Dysregulated erythroid gene expression after TET2 loss is partially corrected by 5-azacytidine in TF-1 cells [RNA-seq]

Using bisulfite padlock probes, mRNA sequencing, and hydroxymethylcytosine pull-down sequencing, we show that TET2 loss particularly influences DNA methylation (5mC) and hydroxymethylation (5hmC) patterns at erythroid gene enhancers and is associated with down-regulation of erythroid gene expression in the human erythroleukemia cell line TF-1. We show that 5-Aza disproportionately induces expression of these down regulated genes in TET2KO cells and that this effect may be related to 5mC changes at erythroid gene enhancers after 5-Aza exposure. This work highlights the role of 5mC and 5hmC changes at distal regulatory elements in regulating the expression of differentiation-associated gene signatures, and sheds light on how 5-Aza may be more effective in patients harboring TET2 mutations. We examine gene expression (bulk mRNAseq) of TF1 cell lines with 2 genetic conditions (TET2 KO vs WT; 2 biological replicates per genotype) at three separate time points (pre-treatment, 72hrs and 264hrs after first treatment) in relation to treatment with 5-azacytidine or DMSO (vehicle). Note: Sample 9 (F4_KO_T72_DMSO_BATCH1) did not pass sequencing QC and was removed prior to downstream analyses.