Cell Genom. 2022 Apr 13. pii: 100119. [Epub ahead of print]2(4):
Y Esther Tak,
Gaylor Boulay,
Lukuo Lee,
Sowmya Iyer,
Nicholas T Perry,
Hayley T Schultz,
Sara P Garcia,
Liliane Broye,
Joy E Horng,
Shruthi Rengarajan,
Beverly Naigles,
Angela Volorio,
Jeffry D Sander,
Jingyi Gong,
Nicolὸ Riggi,
J Keith Joung,
Miguel N Rivera.
Repeat elements can be dysregulated at a genome-wide scale in human diseases. For example, in Ewing sarcoma, hundreds of inert GGAA repeats can be converted into active enhancers when bound by EWS-FLI1. Here we show that fusions between EWS and GGAA-repeat-targeted engineered zinc finger arrays (ZFAs) can function at least as efficiently as EWS-FLI1 for converting hundreds of GGAA repeats into active enhancers in a Ewing sarcoma precursor cell model. Furthermore, a fusion of a KRAB domain to a ZFA can silence GGAA microsatellite enhancers genome wide in Ewing sarcoma cells, thereby reducing expression of EWS-FLI1-activated genes. Remarkably, this KRAB-ZFA fusion showed selective toxicity against Ewing sarcoma cells compared with non-Ewing cancer cells, consistent with its Ewing sarcoma-specific impact on the transcriptome. These findings demonstrate the value of ZFAs for functional annotation of repeats and illustrate how aberrant microsatellite activities might be regulated for potential therapeutic applications.