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  1. Article ; Online: Natural and Experimental Rewiring of Gene Regulatory Regions.

    Downes, Damien J / Hughes, Jim R

    Annual review of genomics and human genetics

    2022  Volume 23, Page(s) 73–97

    Abstract: The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription ... ...

    Abstract The successful development and ongoing functioning of complex organisms depend on the faithful execution of the genetic code. A critical step in this process is the correct spatial and temporal expression of genes. The highly orchestrated transcription of genes is controlled primarily by
    MeSH term(s) Enhancer Elements, Genetic ; Gene Expression Regulation ; Gene Regulatory Networks ; Humans ; Mutation ; Promoter Regions, Genetic
    Language English
    Publishing date 2022-04-26
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2037670-4
    ISSN 1545-293X ; 1527-8204
    ISSN (online) 1545-293X
    ISSN 1527-8204
    DOI 10.1146/annurev-genom-112921-010715
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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: Assessment of Multiway Interactions with Tri-C.

    Oudelaar, A Marieke / Downes, Damien J / Hughes, Jim R

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2532, Page(s) 95–112

    Abstract: Tri-C is a chromosome conformation capture (3C) approach that can efficiently identify multiway chromatin interactions with viewpoints of interest. As opposed to pair-wise interactions identified in methods such as Hi-C, 4C, and Capture-C, the detection ... ...

    Abstract Tri-C is a chromosome conformation capture (3C) approach that can efficiently identify multiway chromatin interactions with viewpoints of interest. As opposed to pair-wise interactions identified in methods such as Hi-C, 4C, and Capture-C, the detection of multiway interactions allows researchers to investigate how multiple cis-regulatory elements interact together in higher-order structures in single nuclei and address questions regarding structural cooperation between these elements. Here, we describe the procedure for designing and performing a Tri-C experiment.
    MeSH term(s) Chromatin/genetics ; Chromosomes ; Regulatory Sequences, Nucleic Acid
    Chemical Substances Chromatin
    Language English
    Publishing date 2022-07-20
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2497-5_6
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  3. Article ; Online: Erratum

    Daniels, Deborah E / Downes, Damien J / Ferrer-Vicens, Ivan / Ferguson, Daniel C J / Singleton, Belinda K / Wilson, Marieangela C / Trakarnsanga, Kongtana / Kurita, Ryo / Nakamura, Yukio / Anstee, David J / Frayne, Jan

    Haematologica

    2024  Volume 109, Issue 1, Page(s) 364

    Language English
    Publishing date 2024-01-01
    Publishing country Italy
    Document type Journal Article ; Published Erratum
    ZDB-ID 2333-4
    ISSN 1592-8721 ; 0017-6567 ; 0390-6078
    ISSN (online) 1592-8721
    ISSN 0017-6567 ; 0390-6078
    DOI 10.3324/haematol.2023.284510
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  4. Article ; Online: Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans.

    Steyer, Joel T / Downes, Damien J / Hunter, Cameron C / Migeon, Pierre A / Todd, Richard B

    mBio

    2021  Volume 12, Issue 3, Page(s) e0076821

    Abstract: Fungi, bacteria, and plants, but not animals, synthesize the branched-chain amino acids: leucine, isoleucine, and valine. While branched-chain amino acid (BCAA) biosynthesis has been well characterized in the yeast Saccharomyces cerevisiae, it is ... ...

    Abstract Fungi, bacteria, and plants, but not animals, synthesize the branched-chain amino acids: leucine, isoleucine, and valine. While branched-chain amino acid (BCAA) biosynthesis has been well characterized in the yeast Saccharomyces cerevisiae, it is incompletely understood in filamentous fungi. The three BCAAs share several early biosynthesis steps before divergence into specific pathways. In Aspergillus nidulans, the genes for the first two dedicated steps in leucine biosynthesis have been characterized, but the final two have not. We used sequence searches of the A. nidulans genome to identify two genes encoding β-isopropylmalate dehydrogenase, which catalyzes the penultimate step of leucine biosynthesis, and six genes encoding BCAA aminotransferase, which catalyzes the final step in biosynthesis of all three BCAA. We have used combinations of gene knockouts to determine the relative contribution of each of these genes to BCAA biosynthesis. While both β-isopropylmalate dehydrogenase genes act in leucine biosynthesis, the two most highly expressed BCAA aminotransferases are responsible for BCAA biosynthesis. We have also characterized the expression of leucine biosynthesis genes using reverse transcriptase-quantitative PCR and found regulation in response to leucine availability is mediated through the Zn(II)
    MeSH term(s) Amino Acids, Branched-Chain/biosynthesis ; Amino Acids, Branched-Chain/genetics ; Amino Acids, Branched-Chain/metabolism ; Aspergillus nidulans/chemistry ; Aspergillus nidulans/genetics ; Biosynthetic Pathways/genetics ; Gene Expression Regulation, Fungal ; Leucine/biosynthesis ; Transaminases/genetics ; Transaminases/metabolism
    Chemical Substances Amino Acids, Branched-Chain ; Transaminases (EC 2.6.1.-) ; branched-chain-amino-acid transaminase (EC 2.6.1.42) ; Leucine (GMW67QNF9C)
    Language English
    Publishing date 2021-06-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.00768-21
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  5. Article ; Online: Multi Locus View: an extensible web-based tool for the analysis of genomic data.

