Assay for Transposase Accessible Chromatin (ATAC)-sequencing of the AML cell line U937

All-trans retinoic acid (ATRA, RA) has powerful activity in APL; its efficacy in non-APL AML is still unclear, but may be boosted by epigenetic drugs such azanucleoside DNMT inhibitors (Blagitko-Dorfs et al. PLoS ONE 2013). In a randomized phase II study (DECIDER trial, NCT00867672) the addition of RA to decitabine (DAC) in newly diagnosed non-fit older AML patients resulted in a clinically meaningful extension of survival. We hypothesize that in vitro, the add-on of RA to DAC results in cooperative transcriptome and chromatin accessibility changes (possibly associated with demethylation), which may explain at least in part this clinical result. Overall design: The AML cell line U937 was treated with decitabine (DAC) ± ATRA in technical triplicates for 3 consecutive days (with daily change of media and DAC add-on). For ATAC-sequencing (ATAC-seq), 50.000 fresh cells were processed in triplicates as described in the Omni-ATAC protocol by Corces et al. Size selection and purification was performed using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA). Validation of enriched open chromatin sites was determined by qPCR and paired-end libraries were sequenced with 40 million read/sample.