DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops

• DOI: 10.1016/j.celrep.2023.112148
• Publication Date: 2023-02-23T04:59:11Z
• Authors: Esther Marchena-Cruz; Lola P. Camino; Jay Bhandari; Sónia Silva; José Javier Marqu...; Shahad A. Amdeen; Cristina Guillén-...; María L. García-R...; José M. Calderón-...; Xiaoyu Xue; Rosa Luna; Andrés Aguilera
• Keywords: Proteomics; 0301 basic medicine; R loop; QH301-705.5; Molecular biology; DNA Helicases; Genome instability; Helicase-unwinding activity; Article; Chromatin; Chromosomes; Genomic Instability; 3. Good health; 03 medical and health sciences; CP; Humans; CP: Molecular biology; Biology (General); R-Loop Structures; Transcription; DDX47; MeCP2

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 an R-loop resolvase, whereas the MeCP2 methyl-CpG-binding protein uncovers a link between DNA methylation and R loops. Thus, our results suggest that a plethora of gene dysfunctions can alter cell physiology via affecting R-loop homeostasis by different mechanisms.