Chromatin accessibility, p300 and histone acetylation define PML-RARalpha- and AML1-ETO-binding sites

Chromatin accessibility is a key determinant of cell-type-specific gene expression. Here, we have investigated the chromatin architecture of different acute myeloid leukemia (AML) cells and the changes in accessibility when NB4 (APL) cells undergo the process of differentiation. Overall design: For nuclease-accessible site sequencing (NA-seq; Gargiulo et al. 2009), chromatin-accessible libraries were generated in different AML leukemic cells by using restriction enzymes NlaIII and HpaII. In the case of NB4 cells, accessibility was mapped both before and after treatment with all-trans retinoic acid (ATRA) for 48hr. Differences were observed between the two conditions, and chromatin accessibility was correlated with underlying epigenetic modifications. For validation purposes, NA-seq libraries (using the NlaIII enzyme) were generated in APL and AML M1 patient''s blasts. All of the ChIP-seq (Martens et al. 2010) studies were performed in leukemic NB4 and SKNO-1 cells. Supplementary file ''GSE30254_All_accessibleregions_ATRA_NB4_fseq.wig'' includes data for Samples GSM749512, GSM749513, GSM749516, and GSM749517. Supplementary file ''GSE30254_All_accessibleregions_untreated_NB4_fseq.wig'' includes data for Samples GSM749510, GSM749511, GSM749514, and GSM749515.