally show that many Pdx-1 targets also interact with NeuroD1/BETA2, including the micro-RNA miR-375, a known regulator of insulin secretion. . 2 The abbreviations used are: ChIP, chromatin immunoprecipitation; Dox, doxycycline; GO, gene ontology; GST, genomic signature tag; Pdx-1, pancreatic and duodenal homeobox protein-1; SACO, serial analysis of chromatin occupancy; qRT-PCR, quantitative real-time PCR; RT, reverse transcriptase; DN, dominant negative; HBSS, Hanks' balanced salt solution; FBS, fetal bovine serum.