Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR

• Published in: Genome Biology Vol. 25; no. 1; pp. 237 - 10
• Main Authors: Flynn, Sean M, Dhir, Somdutta, Herka, Krzysztof, Doyle, Colm, Melidis, Larry, Simeone, Angela, Hui, Winnie W I, Araujo Tavares, Rafael de Cesaris, Schoenfelder, Stefan, Tannahill, David, Balasubramanian, Shankar
• Format: Journal Article
• Language: English
• Published: England BioMed Central 03.09.2024; BMC
• Subjects: 3D genome structure; Antibodies; Chromatin; Chromatin - metabolism; DNA structure; Epigenesis, Genetic; Epigenetics; Epigenomics - methods; G-quadruplex DNA; G-Quadruplexes; Gene mapping; Genes; Genomes; Hi-C; Histone Code; Histone marks; Histones; Histones - metabolism; Humans; Peptide mapping; Short Report; Stem cells; G-quadruplex DNA; Hi-C; 3D genome structure; Histone marks
• ISSN: 1474-760X; 1474-7596; 1474-760X
• DOI: 10.1186/s13059-024-03377-6

Methods to measure chromatin contacts at genomic regions bound by histone modifications or proteins are important tools to investigate chromatin organization. However, such methods do not capture the possible involvement of other epigenomic features such as G-quadruplex DNA secondary structures (G4s). To bridge this gap, we introduce ViCAR (viewpoint HiCAR), for the direct antibody-based capture of chromatin interactions at folded G4s. Through ViCAR, we showcase the first G4-3D interaction landscape. Using histone marks, we also demonstrate how ViCAR improves on earlier approaches yielding increased signal-to-noise. ViCAR is a practical and powerful tool to explore epigenetic marks and 3D genome interactomes.