biostudies-literatureMarchena-Cruz ENIEHS NIH HHSSecretaría de Estado de Investigacion, Desarrollo e InnovacionFederación Española de Enfermedades RarasNational Institutes of HealthMinisterio de Educación, Cultura y DeporteEuropean CommissionGobierno de Espana Ministerio de Educación Cultura y DeporteEuropean Research CouncilGobierno de Espana Ministerio de Economia y CompetitividadMinisterio de Ciencia e InnovaciónMinisterio de Economía y CompetitividadAgencia Estatal de InvestigacionNIGMS NIH HHS112148https://www.ebi.ac.uk/biostudies/studies/S-EPMC10066596biostudies-literatureUnknown42(3)Unscheduled R loops can be a source of genome instability, a hallmark of cancer cells. Although targeted proteomic approaches and cellular analysis of specific mutants have uncovered factors potentially involved in R-loop homeostasis, we report a more open screening of factors whose depletion causes R loops based on the ability of activation-induced cytidine deaminase (AID) to target R loops. Immunofluorescence analysis of γH2AX caused by small interfering RNAs (siRNAs) covering 3,205 protein-coding genes identifies 59 potential candidates, from which 13 are analyzed further and show a significant increase of R loops. Such candidates are enriched in factors involved in chromatin, transcription, and RNA biogenesis and other processes. A more focused study shows that the DDX47 helicase is anCell reportsDDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops.PMC10066596R25 GM102783R15 GM139135PID2019-104270GB-I00/BMCERC2014 AdG669898 TARLOOPBFU2016-75058-PR21 ES028792Marqueta-Gracia JJAmdeen SAGarcia-Rubio MLAguilera AGuillen-Mendoza CCamino LPCalderon-Montano JMLuna RMarchena-Cruz EBhandari JXue XSilva SfalseDDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops.Unscheduled R loops can be a source of genome instability, a hallmark of cancer cells. Although targeted proteomic approaches and cellular analysis of specific mutants have uncovered factors potentially involved in R-loop homeostasis, we report a more open screening of factors whose depletion causes R loops based on the ability of activation-induced cytidine deaminase (AID) to target R loops. Immunofluorescence analysis of γH2AX caused by small interfering RNAs (siRNAs) covering 3,205 protein-coding genes identifies 59 potential candidates, from which 13 are analyzed further and show a significant increase of R loops. Such candidates are enriched in factors involved in chromatin, transcription, and RNA biogenesis and other processes. A more focused study shows that the DDX47 helicase is an2023-01-01T00:00:00Z2023 Mar2026-05-29T03:31:38.41Z2024-12-03T17:18:02.383ZS-EPMC100665963682718410.1016/j.celrep.2023.112148