Cell lines
Antibodies
Protein extraction and coimmunoprecipitation
Histone extraction
ChIP, sequencing, and data analysis
Nascent RNA, total RNA, and mRNA sequencing, microarrays, and data analyses
Gene set enrichment analysis
Functional analyses
Enhancer RNA expression analysis
Cell proliferation, cell cycle, and annexin V assays
qPCR
DOT1L knockdown
Miniaturized organotypic 3D cultures
Xenograft experiments
Statistical analysis
ChIP-MS was performed as described by Mohammed et al. (18), with some modifications. Tryptic digestion liquid chromatography–MS/MS and data analysis were performed as previously described (see the Supplementary Materials and Methods for additional details) (46). The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRoteomics IDEntifications (47) partner repository with the dataset identifier PXD010314.