Characterization of pancreatic transcription factor Pdx-1 binding sites using promoter microarray and serial analysis of chromatin occupancy.
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 termed 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.
Keller
David M
DM
Vollum Institute, and Division of Biostatistics, Department of Public Health and Preventative Medicine, Oregon Health & Science University, Portland, Oregon 97239, USA. kellerd@ohsu.edu
McWeeney
Shannon
S
Arsenlis
Athanasios
A
Drouin
Jacques
J
Wright
Christopher V E
CV
Wang
Haiyan
H
Wollheim
Claes B
CB
White
Peter
P
Kaestner
Klaus H
KH
Goodman
Richard H
RH
D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000378:metabolism; D001665:Binding Sites; D002454:Cell Differentiation; D002843:Chromatin / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D018398:Homeodomain Proteins / Q000378:metabolism*; D007328:Insulin; D050417:Insulin-Secreting Cells / Q000166:cytology / Q000378:metabolism*; D051379:Mice; D008810:Mice, Inbred C57BL; D035683:MicroRNAs / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic; D015534:Trans-Activators / Q000378:metabolism*; D014158:Transcription, Genetic
D051792:Basic Helix-Loop-Helix Proteins; D002843:Chromatin; D018398:Homeodomain Proteins; D007328:Insulin; D035683:MicroRNAs; D015534:Trans-Activators; C501008:Neurod1 protein, mouse; C084010:pancreatic and duodenal homeobox 1 protein