Heat shock factor binds to its cognate site in Alu repeats. The binding of a HSF to the heat shock element sequence present within the Alu repeat of HIST1H4A, SPINK6 and ANKRD33 genes in the promoter region was confirmed by ChIP-PCR after heat shock treatment. HSPA1A, with a HSF binding site in a non-Alu region, was used as a positive control. Input chromatin was used to ascertain that equal amounts of chromatin were applied in each reaction. Enrichment in heat shock treated samples compared to untreated and no antibody (Ab) ChIP samples is clearly visible. The faint band in the untreated HSPA1A sample confirms earlier reports of binding of HSF to this promoter, although this is not induced. As negative controls we considered regions of the genome that do not contain an HSF site. The negative controls do not show any band in the treated/untreated ChIP or 'no Ab' lanes, although the band in the input chromatin lane confirms the genomic presence of the queried region.
Pandey et al. Genome Biology 2011 12:R117 doi:10.1186/gb-2011-12-11-r117