Work

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

Year: 2024

Type: article

Abstract: 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.

Source: Genome biology

DOI: 10.1186/s13059-024-03377-6

Authors: Sean M. Flynn, Somdutta Dhir, Krzysztof Herka, Colm Doyle, Larry Melidis, Angela Simeone, Winnie W. I. Hui, Rafael de Cesaris Araujo Tavares, Stefan Schoenfelder, David Tannahill, Shankar Balasubramanian

Institutions: Cancer Research UK, Babraham Institute, University of Cambridge, Cancer Research UK Cambridge Center

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $5,290

Funders: Wellcome Trust, UK Research and Innovation, Cancer Research UK, Leverhulme Trust, Medical Research Council, Biotechnology and Biological Sciences Research Council, Cancer Research UK Cambridge Institute, University of Cambridge

Awards: To study epigenetic mechanisms regulating lineage commitment and cell potency, G339059223, G3594106981, Higher-order chromatin structure and regulatory sequence variation in human induced pluripotent stem cell (iPSC) self-renewal and differentiation, G4002907240, G5043583218, G5410182794, G63586632, G7064146384, G7101412424, G7471487811, G7567962354, G7887713238, The chemical biology and function of natural modified DNA bases in genomes, G823736304, G8418559812, G8550030593, The chemical biology and function of natural modified DNA bases in genomes

OpenAlex ID: W4402178419

FWCI: 1.385

Cites: 52

Cited by: 12

Related to: 10