Location of validated heat shock factor sites within Alus in the promoter region of up-regulated genes. A substantial fraction of up-regulated genes harbor high score (≥8.7) HSF sites within Alus in the upstream region. All the validated genes (SPINK6, HIST1H4A and ANKRD33) have their first HSF site within Alus in the promoter region from the transcription start site. Functional validation of such HSF sites through cloning, site-directed mutagenesis, transient transfection in a cell line and chromatin immunoprecipitation (ChIP) followed by PCR confirmed their role in the heat shock response.
Pandey et al. Genome Biology 2011 12:R117 doi:10.1186/gb-2011-12-11-r117