Yan, QingqingWulfridge, PhillipDoherty, JohnFernandez-Luna, Jose LReal, Pedro JTang, Hsin-YaoSarma, Kavitha2023-05-032023-05-032022-01-10http://hdl.handle.net/10668/19536R-loops are three-stranded nucleic acid structures that accumulate on chromatin in neurological diseases and cancers and contribute to genome instability. Using a proximity-dependent 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.enAttribution 4.0 Internationalhttp://creativecommons.org/licenses/by/4.0/AnimalsCell DifferentiationChromatinEmbryonic Stem CellsGenomic InstabilityHEK293 CellsHomeodomain ProteinsHumansInduced Pluripotent Stem CellsMiceMutationNerve Tissue ProteinsNeuronsProteomicsR-Loop StructuresRNAZinc Fingersresearch article35013239open access10.1038/s41467-021-27722-62041-1723PMC8748879https://www.nature.com/articles/s41467-021-27722-6.pdfhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8748879/pdf