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Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.

Motallebipour M, Ameur A, Reddy Bysani MS, Patra K, Wallerman O, Mangion J, Barker MA, McKernan KJ, Komorowski J, Wadelius C - Genome Biol. (2009)

Bottom Line: 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.Finally, several SNPs associated with diseases and quantitative traits were located in the enriched regions.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds väg 20, Uppsala SE-75185, Sweden. mehdi.motallebipour@imperial.ac.uk

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.

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Genomic localization of common binding regions for FOXA1, FOXA2, and FOXA3. (a) FOXA1-2, (b) FOXA2-3, (c) FOXA1-3, and (d) FOXA1-2-3. Each region was mapped to all UCSC gene coordinates and sequentially matched to the categories 500 bp from TSS, 500 bp to 1 kb from TSS, 1 to 5 kb from TSS, 1 kb from 3'-end, 1 to 5 kb from 3'-end and intragenic. The intergenic group consists of those regions not matching any of the mentioned categories.
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Figure 3: Genomic localization of common binding regions for FOXA1, FOXA2, and FOXA3. (a) FOXA1-2, (b) FOXA2-3, (c) FOXA1-3, and (d) FOXA1-2-3. Each region was mapped to all UCSC gene coordinates and sequentially matched to the categories 500 bp from TSS, 500 bp to 1 kb from TSS, 1 to 5 kb from TSS, 1 kb from 3'-end, 1 to 5 kb from 3'-end and intragenic. The intergenic group consists of those regions not matching any of the mentioned categories.

Mentions: We have previously examined the genome-wide location of FOXA2 binding in HepG2 cells, where we found 7,253 binding sites for this factor [25]. Comparison of the FOXA2 data with that for FOXA1 and FOXA3 revealed 2,304 regions in common for all three factors. Here, a common binding is reported when the distance between the peak centers is less than 1 kb. Furthermore, when the genomic localization of different combinations of these factors was examined, we found around 100 regions of common binding for each pair (Figure 3). While 12 of 121 (10%) FOXA1-2 regions were within 5 kb of a TSS of a known gene (Figure 3a), 49 of 96 (51%) FOXA2-3 regions were within the same distance (Figure 3b). For FOXA1-3, 14 of 102 (14%) regions are within 5 kb, although there are no common binding sites for this pair within the first kilobase of a TSS (Figure 3c). The corresponding number for all three factors together is 22% (505 of 2,304; Figure 3d).


Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq.

Motallebipour M, Ameur A, Reddy Bysani MS, Patra K, Wallerman O, Mangion J, Barker MA, McKernan KJ, Komorowski J, Wadelius C - Genome Biol. (2009)

Genomic localization of common binding regions for FOXA1, FOXA2, and FOXA3. (a) FOXA1-2, (b) FOXA2-3, (c) FOXA1-3, and (d) FOXA1-2-3. Each region was mapped to all UCSC gene coordinates and sequentially matched to the categories 500 bp from TSS, 500 bp to 1 kb from TSS, 1 to 5 kb from TSS, 1 kb from 3'-end, 1 to 5 kb from 3'-end and intragenic. The intergenic group consists of those regions not matching any of the mentioned categories.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091322&req=5

Figure 3: Genomic localization of common binding regions for FOXA1, FOXA2, and FOXA3. (a) FOXA1-2, (b) FOXA2-3, (c) FOXA1-3, and (d) FOXA1-2-3. Each region was mapped to all UCSC gene coordinates and sequentially matched to the categories 500 bp from TSS, 500 bp to 1 kb from TSS, 1 to 5 kb from TSS, 1 kb from 3'-end, 1 to 5 kb from 3'-end and intragenic. The intergenic group consists of those regions not matching any of the mentioned categories.
Mentions: We have previously examined the genome-wide location of FOXA2 binding in HepG2 cells, where we found 7,253 binding sites for this factor [25]. Comparison of the FOXA2 data with that for FOXA1 and FOXA3 revealed 2,304 regions in common for all three factors. Here, a common binding is reported when the distance between the peak centers is less than 1 kb. Furthermore, when the genomic localization of different combinations of these factors was examined, we found around 100 regions of common binding for each pair (Figure 3). While 12 of 121 (10%) FOXA1-2 regions were within 5 kb of a TSS of a known gene (Figure 3a), 49 of 96 (51%) FOXA2-3 regions were within the same distance (Figure 3b). For FOXA1-3, 14 of 102 (14%) regions are within 5 kb, although there are no common binding sites for this pair within the first kilobase of a TSS (Figure 3c). The corresponding number for all three factors together is 22% (505 of 2,304; Figure 3d).

Bottom Line: 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.Finally, several SNPs associated with diseases and quantitative traits were located in the enriched regions.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Dag Hammarskjölds väg 20, Uppsala SE-75185, Sweden. mehdi.motallebipour@imperial.ac.uk

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.

Show MeSH