Nat Commun. 2022 Jan 10;13(1):53. doi: 10.1038/s41467-021-27722-6.

Proximity labeling identifies a repertoire of site-specific R-loop modulators.

Nature communications

Qingqing Yan, Phillip Wulfridge, John Doherty, Jose L Fernandez-Luna, Pedro J Real, Hsin-Yao Tang, Kavitha Sarma

PMID: 35013239 DOI: 10.1038/s41467-021-27722-6

Abstract

R-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.

© 2022. The Author(s).

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• Journal Article

Grant support

• 1DP2NS105576/U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD)
• 670739/Simons Foundation