ARID1A IDR Targets EWS-FLI1 Condensates and Finetunes Productive Chromatin Remodeling

The chimeric transcription factor EWS-FLI1 undergoes liquid-liquid phase separation (LLPS) and binds to neomorphic microsatellite DNA regions, which in turn recruits cBAF to activate an oncogenic transcriptional program in Ewing sarcoma. To identify the specific subunit of cBAF involved in this interaction, we employed unbiased TurboID analysis, revealing ARID1A as a potential mediator. We discovered that an intrinsic disordered region of ARID1A, known as IDR1, undergoes homotypic phase separation and incorporates into EWS-FLI1 droplets. This finding suggests the direct involvement of IDR1 in recruiting cBAF to phase-separated EWS-FLI1. Additionally, we uncovered a surprising function of IDR1 in regulating the productive chromatin remodeling activity of cBAF. This novel discovery of ARID1A IDR1's dual role opens avenues for developing effective treatment strategies for relevant tumors. To investigate the role of ARID1A IDR1b in EWS-FLI1 mediated gene transcriptional regulation, we overexpressed EWS-FLI1 and ARID1A WT or ΔIDR1b in ARID1A-knockout 293T (named 12KO) cell line.