Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance

Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy

Recent studies have shown that active enhancers are transcribed to produce enhancer RNAs (eRNAs; Kim et al., 2010; De Santa et al., 2010) . Genome-wide identification of enhancers by detection of eRNAs has recently become possible by coupling nascent transcription (run-on) assays with high throughput sequencing (e.g., global run-on [GRO-seq] and precision run-on sequencing [PRO-seq] ). GRO-seq (Core et al., 2008) and PRO-seq (Kwak et al., 2013) require isolation of cellular nuclei making the application of these methods to primary tissue extraordinarily difficult. To overcome this limitation, chromatin run-on sequencing (ChRO-seq), was developed to extend the technique and permit analysis of primary fresh or frozen tissue (Chu et al., 2018) . Additionally, the advent of a sister technique called length extension ChRO-seq (leChRO-seq) permits investigation of samples with degraded RNA (Chu et al., 2018) . These technical advances finally enable the study of nascent transcription at enhancer, promoter, and gene loci in fresh or archived primary human tumor tissues. ChRO-seq was recently successfully used to identify distinct transcriptional programs in different subtypes of glioblastoma multiforme (Chu et al., 2018) .