File S1 - Alterations of Epigenetic Signatures in Hepatocyte Nuclear Factor 4α Deficient Mouse Liver Determined by Improved ChIP-qPCR and (h)MeDIP-qPCR Assays

Figure S1, Effects of Hnf4a deficiency on histone H3 lysine 4 dimethyl (H3K4me2) and histone H3 lysine 4 trimethyl (H3K4me3) in female mouse livers. Enrichment of H3K4me2 and H3K4me3 at specific loci relative to input in ChIPed DNA fragments in livers from female Hnf4a-LivKO and wild-type mice was normalized by the positive control. Insets, the percentage of total ChIPed DNA fragments relative to input for H3K4me2 and H3K4me3 in livers from female Hnf4a-LivKO and wild-type mice. Negative = negative control. Mean ± S.E., N = 3 biological replicates. *, p<0.05 versus wild-type. Figure S2, Effects of Hnf4a deficiency on histone H3 lysine 9 dimethyl (H3K9me2) and histone H3 lysine 9 trimethyl (H3K9me3) in female mouse livers. Enrichment of H3K9me2 and H3K9me3 at specific loci relative to input in ChIPed DNA fragments in livers from female Hnf4a-LivKO and wild-type mice was normalized by the positive control. Insets, the percentage of total ChIPed DNA fragments relative to input for H3K9me2 and H3K9me3 in livers from female Hnf4a-LivKO and wild-type mice. Negative = negative control. Mean ± S.E., N = 3 biological replicates. *, p<0.05 versus wild-type. Figure S3, Effects of Hnf4a deficiency on histone H3 lysine 27 trimethyl (H3K27me3) and histone H3 lysine 4 acetylation (H3K4ac) in female mouse livers. Enrichment of H3K27me3 and H3K4acat specific loci relative to input for ChIPed DNA fragments in livers from female Hnf4a-LivKO and wild-type mice was normalized by the positive control. Insets, the percentage of total ChIPed DNA fragments relative to input for H3K27me3 and H3K4ac in livers from female Hnf4a-LivKO and wild-type mice. Negative = negative control. Mean ± S.E., N = 3 biological replicates. *, p<0.05 versus wild-type. Table S1, The efficiency (E) and coefficient of variation (CV) for Cq values in real-time PCR reactions in the presence/absence of input DNA sample and positive control. Table S2, The list of functions of genes tested in histone modifications due to Hnf4a deficiency. Table S3, List of qPCR primers used for IPed DNA fragments and cDNA.
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