Limits...
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.

Show MeSH
H3K4me3 signals around 2,303 FOXA1-2-3 regions. (a) Enrichment of H3K4me3 in a window surrounding the center of FOXA1-2-3 regions. The regions were grouped into four clusters (I to IV) by their H3K4me3 patterns. The enrichment scale is from high (yellow) to low (blue), and the red vertical line represents the FOXA1-2-3 centers. Negative x-coordinates are upstream of the centers and positive are downstream. (b) Average H3K4me3 signal footprints for the four clusters in (a). (c) Average H3K4me3 signal footprints for regions with a TSS within 5 kb independent of direction (green) and regions lacking a TSS within this distance (purple).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3091322&req=5

Figure 6: H3K4me3 signals around 2,303 FOXA1-2-3 regions. (a) Enrichment of H3K4me3 in a window surrounding the center of FOXA1-2-3 regions. The regions were grouped into four clusters (I to IV) by their H3K4me3 patterns. The enrichment scale is from high (yellow) to low (blue), and the red vertical line represents the FOXA1-2-3 centers. Negative x-coordinates are upstream of the centers and positive are downstream. (b) Average H3K4me3 signal footprints for the four clusters in (a). (c) Average H3K4me3 signal footprints for regions with a TSS within 5 kb independent of direction (green) and regions lacking a TSS within this distance (purple).

Mentions: We looked further into this double peak by k-means clustering of the signal for H3K4me3 in four different clusters (Figure 6a, b). Two of these clusters, clusters I and II, revealed patterns that resembled those at the TSS (Figure 2c), with each of the curves on either side of the FOXA1-2-3 binding. Due to the observed pattern, we decided to look for TSSs within a 5 kb distance from the combined FOXA1-2-3 binding site. Of the 2,304 regions with triple binding, 505 contained a known TSS within this distance (Figure 3d), with a similar number of TSSs on the two strands (Table S6 in Additional data file 1). A majority of regions in clusters I and II were within 5 kb of a TSS and these clusters showed the highest levels of H3K4me3. The H3K4me3 peaks in these clusters are located at opposite sides of the FOXA1-2-3 binding, and this would suggest that the H3K4me3 signals are biased towards the direction of transcription (Figure 6b; Table S6 in Additional data file 1).


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)

H3K4me3 signals around 2,303 FOXA1-2-3 regions. (a) Enrichment of H3K4me3 in a window surrounding the center of FOXA1-2-3 regions. The regions were grouped into four clusters (I to IV) by their H3K4me3 patterns. The enrichment scale is from high (yellow) to low (blue), and the red vertical line represents the FOXA1-2-3 centers. Negative x-coordinates are upstream of the centers and positive are downstream. (b) Average H3K4me3 signal footprints for the four clusters in (a). (c) Average H3K4me3 signal footprints for regions with a TSS within 5 kb independent of direction (green) and regions lacking a TSS within this distance (purple).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: H3K4me3 signals around 2,303 FOXA1-2-3 regions. (a) Enrichment of H3K4me3 in a window surrounding the center of FOXA1-2-3 regions. The regions were grouped into four clusters (I to IV) by their H3K4me3 patterns. The enrichment scale is from high (yellow) to low (blue), and the red vertical line represents the FOXA1-2-3 centers. Negative x-coordinates are upstream of the centers and positive are downstream. (b) Average H3K4me3 signal footprints for the four clusters in (a). (c) Average H3K4me3 signal footprints for regions with a TSS within 5 kb independent of direction (green) and regions lacking a TSS within this distance (purple).
Mentions: We looked further into this double peak by k-means clustering of the signal for H3K4me3 in four different clusters (Figure 6a, b). Two of these clusters, clusters I and II, revealed patterns that resembled those at the TSS (Figure 2c), with each of the curves on either side of the FOXA1-2-3 binding. Due to the observed pattern, we decided to look for TSSs within a 5 kb distance from the combined FOXA1-2-3 binding site. Of the 2,304 regions with triple binding, 505 contained a known TSS within this distance (Figure 3d), with a similar number of TSSs on the two strands (Table S6 in Additional data file 1). A majority of regions in clusters I and II were within 5 kb of a TSS and these clusters showed the highest levels of H3K4me3. The H3K4me3 peaks in these clusters are located at opposite sides of the FOXA1-2-3 binding, and this would suggest that the H3K4me3 signals are biased towards the direction of transcription (Figure 6b; Table S6 in Additional data file 1).

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