    Sergeant, Martin J / Hughes, Jim R / Hentges, Lance / Lunter, Gerton / Downes, Damien J / Taylor, Stephen

    Communications biology

    2021  Volume 4, Issue 1, Page(s) 623

    Abstract: Tracking and understanding data quality, analysis and reproducibility are critical concerns in the biological sciences. This is especially true in genomics where next generation sequencing (NGS) based technologies such as ChIP-seq, RNA-seq and ATAC-seq ... ...

    Abstract Tracking and understanding data quality, analysis and reproducibility are critical concerns in the biological sciences. This is especially true in genomics where next generation sequencing (NGS) based technologies such as ChIP-seq, RNA-seq and ATAC-seq are generating a flood of genome-scale data. However, such data are usually processed with automated tools and pipelines, generating tabular outputs and static visualisations. Interpretation is normally made at a high level without the ability to visualise the underlying data in detail. Conventional genome browsers are limited to browsing single locations and do not allow for interactions with the dataset as a whole. Multi Locus View (MLV), a web-based tool, has been developed to allow users to fluidly interact with genomics datasets at multiple scales. The user is able to browse the raw data, cluster, and combine the data with other analysis and annotate the data. User datasets can then be shared with other users or made public for quick assessment from the academic community. MLV is publically available at https://mlv.molbiol.ox.ac.uk .
    MeSH term(s) Chromatin Immunoprecipitation Sequencing/methods ; Computational Biology/methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Internet ; Numerical Analysis, Computer-Assisted ; RNA-Seq/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; Sequence Analysis, RNA/methods ; Software
    Language English
    Publishing date 2021-05-25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ISSN 2399-3642
    ISSN (online) 2399-3642
    DOI 10.1038/s42003-021-02097-y
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  6. Article ; Online: LanceOtron: a deep learning peak caller for genome sequencing experiments.

    Hentges, Lance D / Sergeant, Martin J / Cole, Christopher B / Downes, Damien J / Hughes, Jim R / Taylor, Stephen

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 18, Page(s) 4255–4263

    Abstract: Motivation: Genome sequencing experiments have revolutionized molecular biology by allowing researchers to identify important DNA-encoded elements genome wide. Regions where these elements are found appear as peaks in the analog signal of an assay's ... ...

    Abstract Motivation: Genome sequencing experiments have revolutionized molecular biology by allowing researchers to identify important DNA-encoded elements genome wide. Regions where these elements are found appear as peaks in the analog signal of an assay's coverage track, and despite the ease with which humans can visually categorize these patterns, the size of many genomes necessitates algorithmic implementations. Commonly used methods focus on statistical tests to classify peaks, discounting that the background signal does not completely follow any known probability distribution and reducing the information-dense peak shapes to simply maximum height. Deep learning has been shown to be highly accurate for many pattern recognition tasks, on par or even exceeding human capabilities, providing an opportunity to reimagine and improve peak calling.
    Results: We present the peak calling framework LanceOtron, which combines deep learning for recognizing peak shape with multifaceted enrichment calculations for assessing significance. In benchmarking ATAC-seq, ChIP-seq and DNase-seq, LanceOtron outperforms long-standing, gold-standard peak callers through its improved selectivity and near-perfect sensitivity.
    Availability and implementation: A fully featured web application is freely available from LanceOtron.molbiol.ox.ac.uk, command line interface via python is pip installable from PyPI at https://pypi.org/project/lanceotron/, and source code and benchmarking tests are available at https://github.com/LHentges/LanceOtron.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Humans ; Deep Learning ; Sequence Analysis, DNA/methods ; Software ; Chromatin Immunoprecipitation Sequencing ; Base Sequence ; High-Throughput Nucleotide Sequencing/methods
    Language English
    Publishing date 2022-07-08
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac525
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    Zs.A 2374: Show issues Location:
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    Jg. 1995 - 2021: Lesesall (2.OG)
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  7. Article: Inferring causal genes at type 2 diabetes GWAS loci through chromosome interactions in islet cells.

    Torres, Jason M / Sun, Han / Nylander, Vibe / Downes, Damien J / van de Bunt, Martijn / McCarthy, Mark I / Hughes, Jim R / Gloyn, Anna L

    Wellcome open research

    2023  Volume 8, Page(s) 165

    Abstract: Background: ...

