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Genome-wide analysis of FoxO1 binding in hepatic chromatin: potential involvement of FoxO1 in linking retinoid signaling to hepatic gluconeogenesis.

Shin DJ, Joshi P, Hong SH, Mosure K, Shin DG, Osborne TF - Nucleic Acids Res. (2012)

Bottom Line: We show here that FoxO1 directly binds to the genomic sites for the genes in retinoid metabolism.Notably, deletion of FoxO1 caused a significantly reduced induction of Pck1 and Pdk4 in response to retinoids.As Pck1 and Pdk4 are downstream targets of retinoid signaling, these results suggest that FoxO1 plays a potential role in linking retinoid metabolism to hepatic gluconeogenesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. djshin@sanfordburnham.org

ABSTRACT
The forkhead transcription factor FoxO1 is a critical regulator of hepatic glucose and lipid metabolism, and dysregulation of FoxO1 function has been implicated in diabetes and insulin resistance. We globally identified FoxO1 occupancy in mouse hepatic chromatin on a genome-wide level by chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq). To establish the specific functional significance of FoxO1 against other FoxO proteins, ChIP-seq was performed with chromatin from liver-specific FoxO1 knockout and wild-type mice. Here we identified 401 genome-wide FoxO1-binding locations. Motif search reveals a sequence element, 5' GTAAACA 3', consistent with a previously known FoxO1-binding site. Gene set enrichment analysis shows that the data from FoxO1 ChIP-seq are highly correlated with the global expression profiling of genes regulated by FoxO1, demonstrating the functional relevance of our FoxO1 ChIP-seq study. Interestingly, gene ontology analysis reveals the functional significance of FoxO1 in retinoid metabolic processes. We show here that FoxO1 directly binds to the genomic sites for the genes in retinoid metabolism. Notably, deletion of FoxO1 caused a significantly reduced induction of Pck1 and Pdk4 in response to retinoids. As Pck1 and Pdk4 are downstream targets of retinoid signaling, these results suggest that FoxO1 plays a potential role in linking retinoid metabolism to hepatic gluconeogenesis.

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Representative view of a ChIP-seq peak. FoxO1-binding peaks were mapped onto the mouse reference genome mm9 and visualized using the UCSC Genome Browser. Arrows indicate peaks associated with genes: (A), Elk4; (B), Pck1; (C), Pdk4. WT = wild-type; KO = l-FoxO1 KO; Fx = FoxO1.
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gks932-F2: Representative view of a ChIP-seq peak. FoxO1-binding peaks were mapped onto the mouse reference genome mm9 and visualized using the UCSC Genome Browser. Arrows indicate peaks associated with genes: (A), Elk4; (B), Pck1; (C), Pdk4. WT = wild-type; KO = l-FoxO1 KO; Fx = FoxO1.

Mentions: ChIPed DNA was processed for sequencing by Solexa/Illumina Genome Analyzer II, which generated a data set of 5–6 million reads in each group (Figure 1A). The peaks were mapped onto the mouse reference genome mm9 in the UCSC Genome Browser Database. FoxO1-binding peaks were identified by SEAN (Supplementary Materials and Methods S1) with the threshold P-value 1 × 10−5. We found 583 peaks in FoxO1-enriched chromatin compared with IgG in WT (WT-FoxO1/WT-IgG), designated FoxO1/IgG, whereas 460 peaks were identified in FoxO1-enriched chromatin in WT compared with that in l-FoxO1 KO (WT-FoxO1/l-FoxO1 KO-FoxO1), designated WT/KO (Figure 1B). Notably, the overlapping peaks were 401, accounting for as much as 69% of peaks in FoxO1/IgG and 87% of peaks in WT/KO. The genomic locations of the 401 peaks are shown in Supplementary Table S9. We used the overlapping peaks as a reference for further analysis of genome-wide FoxO1-binding sites. We randomly selected three representative examples of ChIP-seq peaks, as shown in Figure 2. The location of the peaks for Pdk4 and Pck1-a encompasses the previously known FoxO1-binding sites (3,27), whereas the peaks for Elk4 and Pck1-b are newly found as putative FoxO1-binding sites in the current studies.Figure 1.


