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ChIP-on-chip of Pdx1 binding in Min6 cells - Study GBCO3979


Genomics Study Specifications

Study Name ChIP-on-chip of Pdx1 binding in Min6 cells
Contact Name David Groff (University of Pennsylvania)
Publication http://www.ncbi.nlm.nih.gov/pubmed/19855005
My Strategies Return to My Strategies page
Classification Islet/beta-cell stimulation/injury; Targets and roles of transcriptional regulators; Cell stimulation/injury
Links
BCBC Release Date July 21, 2010
Public Release Date July 21, 2010
Citation Sachdeva MM, Claiborn KC, Khoo C, Yang J, Groff DN, Mirmira RG, Stoffers DA. Pdx1 (MODY4) regulates pancreatic beta cell susceptibility to ER stress. Proc Natl Acad Sci U S A. 2009. 106:19090-5
Synopsis
The aim of this experiment was to use highthroughput chromatin immunoprecipitation followed by hybridization to promoter microarrays to obtain a comprehensive list of sites in the genome that are physically occupied by Pdx1. Chromatin was prepared from Min6 insulinoma cells and immunoprecipitated with Pdx1 or control antiserum. The precipitated chromatin was then purified, amplified and directly sequenced using Illumina technology.
Identify Pdx1 transcriptional targets involved in ER function as part of a larger study to define the role of Pdx1 in compensatory beta cell mass expansion that occurs in the progression to type 2 diabetes in humans.
Microarray expression results were integrated with the results of a ChIP-on-chip experiment of Pdx1 occupancy, also in Min6 cells using Mouse PromoterChip BCBC-5A.
The proximal promoters of ER target genes, Atf4 and Wfs1, were directly occupied by Pdx1. Two evolutionarily-conserved genomic sequences were found within 1.5 kb upstream of the Atf4 transcriptional start site, each of which contain at least one conserved Pdx1 consensus binding motif T(T/A)AT. ChIP assays demonstrated Pdx1 occupancy of both regions in Min6 cells. Occupancy of the Wfs1 promoter by Pdx1 was also confirmed both in Min6 cells and in primary mouse islets.
Pdx1 regulates a broad array of genes involved in diverse functions of the ER, including proper disulfide bond formation, protein folding, and the unfolded protein response. These findings suggest that Pdx1 deficiency leads to a failure of beta cell compensation for insulin resistance at least in part by impairing critical functions of the ER.
Platform types TF Binding ChIP-chip, TF Binding
Platforms Show platform Mouse PromoterChip
Study Design Type
  • binding_site_identification_design
  • dye_swap_design
Study Factors Show study factors
Study Assays Show study assays


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Repositories

Stoffers Lab
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Resource Tags

Atf4, Mouse PromoterChip 5A.0, Pdx1, Wfs1

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Resource History & Actions

Approved on Jul 21, 2010
Last modified on Jan 17, 2012
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