Transcriptional repression by a secondary DNA binding surface of DNA topoisomerase I safeguards against hypertranscription

• Published in: Nature communications Vol. 14; no. 1; p. 6464
• Main Authors: Lau, Mei Sheng, Hu, Zhenhua, Zhao, Xiaodan, Tan, Yaw Sing, Liu, Jinyue, Huang, Hua, Yeo, Clarisse Jingyi, Leong, Hwei Fen, Grinchuk, Oleg V., Chan, Justin Kaixuan, Yan, Jie, Tee, Wee-Wei
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13.10.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/15; 38/23; 38/39; 38/91; 42/109; 45; 45/100; 45/90; 631/337/572; 631/45/173; 9/74; Binding; Chromatin; Deoxyribonucleic acid; DNA; DNA topoisomerase; Embryo cells; Enzymatic activity; Gene regulation; Gene silencing; Humanities and Social Sciences; multidisciplinary; Mutation; Proteins; Science; Science (multidisciplinary); Stem cells; Supercoiling
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-42078-9

Regulation of global transcription output is important for normal development and disease, but little is known about the mechanisms involved. DNA topoisomerase I (TOP1) is an enzyme well-known for its role in relieving DNA supercoils for enabling transcription. Here, we report a non-enzymatic function of TOP1 that downregulates RNA synthesis. This function is dependent on specific DNA-interacting residues located on a conserved protein surface. A loss-of-function knock-in mutation on this surface, R548Q, is sufficient to cause hypertranscription and alter differentiation outcomes in mouse embryonic stem cells (mESCs). Hypertranscription in mESCs is accompanied by reduced TOP1 chromatin binding and change in genomic supercoiling. Notably, the mutation does not impact TOP1 enzymatic activity; rather, it diminishes TOP1-DNA binding and formation of compact protein-DNA structures. Thus, TOP1 exhibits opposing influences on transcription through distinct activities which are likely to be coordinated. This highlights TOP1 as a safeguard of appropriate total transcription levels in cells. Aberrant hypertranscription in cells can affect development and disease. Here, the authors show that DNA topoisomerase I prevents hypertranscription; not through its catalytic function, but through a DNA binding mechanism.