ORCID Profile
0000-0002-4108-4357
Current Organisation
University of Oxford
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Publisher: Bio-Protocol, LLC
Date: 2017
Publisher: Springer Science and Business Media LLC
Date: 29-03-2023
Publisher: Springer Science and Business Media LLC
Date: 22-01-2021
DOI: 10.1038/S41467-020-20809-6
Abstract: Chromosome conformation capture (3C) provides an adaptable tool for studying erse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at limited numbers of loci. Due to technical limitations, generation of reproducible high-resolution interaction profiles has not been achieved at genome-wide scale. Here, to overcome this barrier, we systematically test each step of 3C and report two improvements over current methods. We show that up to 30% of reporter events generated using the popular in situ 3C method arise from ligations between two in idual nuclei, but this noise can be almost entirely eliminated by isolating intact nuclei after ligation. Using Nuclear-Titrated Capture-C, we generate reproducible high-resolution genome-wide 3C interaction profiles by targeting 8055 gene promoters in erythroid cells. By pairing high-resolution 3C interaction calls with nascent gene expression we interrogate the role of promoter hubs and super-enhancers in gene regulation.
Publisher: Cold Spring Harbor Laboratory
Date: 02-03-2020
DOI: 10.1101/2020.03.02.953745
Abstract: Chromosome conformation capture (3C) provides an adaptable tool for studying erse biological questions. Current 3C methods provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at up to several hundred loci. All 3C methods are affected to varying degrees by inefficiency, bias and noise. As such, generation of reproducible high-resolution interaction profiles has not been achieved at scale. To overcome this barrier, we systematically tested and improved upon current methods. We show that isolation of 3C libraries from intact nuclei, as well as shortening and titration of enrichment oligonucleotides used in high-resolution methods reduces noise and increases on-target sequencing. We combined these technical modifications into a new method Nuclear-Titrated (NuTi) Capture-C, which provides a -fold increase in informative sequencing content over current Capture-C protocols. Using NuTi Capture-C we target 8,061 promoters in triplicate, demonstrating that this method generates reproducible high-resolution genome-wide 3C interaction profiles at scale.
Publisher: Springer Science and Business Media LLC
Date: 09-06-2021
DOI: 10.1038/S41586-021-03639-4
Abstract: In higher eukaryotes, many genes are regulated by enhancers that are 10
Publisher: Oxford University Press (OUP)
Date: 09-2019
DOI: 10.1093/QJMED/HCZ175
Publisher: Springer Science and Business Media LLC
Date: 27-06-2023
Publisher: Cold Spring Harbor Laboratory
Date: 24-10-2019
DOI: 10.1101/813618
Abstract: Genome-wide association studies (GWAS) have identified over 150,000 links between common genetic variants and human traits or complex diseases. Over 80% of these associations map to polymorphisms in non-coding DNA. Therefore, the challenge is to identify disease-causing variants, the genes they affect, and the cells in which these effects occur. We have developed a platform using ATAC-seq, DNaseI footprints, NG Capture-C and machine learning to address this challenge. Applying this approach to red blood cell traits identifies a significant proportion of known causative variants and their effector genes, which we show can be validated by direct in vivo modelling.
Publisher: Springer Science and Business Media LLC
Date: 02-2022
Publisher: Oxford University Press (OUP)
Date: 08-2006
DOI: 10.1093/QJMED/HCL065
Publisher: Cold Spring Harbor Laboratory
Date: 18-02-2020
DOI: 10.1101/2020.02.17.952572
Abstract: DNA folding within nuclei is a highly ordered process, with implications for gene regulation and development. An array of chromosome conformation capture (3C) methods have been developed to investigate how DNA is packaged within nuclei and to interrogate specific interactions. While these methods use different approaches to examine target loci (many-versus-all) or the entire genome (all-versus-all), they all rely on the core principle of endonuclease digestion and proximity-based ligation to re-arrange genomic order to reflect the three-dimensional nuclear conformation. This sequence reorganization creates novel chimeric DNA fragments which require specialist bioinformatic tools to analyze and visualize. Despite this need for specialist bioinformatic skills, the core biological importance of genome folding has seen widespread methodological uptake. To service the needs of experimentalists using the many-versus-all Capture-C family of methods we have developed CaptureCompendium a toolkit of software to simplify the design, analysis and presentation of 3C experiments.
Publisher: Springer Science and Business Media LLC
Date: 11-2021
Publisher: Oxford University Press (OUP)
Date: 23-11-2017
DOI: 10.1093/NAR/GKX1194
Publisher: American Society of Hematology
Date: 28-01-2021
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for James Davies.