Before and after DUX4: deconstructing its web of silencers and defining its long-term impact on cellular processes

Abstract

Facioscapulohumeral dystrophy (FSHD) is driven by a loss of epigenetic repression at the D4Z4 repeat region, leading to aberrant expression of early embryonic transcription factor Double Homeobox 4 (DUX4) and an embryonic transcriptional program in skeletal muscle. Mechanisms that initiate and maintain epigenetic repression at the D4Z4 are complex and incompletely understood. Here, I designed a functional silencing reporter system to identify specific D4Z4 sequences that drive silencing activity and discovered that one discrete sequence, termed D4Z4-S5, was sufficient for sequence-dependent silencer recruitment. This sequence drives silencing activity through both de novo DNA methylation and repressive histone modifications, driven specifically by several previously identified D4Z4 silencers: SETDB1, ATF7IP, SIN3A/3B, and LRIF1. The reporter system also showed promise as a robust platform for further discovery of FSHD therapeutics and disease modifiers, with candidate therapeutic p38 pathway inhibitors showing increased repression in D4Z4-S5. Our findings identify a key D4Z4 regulatory sequence that drives epigenetic repression and proposes a novel system for further screening of FSHD disease modifiers and therapeutics. The second focus of this work is based on the long-term effects of DUX4 in cancer. Expression of DUX4 has been identified in a wide variety of solid tissue cancers. DUX4 was recently found to be a driver of immune evasion and is associated with poor prognosis in response to immune-mediated cancer therapies due to a loss of antigen presentation machinery. Though the transcriptional activity of DUX4 has been well characterized, recent studies have implicated DUX4 in post-transcriptional modulation of cellular processes. Here, I describe the mechanism of DUX4-mediated translational suppression, leading to translational reprogramming. I also describe optimization attempts to develop a DUX4-lineage tracing system for further study of long-term effects of DUX4 activity in cancer and FSHD.