Genes & Cancer

Transcriptomic analysis functionally maps the intrinsically disordered domain of EWS/FLI and reveals novel transcriptional dependencies for oncogenesis

Emily R. Theisen1, Kyle R. Miller1, Iftekhar A. Showpnil1,2, Cenny Taslim1, Kathleen I. Pishas1 and Stephen L. Lessnick1,2,3

1 Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children’s Hospital, Columbus, OH, USA

2 Molecular, Cellular, and Developmental Biology Program, The Ohio State University, Columbus, OH, USA

3 Division of Pediatric Hematology/Oncology/Blood & Marrow Transplant, The Ohio State University, Columbus, OH, USA


Stephen L. Lessnick, email:

Keywords: Ewing sarcoma; EWS/FLI; RNA-seq; structure-function; intrinsically disordered domains

Received: December 10, 2018 Accepted: February 05, 2019 Published: February 17, 2019


EWS/FLI is the pathognomic fusion oncoprotein that drives Ewing sarcoma. The amino-terminal EWS portion coordinates transcriptional regulation and the carboxy-terminal FLI portion contains an ETS DNA-binding domain. EWS/FLI acts as an aberrant transcription factor, orchestrating a complex mix of gene activation and repression, from both high affinity ETS motifs and repetitive GGAA-microsatellites. Our overarching hypothesis is that executing multi-faceted transcriptional regulation requires EWS/FLI to use distinct molecular mechanisms at different loci. Many attempts have been made to map distinct functions to specific features of the EWS domain, but described deletion mutants are either fully active or completely “dead” and other approaches have been limited by the repetitive and disordered nature of the EWS domain. Here, we use transcriptomic approaches to show an EWS/FLI mutant, called DAF, previously thought to be nonfunctional, displays context-dependent and partial transcriptional activity but lacks transforming capacity. Using transcriptomic and phenotypic anchorage-independent growth profiles of other EWS/FLI mutants coupled with reported EWS/FLI localization data, we have mapped the critical structure-function requirements of the EWS domain for EWS/FLI-mediated oncogenesis. This approach defined unique classes of EWS/FLI response elements and revealed novel structure-function relationships required for EWS/FLI activation at these response elements.

PII: 188