Figure 3.

HNF4α binds Alu elements in vivo. A. HNF4α chromatin immunoprecipitation (ChIP) of HepG2 cells using 16 sets of PCR primers as indicated. Shown is an ethidium-bromide-stained agarose gel of the qPCR products after ~40 cycles for graphical representation only. In, input control of genomic DNA. IgG, control IP with normal rabbit IgG. H4, IP with HNF4α antibody raised in rabbit. Fold change, ratio of the H4 to IgG signal determined by quantitative real time PCR (qPCR). Pos and neg control, regions of the CDKN1A promoter in which HNF4α was shown previously to bind or not, respectively [71]; Alu generic, amplification with generic primers that recognize all Alu elements. Shown are the results from one of two or more independent ChIP experiments performed in duplicate, except for APOM, GSTM4, PRLR and SOCS2 which are from one ChIP experiment. The largest fold change values obtained for a given gene are indicated. B. Schematic diagram of promoters of HNF4α target genes. Diamonds, position of HNF4α binding sites in Alu elements identified in this study; triangles, other HNF4α binding sites predicted by PBM from Bolotin et al. [42]; vertical lines, position of the PCR primers used in the ChIP; arrows, start sites of transcription. See additional file 2: Table S2 for sequences of all the PCR primers.

Bolotin et al. BMC Genomics 2011 12:560   doi:10.1186/1471-2164-12-560
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