BioProject

The growth of human cancer cells is driven by aberrant enhancer and gene transcription activity. More...

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. Overall design: 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. Less...