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. Author manuscript; available in PMC: 2011 Dec 1.
Published in final edited form as: Nat Struct Mol Biol. 2011 May 29;18(6):742–746. doi: 10.1038/nsmb.2060

Figure 4.

Figure 4

The maintenance of nucleosome position and chromatin structure is independent of Foxa1/2 in the adult liver. (a) Promoter-proximal Foxa2 binding sites are frequently surrounded by CpG islands. Distribution of CpG islands and nucleosomes surrounding Foxa2 binding sites. (b) Distribution of CpG bounded Foxa2 binding sites upstream and downstream of transcriptional start sites. (c) Intersection of differentially expressed genes in Foxa1/2 mutant liver and Foxa2 ChIP-Seq data. Gene expression data were differentially expressed genes from microarray analysis between Foxa1loxP/loxP;Foxa2loxP/loxP;AlfpCre (Mutant) and control mice; Foxa2 targets were Foxa2-targeted genes from ChIP-Seq analysis. (d) Distribution of Foxa2 binding sites upstream and downstream of transcriptional start sites for those sites associated with directly-regulated genes. A total of 369 Foxa2 binding sites were associated with the 197 differentially expressed genes. (e) Nucleosome occupancy surrounding Foxa2 binding sites associated with genes including thymocyte selection-associated high mobility group box (Tox), cAMP specific phosphodiesterase 4B (Pde4b), hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 5 (Hsd3b5), transthyretin (Ttr), glutathionine S-transferase m1 (Gstm1), albumin promoter (Alb_p), alpha fetoprotein enhancer (Afp_e), sulfotransferase family 3A, member 1 (Sult3a1), the albumin enhancer (Alb1_e), gene model 129 (GM129), ribosomal protein S27A (Rps27a), protein phosphatase 1, regulatory (inhibitor) subunit 3C (Ppp1r3c), COBW domain containing 1 (Cbwd1), poly A polymerase alpha (Pap), ribonuclease L (Rnasel) and PR domain containing 6 (Prdm6), in livers from Foxa1loxP/loxP;Foxa2loxP/loxP;AlfpCre (Mutant) and control mice, mouse heart and mouse embryonic stem cells (ES Cell). (f, g) Distribution of heterochromatin protein 1 (Hp1), CBP, and p300 surrounding Foxa2 binding sites, or Hp1 surrounding H3K9me3 sites in control (f) and Foxa1/2 mutant (g) livers. 0 corresponds to the center of Foxa2 binding sites or H3K9me3 sites, respectively.