Proximity labeling identifies a repertoire of sitespecific R-loop modulators Yan, Qingqing Wulfridge, Phillip Doherty, John Fernández Luna, Juan Manuel Real Luna, Pedro José Tang, Hsin-Yao Sarma, Kavitha R-loops are three-stranded nucleic acid structures that accumulate on chromatin in neurological diseases and cancers and contribute to genome instability. Using a proximitydependent labeling system, we identified distinct classes of proteins that regulate R-loops in vivo through different mechanisms. We show that ATRX suppresses R-loops by interacting with RNAs and preventing R-loop formation. Our proteomics screen also discovered an unexpected enrichment for proteins containing zinc fingers and homeodomains. One of the most consistently enriched proteins was activity-dependent neuroprotective protein (ADNP), which is frequently mutated in ASD and causal in ADNP syndrome. We find that ADNP resolves R-loops in vitro and that it is necessary to suppress R-loops in vivo at its genomic targets. Furthermore, deletion of the ADNP homeodomain severely diminishes R-loop resolution activity in vitro, results in R-loop accumulation at ADNP targets, and compromises neuronal differentiation. Notably, patient-derived human induced pluripotent stem cells that contain an ADNP syndrome-causing mutation exhibit R-loop and CTCF accumulation at ADNP targets. Our findings point to a specific role for ADNP-mediated R-loop resolution in physiological and pathological neuronal function and, more broadly, to a role for zinc finger and homeodomain proteins in R-loop regulation, with important implications for developmental disorders and cancers. 2024-10-02T11:56:49Z 2024-10-02T11:56:49Z 2022-01-10 journal article Yan, S. et. al. Nat Commun 13, 53 (2022). [https://doi.org/10.1038/s41467-021-27722-6] https://hdl.handle.net/10481/95441 10.1038/s41467-021-27722-6 eng http://creativecommons.org/licenses/by/4.0/ open access Atribución 4.0 Internacional Springer Nature