Fig. 2: RNA-seq and methylation analyses show that HN9-R is hypermethylated by DNMT1 on the p62 promoter regions. | Cell Death & Disease

Fig. 2: RNA-seq and methylation analyses show that HN9-R is hypermethylated by DNMT1 on the p62 promoter regions.

From: Epigenetic regulation of p62/SQSTM1 overcomes the radioresistance of head and neck cancer cells via autophagy-dependent senescence induction

Fig. 2

A Heatmap of differentially expressed genes (DEGs) between the HN9-S and HN9-R clones by RNA sequencing analysis (n = 3). The number of genes with increased and reduced in HN9-R relative to HN9-S clones were displayed. B Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with p62 among DEGs between HN9-S and HN9-R clones. The y-axis displays the names and total number of genes of each pathway. DEGs significance was set at FDR ≤ 0.05 and |log2 FC | ≥ 0.5, and pathway significance was set at p ≤ 0.01 (Fisher’s exact test). C Log2 fold change comparison of RNA-seq and qRT-PCR (left) for p62 and western blotting (right) were used to validate the RNA sequencing data. Negative values indicate that p62 gene expression was downregulated in HN9-R compared to HN9-S clones. D Methylation analysis of the p62 promoter by methylation-specific PCR in three HN9 cells (upper) and in HN9-R treated with DNMT1 inhibitor, 5-Aza (bottom). E Immunoblot analysis of p62 level in HN9-R clones after treatment with 5-Aza. F Bisulfite sequencing analysis of the p62 promoter in HN9-S and HN9-R clones. The p62 promoter (from forward 4000 to 5000 bp) was analyzed at nine CpG methylation sites using pyrosequencing.

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