Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors.

Journal: Cell Genomics

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.

Y Tak, Gaylor Boulay, Lukuo Lee, Sowmya Iyer, Nicholas Perry, Hayley Schultz, Sara Garcia, Liliane Broye, Joy Horng, Shruthi Rengarajan, Beverly Naigles, Angela Volorio, Jeffry Sander, Jingyi Gong, Nicolὸ Riggi, J Joung, Miguel Rivera

Similar Publications