Genome-wide maps of acetylated histone 3 lysine 4 in human head and neck squamous cell carcinoma cells under normoxia and hypoxia

Hypoxia-induced EMT involves the interplay between chromatin modifiers histone deacetylase 3 (HDAC3) and WDR5. The histone mark acetylation of histone 3 lysine 4 (H3K4Ac) is observed in the promoter regions of various EMT marker genes (e.g. E-cadherin, vimentin). However, there are only a limited number of EMT marker genes whose promoters were shown to be labeled with H3K4Ac. To further define the genome wide location of H3K4Ac, a chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) analysis was performed using a head and neck squamous cell carcinoma (HNSCC) FADU cell line under normoxia and hypoxia. H3K4Ac was found to be located mainly around the transcription start site (TSS), and was partially removed from transcribed genes under hypoxia, indicating that H3K4Ac is responsible for regulation of gene expression during normoxia and hypoxia. 779 H3K4Ac-labeled genes whose H3K4Ac peaks were decreased under hypoxia were obtained by screening with a FDR< 0.05 and a distance to TSS of -5000~1000 bp. Overall design: Examination of the histone modification H3K4Ac in FADU cells under normoxia and hypoxia