DNA Topoisomerase I differentially modulates R-loops across the human genome

• DOI: 10.1186/s13059-018-1478-1
• Publication Date: 2018-07-30T11:17:28Z
• Authors: Stefano G. Manzo; Stella R. Hartono; Lionel A. Sanz; Jessica Marinello; Sara De Biasi; Andrea Cossarizza; Giovanni Capranico; Frederic Chedin
• Keywords: DNA Replication; 0301 basic medicine; 570; Chromatin Immunoprecipitation; Transcription, Genetic; Bioinformatics; QH301-705.5; 1.1 Normal biological development and functioning; Type I; QH426-470; Small Interfering; Resting Phase, Cell Cycle; Histones; 03 medical and health sciences; Genetic; Underpinning research; Information and Computing Sciences; Heterochromatin; Genetics; Humans; Gene Silencing; Biology (General); RNA, Small Interfering; 0303 health sciences; Genome; Chromatin Immunoprecipitation; DNA; DNA Replication; DNA Topoisomerases, Type I; G1 Phase Cell Cycle Checkpoints; Gene Silencing; HEK293 Cells; Heterochromatin; Histones; Humans; Lamin Type B; Nucleic Acid Conformation; RNA Polymerase II; RNA, Small Interfering; Resting Phase, Cell Cycle; Genome, Human; Transcription, Genetic; Ecology, Evolution, Behavior and Systematics; Genetics; Cell Biology; Lamin Type B; Genome, Human; Research; Cell Cycle; DNA; Biological Sciences; G1 Phase Cell Cycle Checkpoints; Chromatin Immunoprecipitation; DNA; DNA Replication; DNA Topoisomerases, Type I; G1 Phase Cell Cycle Checkpoints; Gene Silencing; HEK293 Cells; Heterochromatin; Histones; Humans; Lamin Type B; Nucleic Acid Conformation; RNA Polymerase II; RNA, Small Interfering; Resting Phase, Cell Cycle; Genome, Human; Transcription, Genetic; HEK293 Cells; DNA Topoisomerases, Type I; RNA; Resting Phase; Nucleic Acid Conformation; Generic health relevance; RNA Polymerase II; Transcription; DNA Topoisomerases; Environmental Sciences; Human

Co-transcriptional R-loops are abundant non-B DNA structures in mammalian genomes. DNA Topoisomerase I (Top1) is often thought to regulate R-loop formation owing to its ability to resolve both positive and negative supercoils. How Top1 regulates R-loop structures at a global level is unknown.Here, we perform high-resolution strand-specific R-loop mapping in human cells depleted for Top1 and find that Top1 depletion results in both R-loop gains and losses at thousands of transcribed loci, delineating two distinct gene classes. R-loop gains are characteristic for long, highly transcribed, genes located in gene-poor regions anchored to Lamin B1 domains and in proximity to H3K9me3-marked heterochromatic patches. R-loop losses, by contrast, occur in gene-rich regions overlapping H3K27me3-marked active replication initiation regions. Interestingly, Top1 depletion coincides with a block of the cell cycle in G0/G1 phase and a trend towards replication delay.Our findings reveal new properties of Top1 in regulating R-loop homeostasis in a context-dependent manner and suggest a potential role for Top1 in modulating the replication process via R-loop formation.