Supporting data for "Long Noncoding Transcriptome in Acute Myeloid Leukaemia"

The landscape of transcribed super-enhancers (SEs) in acute myeloid leukemia (AML) has not been characterized. Established methods for determination of SE landscape rely on chromatin immunoprecipitation of H3K27ac and H3K4me1 followed by sequencing to ascertain chromatin pattern. Enhancer RNA expression represents an independent method to measure functional enhancer activities. Recent strategies focusing on pre-defined enhancer elements have enabled the determination of SE landscape in large cohorts of primary tumor samples using RNA-sequencing. In this study, we performed deep total RNA-sequencing to study the landscape of transcribed SE loci in 185 AML patients and observed transcribed SE activities being closely associated with subtype-specific transcriptional programs in AML, revealing the pervasiveness of SE-associated deregulation of coding genes. Our findings suggest transcribed SE loci are pervasively involved in leukemogenic pathways, with clinical utility as biomarkers for prediction of treatment response.