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

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.

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Publication Details

Journal
Genome biology
Published
2024-09-03
DOI
https://doi.org/10.1186/s13059-024-03377-6
Citations
8
Primary Topic
Genomics and Chromatin Dynamics
Type
article
Field-Weighted Citation Impact
1.87

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article

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

Somdutta Dhir, David Tannahill, Rafael de Cesaris Araujo Tavares, Colm Doyle et al.
8 citations
Genome biology
Genomics and Chromatin Dynamics
1.87
article

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

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

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.

Genome biologyVol. 25(1)
Babraham Institute (GB), University of Cambridge (GB), Cancer Research UK (GB), Cambridge School (PT)
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
Openalex Percentile: Top 14%
Genomics and Chromatin Dynamics
1.87
DOIOpen Access PDFOpenAlex
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Improved simultaneous mapping of epigenetic features and 3D chromatin structure via ViCAR — Somdutta Dhir, David Tannahill, et al. · Genome biology (2024) | TGRS Research Map | TGRS