Characterization of Pancreatic Transcription Factor Pdx-1 Binding Sites Using Promoter Microarray and Serial Analysis of Chromatin Occupancy

David M. Keller, Shannon McWeeney, Athanasios Arsenlis, Jacques Drouin, Christopher V. E. Wright, Haiyan Wang, Claes B. Wollheim, Peter White, Klaus H. Kaestner, Richard H. Goodman
2007 Journal of Biological Chemistry  
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
more » ... 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.
doi:10.1074/jbc.m700899200 pmid:17761679 fatcat:ayhbsbctbbdmvoezmk745cw7hm