Language
English
Publication Date
9-5-2024
Journal
Molecular Cell
DOI
10.1016/j.molcel.2024.07.032
PMID
39173639
PMCID
PMC11380577
PubMedCentral® Posted Date
9-5-2025
PubMedCentral® Full Text Version
Author MSS
Abstract
Topoisomerase I (TOP1) is an essential enzyme that relaxes DNA to prevent and dissipate torsional stress during transcription. However, the mechanisms underlying the regulation of TOP1 activity remain elusive. Using enhanced cross-linking and immunoprecipitation (eCLIP) and ultraviolet-cross-linked RNA immunoprecipitation followed by total RNA sequencing (UV-RIP-seq) in human colon cancer cells along with RNA electrophoretic mobility shift assays (EMSAs), biolayer interferometry (BLI), and in vitro RNA-binding assays, we identify TOP1 as an RNA-binding protein (RBP). We show that TOP1 directly binds RNA in vitro and in cells and that most RNAs bound by TOP1 are mRNAs. Using a TOP1 RNA-binding mutant and topoisomerase cleavage complex sequencing (TOP1cc-seq) to map TOP1 catalytic activity, we reveal that RNA opposes TOP1 activity as RNA polymerase II (RNAPII) commences transcription of active genes. We further demonstrate the inhibitory role of RNA in regulating TOP1 activity by employing DNA supercoiling assays and magnetic tweezers. These findings provide insight into the coordinated actions of RNA and TOP1 in regulating DNA topological stress intrinsic to RNAPII-dependent transcription.
Keywords
DNA Topoisomerases, Type I, Humans, RNA-Binding Proteins, RNA Polymerase II, Protein Binding, DNA, Transcription, Genetic, RNA, Messenger, RNA, Cell Line, Tumor, DNA, Superhelical, HCT116 Cells, Nucleic Acid Conformation, TOP1, RNA binding protein, DNA supercoiling, magnetic tweezers, TOP1 interactome, transcription, topology
Published Open-Access
yes
Recommended Citation
Bhola, Mannan; Abe, Kouki; Orozco, Paola; et al., "RNA Interacts With Topoisomerase I To Adjust DNA Topology" (2024). Faculty and Staff Publications. 3849.
https://digitalcommons.library.tmc.edu/baylor_docs/3849
Graphical Abstract