    Abstract Background:
    Language English
    Publishing date 2023-08-08
    Publishing country England
    Document type Journal Article
    ISSN 2398-502X
    ISSN 2398-502X
    DOI 10.12688/wellcomeopenres.18653.2
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  8. Article ; Online: Author Correction: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.

    Downes, Damien J / Smith, Alastair L / Karpinska, Magdalena A / Velychko, Taras / Rue-Albrecht, Kevin / Sims, David / Milne, Thomas A / Davies, James O J / Oudelaar, A Marieke / Hughes, Jim R

    Nature protocols

    2023  Volume 18, Issue 10, Page(s) 3155

    Language English
    Publishing date 2023-06-27
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-023-00860-5
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  9. Article ; Online: Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture.

    Downes, Damien J / Smith, Alastair L / Karpinska, Magdalena A / Velychko, Taras / Rue-Albrecht, Kevin / Sims, David / Milne, Thomas A / Davies, James O J / Oudelaar, A Marieke / Hughes, Jim R

    Nature protocols

    2022  Volume 17, Issue 2, Page(s) 445–475

    Abstract: Chromosome conformation capture (3C) methods measure the spatial proximity between DNA elements in the cell nucleus. Many methods have been developed to sample 3C material, including the Capture-C family of protocols. Capture-C methods use ... ...

    Abstract Chromosome conformation capture (3C) methods measure the spatial proximity between DNA elements in the cell nucleus. Many methods have been developed to sample 3C material, including the Capture-C family of protocols. Capture-C methods use oligonucleotides to enrich for interactions of interest from sequencing-ready 3C libraries. This approach is modular and has been adapted and optimized to work for sampling of disperse DNA elements (NuTi Capture-C), including from low cell inputs (LI Capture-C), as well as to generate Hi-C like maps for specific regions of interest (Tiled-C) and to interrogate multiway interactions (Tri-C). We present the design, experimental protocol and analysis pipeline for NuTi Capture-C in addition to the variations for generation of LI Capture-C, Tiled-C and Tri-C data. The entire procedure can be performed in 3 weeks and requires standard molecular biology skills and equipment, access to a next-generation sequencing platform, and basic bioinformatic skills. Implemented with other sequencing technologies, these methods can be used to identify regulatory interactions and to compare the structural organization of the genome in different cell types and genetic models.
    MeSH term(s) Chromosomes
    Language English
    Publishing date 2022-02-04
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/s41596-021-00651-w
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  10. Article ; Online: The chromatin remodeller ATRX facilitates diverse nuclear processes, in a stochastic manner, in both heterochromatin and euchromatin.

    Truch, Julia / Downes, Damien J / Scott, Caroline / Gür, E Ravza / Telenius, Jelena M / Repapi, Emmanouela / Schwessinger, Ron / Gosden, Matthew / Brown, Jill M / Taylor, Stephen / Cheong, Pak Leng / Hughes, Jim R / Higgs, Douglas R / Gibbons, Richard J

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 3485

    Abstract: The chromatin remodeller ATRX interacts with the histone chaperone DAXX to deposit the histone variant H3.3 at sites of nucleosome turnover. ATRX is known to bind repetitive, heterochromatic regions of the genome including telomeres, ribosomal DNA and ... ...

    Abstract The chromatin remodeller ATRX interacts with the histone chaperone DAXX to deposit the histone variant H3.3 at sites of nucleosome turnover. ATRX is known to bind repetitive, heterochromatic regions of the genome including telomeres, ribosomal DNA and pericentric repeats, many of which are putative G-quadruplex forming sequences (PQS). At these sites ATRX plays an ancillary role in a wide range of nuclear processes facilitating replication, chromatin modification and transcription. Here, using an improved protocol for chromatin immunoprecipitation, we show that ATRX also binds active regulatory elements in euchromatin. Mutations in ATRX lead to perturbation of gene expression associated with a reduction in chromatin accessibility, histone modification, transcription factor binding and deposition of H3.3 at the sequences to which it normally binds. In erythroid cells where downregulation of α-globin expression is a hallmark of ATR-X syndrome, perturbation of chromatin accessibility and gene expression occurs in only a subset of cells. The stochastic nature of this process suggests that ATRX acts as a general facilitator of cell specific transcriptional and epigenetic programmes, both in heterochromatin and euchromatin.
    MeSH term(s) Chromatin ; DNA Helicases/genetics ; DNA Helicases/metabolism ; Euchromatin/genetics ; Heterochromatin/genetics ; Histones/metabolism ; Mental Retardation, X-Linked ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; X-linked Nuclear Protein/genetics ; X-linked Nuclear Protein/metabolism ; alpha-Thalassemia
    Chemical Substances Chromatin ; Euchromatin ; Heterochromatin ; Histones ; Nuclear Proteins ; DNA Helicases (EC 3.6.4.-) ; X-linked Nuclear Protein (EC 3.6.4.12)
    Language English
    Publishing date 2022-06-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-31194-7
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