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  1. Article ; Online: CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data.

    Riva, Simone G / Georgiades, Emily / Gur, E Ravza / Baxter, Matthew / Hughes, Jim R

    Journal of visualized experiments : JoVE

    2023  , Issue 199

    Abstract: Assay for transposase-accessible chromatin (ATAC) and chromatin immunoprecipitation (ChIP), coupled with next-generation sequencing (NGS), have revolutionized the study of gene regulation. A lack of standardization in the analysis of the highly ... ...

    Abstract Assay for transposase-accessible chromatin (ATAC) and chromatin immunoprecipitation (ChIP), coupled with next-generation sequencing (NGS), have revolutionized the study of gene regulation. A lack of standardization in the analysis of the highly dimensional datasets generated by these techniques has made reproducibility difficult to achieve, leading to discrepancies in the published, processed data. Part of this problem is due to the diverse range of bioinformatic tools available for the analysis of these types of data. Secondly, a number of different bioinformatic tools are required sequentially to convert raw data into a fully processed and interpretable output, and these tools require varying levels of computational skills. Furthermore, there are many options for quality control that are not uniformly employed during data processing. We address these issues with a complete assay for transposase-accessible chromatin sequencing (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) upstream pipeline (CATCH-UP), an easy-to-use, Python-based pipeline for the analysis of bulk ChIP-seq and ATAC-seq datasets from raw fastq files to visualizable bigwig tracks and peaks calls. This pipeline is simple to install and run, requiring minimal computational knowledge. The pipeline is modular, scalable, and parallelizable on various computing infrastructures, allowing for easy reporting of methodology to enable reproducible analysis of novel or published datasets.
    MeSH term(s) Chromatin Immunoprecipitation Sequencing ; Sequence Analysis, DNA/methods ; Reproducibility of Results ; Chromatin Immunoprecipitation/methods ; High-Throughput Nucleotide Sequencing/methods ; Chromatin/genetics ; Transposases
    Chemical Substances Chromatin ; Transposases (EC 2.7.7.-)
    Language English
    Publishing date 2023-09-22
    Publishing country United States
    Document type Journal Article ; Video-Audio Media ; Research Support, Non-U.S. Gov't
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/65633
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Lessons from a ten-year-long journey: building a student-driven computational biology society across Turkey.

    Kaya, Yasin / Karakulak, Tülay / Can Saylan, Cemil / Gür, E Ravza / Tatlıdil, Engin / Güleşen, Sevilay / Betül Dinçaslan, Fatma / Dönertaş, Handan Melike

    F1000Research

    2022  Volume 11

    Abstract: The Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational biology ...

    Abstract The Regional Student Group Turkey (RSG-Turkey) is officially associated with the International Society for Computational Biology (ISCB) Student Council (SC). At the RSG-Turkey, we aim to contribute to the early-career researchers in computational biology and bioinformatics fields by providing opportunities for improving their academic and technical skills in the field. Over the last ten years, we have built a well-known student-driven academic society in Turkey that organizes numerous events every year and continues to grow with over 650 current members. Celebrating the 10th anniversary of RSG-Turkey, in this communication, we share our experiences, five main lessons we learned, and the steps to establish a long-standing academic community: having a clear mission, building a robust structure, effective communication, turning challenges into opportunities, and building collaborations. We believe that our experiences can help students and academics establish long-standing communities in fast-developing areas like bioinformatics.
    MeSH term(s) Communication ; Computational Biology/education ; Humans ; Research Personnel ; Students ; Turkey
    Language English
    Publishing date 2022-01-26
    Publishing country England
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.107886.1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells.

    Turkalj, Sven / Jakobsen, Niels Asger / Groom, Angus / Metzner, Marlen / Riva, Simone G / Gür, E Ravza / Usukhbayar, Batchimeg / Salazar, Mirian Angulo / Hentges, Lance D / Mickute, Gerda / Clark, Kevin / Sopp, Paul / Davies, James O J / Hughes, Jim R / Vyas, Paresh

    Cell stem cell

    2023  Volume 30, Issue 5, Page(s) 722–740.e11

    Abstract: Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin ... ...

    Abstract Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.
    MeSH term(s) Humans ; Chromatin ; Transposases/genetics ; Transposases/metabolism ; Genotype ; Genomics ; Gene Expression Regulation ; Leukemia, Myeloid, Acute
    Chemical Substances Chromatin ; Transposases (EC 2.7.7.-)
    Language English
    Publishing date 2023-05-05
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2375354-7
    ISSN 1875-9777 ; 1934-5909
    ISSN (online) 1875-9777
    ISSN 1934-5909
    DOI 10.1016/j.stem.2023.04.012
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. 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
    Database MEDical Literature Analysis and Retrieval System OnLINE

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