Integration analysis of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome

Our DNA is organized into structures that control gene activity, essential for normal cell function and health. Disruptions in this organization can lead to diseases, including cancer. Long non-coding RNAs (lncRNAs) and R-loops, which are three-stranded DNA-RNA hybrid structure, are molecules that can influence this organization by interacting with DNA-binding proteins like CCTCC-binding factor (CTCF) which is crucial for maintaining chromatin structure. Using advanced computational methods to analyze genomic and genetic public multi-omics data across various human cell types, we have identified 542 candidate regions on human genome where lncRNAs impact gene regulation by modulating CTCF binding and chromatin regulation. This study provides new insights into how lncRNAs and R-loops contribute to the organization of DNA and regulation of genes, enhancing our understanding of cellular mechanisms and shedding light on potential genetic factors involved in health and disease.