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Cited by 150Genomics and Chromatin DynamicsLiver physiology and pathologyGenomics and Phylogenetic Studies

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

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Wederell, Elizabeth D., Bilenky, Mikhail, Cullum, Rebecca, Thiessen, Nina, Dagpinar, Melis, Delaney, Allen, Varhol, Richard, Zhao, YongJun +8 more·2008·Nucleic Acids Research
DOI 10.1093/nar/gkn382PMC PMC2504304
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Abstract

Foxa2 (HNF3 beta) is a one of three, closely related transcription factors that are critical to the development and function of the mouse liver. We have used chromatin immunoprecipitation and massively parallel Illumina 1G sequencing (ChIP-Seq) to create a genome-wide profile of in vivo Foxa2-binding sites in the adult liver. More than 65% of the approximately 11.5 k genomic sites associated with Foxa2 binding, mapped to extended gene regions of annotated genes, while more than 30% of intragenic sites were located within first introns. 20.5% of all sites were further than 50 kb from any annotated gene, suggesting an association with novel gene regions. QPCR analysis demonstrated a strong positive correlation between peak height and fold enrichment for Foxa2-binding sites. We measured the relationship between Foxa2 and liver gene expression by overlapping Foxa2-binding sites with a SAGE transcriptome profile, and found that 43.5% of genes expressed in the liver were also associated with Foxa2 binding. We also identified potential Foxa2-interacting transcription factors whose motifs were enriched near Foxa2-binding sites. Our comprehensive results for in vivo Foxa2-binding sites in the mouse liver will contribute to resolving transcriptional regulatory networks that are important for adult liver function.

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Authors
Wederell, E. D., Bilenky, M., Cullum, R., Thiessen, N., Dagpinar, M., Delaney, A., Varhol, R., Zhao, Y., Zeng, T., Bernier, B., Ingham, M., Hirst, M., Robertson, G., Marra, M. A., Jones, S., & Hoodless, P. A.
Affiliations
BC Cancer Agency (CA)
Corresponding author
Hoodless, Pamela A.
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2008-07-08
Volume
36
Issue
14
Pages
4549-4564
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkn382
PMC
PMC2504304
OpenAlex
W2038697069
Cited by
150
References
7
Citations by year
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FWCI
10.16
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • eSpace (Curtin University) (submittedVersion)
Funders
  • Genome Canada
  • Genome British Columbia
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Health Sciences › Medicine › Hepatology › Liver physiology and pathology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
FOXA2, transcription factor binding sites, liver, transcriptional regulatory networks, gene expression, transcription factor binding motifs, mice
MeSH terms
Animals, Binding Sites, Female, Liver, Mice, Inbred C57BL, Transcription Factors, Gene Expression, Sequence Analysis, DNA, Computational Biology, Genomics, RNA Interference, Chromatin Immunoprecipitation, Regulatory Elements, Transcriptional, Mice, Hepatocyte Nuclear Factor 3-beta, Gene Regulatory Networks

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