Genome-wide analysis of FoxO1 binding in hepatic chromatin: potential involvement of FoxO1 in linking retinoid signaling to hepatic gluconeogenesis.

Shin DJ, Joshi P, Hong SH, Mosure K, Shin DG, Osborne TF - Nucleic Acids Res. (2012)

Representative view of a ChIP-seq peak. FoxO1-binding peaks were mapped onto the mouse reference genome mm9 and visualized using the UCSC Genome Browser. Arrows indicate peaks associated with genes: (A), Elk4; (B), Pck1; (C), Pdk4. WT = wild-type; KO = l-FoxO1 KO; Fx = FoxO1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3526316&req=5

gks932-F2: Representative view of a ChIP-seq peak. FoxO1-binding peaks were mapped onto the mouse reference genome mm9 and visualized using the UCSC Genome Browser. Arrows indicate peaks associated with genes: (A), Elk4; (B), Pck1; (C), Pdk4. WT = wild-type; KO = l-FoxO1 KO; Fx = FoxO1.
Mentions: ChIPed DNA was processed for sequencing by Solexa/Illumina Genome Analyzer II, which generated a data set of 5–6 million reads in each group (Figure 1A). The peaks were mapped onto the mouse reference genome mm9 in the UCSC Genome Browser Database. FoxO1-binding peaks were identified by SEAN (Supplementary Materials and Methods S1) with the threshold P-value 1 × 10−5. We found 583 peaks in FoxO1-enriched chromatin compared with IgG in WT (WT-FoxO1/WT-IgG), designated FoxO1/IgG, whereas 460 peaks were identified in FoxO1-enriched chromatin in WT compared with that in l-FoxO1 KO (WT-FoxO1/l-FoxO1 KO-FoxO1), designated WT/KO (Figure 1B). Notably, the overlapping peaks were 401, accounting for as much as 69% of peaks in FoxO1/IgG and 87% of peaks in WT/KO. The genomic locations of the 401 peaks are shown in Supplementary Table S9. We used the overlapping peaks as a reference for further analysis of genome-wide FoxO1-binding sites. We randomly selected three representative examples of ChIP-seq peaks, as shown in Figure 2. The location of the peaks for Pdk4 and Pck1-a encompasses the previously known FoxO1-binding sites (3,27), whereas the peaks for Elk4 and Pck1-b are newly found as putative FoxO1-binding sites in the current studies.Figure 1.

Bottom Line: We show here that FoxO1 directly binds to the genomic sites for the genes in retinoid metabolism.Notably, deletion of FoxO1 caused a significantly reduced induction of Pck1 and Pdk4 in response to retinoids.As Pck1 and Pdk4 are downstream targets of retinoid signaling, these results suggest that FoxO1 plays a potential role in linking retinoid metabolism to hepatic gluconeogenesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA. djshin@sanfordburnham.org

ABSTRACT
The forkhead transcription factor FoxO1 is a critical regulator of hepatic glucose and lipid metabolism, and dysregulation of FoxO1 function has been implicated in diabetes and insulin resistance. We globally identified FoxO1 occupancy in mouse hepatic chromatin on a genome-wide level by chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq). To establish the specific functional significance of FoxO1 against other FoxO proteins, ChIP-seq was performed with chromatin from liver-specific FoxO1 knockout and wild-type mice. Here we identified 401 genome-wide FoxO1-binding locations. Motif search reveals a sequence element, 5' GTAAACA 3', consistent with a previously known FoxO1-binding site. Gene set enrichment analysis shows that the data from FoxO1 ChIP-seq are highly correlated with the global expression profiling of genes regulated by FoxO1, demonstrating the functional relevance of our FoxO1 ChIP-seq study. Interestingly, gene ontology analysis reveals the functional significance of FoxO1 in retinoid metabolic processes. We show here that FoxO1 directly binds to the genomic sites for the genes in retinoid metabolism. Notably, deletion of FoxO1 caused a significantly reduced induction of Pck1 and Pdk4 in response to retinoids. As Pck1 and Pdk4 are downstream targets of retinoid signaling, these results suggest that FoxO1 plays a potential role in linking retinoid metabolism to hepatic gluconeogenesis.

Show MeSH
Related in: MedlinePlus