title: Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.
abstract: BACKGROUND
  The forkhead box/winged helix family members FOXA1, FOXA2, and FOXA3 are of high importance in development and specification of the hepatic linage and the continued expression of liver-specific genes.
  
  
  RESULTS
  Here, we present a genome-wide location analysis of FOXA1 and FOXA3 binding sites in HepG2 cells through chromatin immunoprecipitation with detection by sequencing (ChIP-seq) studies and compare these with our previous results on FOXA2. We found that these factors often bind close to each other in different combinations and consecutive immunoprecipitation of chromatin for one and then a second factor (ChIP-reChIP) shows that this occurs in the same cell and on the same DNA molecule, suggestive of molecular interactions. Using co-immunoprecipitation, we further show that FOXA2 interacts with both FOXA1 and FOXA3 in vivo, while FOXA1 and FOXA3 do not appear to interact. Additionally, we detected diverse patterns of trimethylation of lysine 4 on histone H3 (H3K4me3) at transcriptional start sites and directionality of this modification at FOXA binding sites. Using the sequence reads at polymorphic positions, we were able to predict allele specific binding for FOXA1, FOXA3, and H3K4me3. Finally, several SNPs associated with diseases and quantitative traits were located in the enriched regions.
  
  
  CONCLUSIONS
  We find that ChIP-seq can be used not only to create gene regulatory maps but also to predict molecular interactions and to inform on the mechanisms for common quantitative variation.
authors.affiliation: Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds väg 20, Uppsala SE-75185, Sweden. mehdi.motallebipour@imperial.ac.uk
authors.forename: Mehdi
authors.initials: M
authors.lastname: Motallebipour
authors.forename: Adam
authors.initials: A
authors.lastname: Ameur
authors.forename: Madhu Sudhan
authors.initials: MS
authors.lastname: Reddy Bysani
authors.forename: Kalicharan
authors.initials: K
authors.lastname: Patra
authors.forename: Ola
authors.initials: O
authors.lastname: Wallerman
authors.forename: Jonathan
authors.initials: J
authors.lastname: Mangion
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Barker
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: McKernan
authors.forename: Jan
authors.initials: J
authors.lastname: Komorowski
authors.forename: Claes
authors.initials: C
authors.lastname: Wadelius
mesh_terms: D000483:Alleles; D019070:Cell Lineage; D047369:Chromatin Immunoprecipitation; D020869:Gene Expression Profiling; D015723:Gene Library; D016678:Genome; D056945:Hep G2 Cells; D051541:Hepatocyte Nuclear Factor 3-alpha / Q000235:genetics* / Q000378:metabolism; D051542:Hepatocyte Nuclear Factor 3-beta / Q000235:genetics / Q000378:metabolism; D051543:Hepatocyte Nuclear Factor 3-gamma / Q000235:genetics* / Q000378:metabolism; D006657:Histones / Q000737:chemistry*; D006801:Humans; D008099:Liver / Q000166:cytology / Q000378:metabolism; D008957:Models, Genetic; D011401:Promoter Regions, Genetic
chemical_list: C496499:FOXA1 protein, human; C496502:FOXA2 protein, human; C496505:FOXA3 protein, human; D051541:Hepatocyte Nuclear Factor 3-alpha; D006657:Histones; D051543:Hepatocyte Nuclear Factor 3-gamma; D051542:Hepatocyte Nuclear Factor 3-beta