Transcriptionally active enhancers in human cancer cells

The growth of human cancer cells is driven by aberrant enhancer and gene transcription activity. Here we use Transient Transcriptome sequencing (TT-seq) to map thousands of transcriptionally active putative enhancers in fourteen human cancer cell lines covering seven cancer types. We conducted an in-depth analysis of the data, derived thousands of putative enhancer-promoter pairs, and extracted general features of active enhancer and transcription landscapes in cancer cells. We provide a comprehensive catalog of transcribed candidate enhancers with cancer-associated somatic mutations and putative enhancer-promoter pairs involving cancer-associated genes. Overall our results serve as a resource to study enhancer activity and gene regulation, and to select candidate enhancers for functional studies. Twelve human cancer cell lines (M059J, U-118 MG, BT-20, MDA-MB-231, GP5d, HCT 116, LoVo, 769-P, 786-O, DU 145, PC-3, SK-UT-1) were labeled with 500 µM 4-thiouridine for 5 min in biological duplicates. For each duplicate libraries of total fragmented RNA (RNA-seq) and 4sU-labelled RNA (TT-seq) were sequenced. Total number of samples sequenced: 48. Published TT-seq data sets of two additional cancer cell lines, K562 (Schwalb et al. 2016) and Jurkat (Michel et al. 2017) were incorporated in the eRNA and enhancer annotation data.