A functional LSD1 coregulator screen reveals a novel transcriptional regulatory cascade connecting R-loop homeostasis with epigenetic regulation

• Published in: Nucleic acids research 2021-05, Vol.49 (8), p.4350-4370
• Main Authors: Pinter, Sabine, Knodel, Franziska, Choudalakis, Michel, Schnee, Philipp, Kroll, Carolin, Fuchs, Marina, Broehm, Alexander, Weirich, Sara, Roth, Mareike, Eisler, Stephan A, Zuber, Johannes, Jeltsch, Albert, Rathert, Philipp
• Format: Article
• Language: English
• Subjects: Animals; Binding Sites; Enhancer Elements, Genetic; Gene Expression Regulation, Neoplastic; Gene regulation, Chromatin and Epigenetics; Gene Silencing; Genes, Reporter; Histone Demethylases - genetics; Histones - metabolism; Homeostasis; Humans; Methylation; Mice; Neoplasms - genetics; NIH 3T3 Cells; Nucleocytoplasmic Transport Proteins - genetics; Nucleocytoplasmic Transport Proteins - metabolism; Promoter Regions, Genetic; R-Loop Structures - genetics; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; RNA Interference; Transcription, Genetic
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkab180

Abstract The lysine specific demethylase 1 (LSD1) plays a pivotal role in cellular differentiation by regulating the expression of key developmental genes in concert with different coregulatory proteins. This process is impaired in different cancer types and incompletely understood. To comprehensively identify functional coregulators of LSD1, we established a novel tractable fluorescent reporter system to monitor LSD1 activity in living cells. Combining this reporter system with a state-of-the-art multiplexed RNAi screen, we identify the DEAD-box helicase 19A (DDX19A) as a novel coregulator and demonstrate that suppression of Ddx19a results in an increase of R-loops and reduced LSD1-mediated gene silencing. We further show that DDX19A binds to tri-methylated lysine 27 of histone 3 (H3K27me3) and it regulates gene expression through the removal of transcription promoting R-loops. Our results uncover a novel transcriptional regulatory cascade where the downregulation of genes is dependent on the LSD1 mediated demethylation of histone H3 lysine 4 (H3K4). This allows the polycomb repressive complex 2 (PRC2) to methylate H3K27, which serves as a binding site for DDX19A. Finally, the binding of DDX19A leads to the efficient removal of R-loops at active promoters, which further de-represses LSD1 and PRC2, establishing a positive feedback loop leading to a robust repression of the target gene. Graphical Abstract Graphical Abstract Model of the regulatory cascade for transcriptional repression, which depends on the removal of transcription-associated R-loops downstream of LSD1 activity.