Systematic Characterization of Mutations Altering Protein Degradation in Human Cancers

The Ubiquitin-Proteasome System (UPS) is the primary route for selective protein degradation in human cells. We implicate transcription factors as important substrates. By developing a deep learning model (deepDegron) to identify mutations that result in degron loss, and experimentally validated predictions that gain-of-function truncating mutations in GATA3 result in increased protein stability. We profiled the DNA binding by ChIP-seq of GATA3 in response to point mutations of the implicated degron. We found an increase in DNA binding, with up-regulating peaks preferentially found near estrogen signaling related genes. To serve as control, we include GATA3 with a c-terminal FLAG-tag that would stabilize GATA3 regardless of mutation status. No significant enrichment was observed in the control. Overall design: Examination of GATA3 ChIP-seq under three condtions in MDA-MB-231 cells: wildtype, p.A442M point mutation, and p.G444E point mutation. Additionally, the three conditions were also assayed with a FLAG-tag at the c-terminus, which stabilizes GATA3 protein levels, regardless of mutation status. Two replicaters per condition.