RT Journal Article
T1 Proximity labeling identifies a repertoire of site-specific R-loop modulators.
A1 Yan, Qingqing
A1 Wulfridge, Phillip
A1 Doherty, John
A1 Fernandez-Luna, Jose L
A1 Real, Pedro J
A1 Tang, Hsin-Yao
A1 Sarma, Kavitha
AB 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.
YR 2022
FD 2022-01-10
LK http://hdl.handle.net/10668/19536
UL http://hdl.handle.net/10668/19536
LA en
DS RISalud
RD Apr 9, 2025