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  1. Article ; Online: Early Insights into Cancer Epigenetics: Gene Promoter Hypermethylation Emerges as a Potential Biomarker for Cancer Detection.

    Clark, Susan J / Molloy, Peter L

    Cancer research

    2021  Volume 82, Issue 8, Page(s) 1461–1463

    Abstract: DNA methylation is one of the most intensely studied epigenetic modifications in mammals. In normal cells, it plays an essential role in core biologic processes by assuring the proper regulation of gene expression and stable gene silencing. In cancer ... ...

    Abstract DNA methylation is one of the most intensely studied epigenetic modifications in mammals. In normal cells, it plays an essential role in core biologic processes by assuring the proper regulation of gene expression and stable gene silencing. In cancer cells, genome-wide DNA methylation patterns are altered and often represent an early and fundamental step in neoplastic transformation. The landmark study from Esteller and colleagues, published in Cancer Research in 2001, was the first to reveal high frequency promoter methylation across multiple cancer types. They highlighted that widespread alterations in DNA methylation may be a key characteristic of oncogenesis and proposed aberrant DNA methylation of gene promoters could provide markers for sensitive detection of nearly all cancer types. The authors used a candidate gene approach to show promoter hypermethylation occurred across 12 cancer-associated genes in DNA from over 600 primary tumor samples, representing 15 major tumor types. The profile of promoter hypermethylation differed in every tumor type, suggesting that alterations in DNA methylation are pervasive, but the genes affected may be tumor-specific and impact multiple signaling pathways. Over the past 20 years since this publication, the cancer epigenetics field has exploded to generate thousands of normal and cancer methylome maps and developed sophisticated informatic tools for genome-wide methylome analyses. These methylomes are providing roadmaps for the study of cancer biology and discovery of DNA methylation biomarkers for early detection and monitoring of cancer. See related article by Esteller and colleagues, Cancer Res 2001;61:3225-29.
    MeSH term(s) Animals ; Biomarkers ; Biomarkers, Tumor/genetics ; Cell Transformation, Neoplastic/genetics ; DNA Methylation ; Epigenesis, Genetic ; Gene Expression Regulation, Neoplastic ; Humans ; Mammals/genetics ; Neoplasms/diagnosis ; Neoplasms/genetics ; Promoter Regions, Genetic/genetics
    Chemical Substances Biomarkers ; Biomarkers, Tumor
    Language English
    Publishing date 2021-10-22
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1432-1
    ISSN 1538-7445 ; 0008-5472
    ISSN (online) 1538-7445
    ISSN 0008-5472
    DOI 10.1158/0008-5472.CAN-22-0657
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Mapping genomic and epigenomic evolution in cancer ecosystems.

    Ushijima, Toshikazu / Clark, Susan J / Tan, Patrick

    Science (New York, N.Y.)

    2021  Volume 373, Issue 6562, Page(s) 1474–1479

    Abstract: Cancer is a major cause of global mortality underpinned by genomic and epigenomic derangements. Here, we highlight the importance of multimodal data integration in understanding the molecular evolution of malignant cell states across the cancer life ... ...

    Abstract Cancer is a major cause of global mortality underpinned by genomic and epigenomic derangements. Here, we highlight the importance of multimodal data integration in understanding the molecular evolution of malignant cell states across the cancer life cycle. The widespread presence of driver mutations and epigenetic alterations in normal-appearing tissues is prompting a reassessment of how cancer initiation is defined. In later-stage cancers, studying the roles of clonal selection, epigenomic adaptation, and persister cells in metastasis and therapy resistance is an emerging field. Finally, the importance of tumor ecosystems in driving cancer development is being unraveled by single-cell and spatial technologies at unprecedented resolution. Improving cancer risk assessment and accelerating therapeutic discovery for patients will require robust, comprehensive, and integrated temporal, spatial, and multilevel tumor atlases across the cancer life cycle.
    MeSH term(s) Carcinogenesis ; Epigenesis, Genetic ; Epigenome ; Evolution, Molecular ; Humans ; Mutation ; Neoplasm Metastasis ; Neoplasms/genetics ; Neoplasms/pathology ; Neoplasms/therapy ; Precancerous Conditions/genetics ; Precancerous Conditions/pathology ; Tumor Microenvironment
    Language English
    Publishing date 2021-09-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 128410-1
    ISSN 1095-9203 ; 0036-8075
    ISSN (online) 1095-9203
    ISSN 0036-8075
    DOI 10.1126/science.abh1645
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: The H2A.Z-nucleosome code in mammals: emerging functions.

    Colino-Sanguino, Yolanda / Clark, Susan J / Valdes-Mora, Fatima

    Trends in genetics : TIG

    2022  Volume 38, Issue 5, Page(s) 516

    Language English
    Publishing date 2022-02-26
    Publishing country England
    Document type Published Erratum
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2022.02.004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: The H2A.Z-nuclesome code in mammals: emerging functions.

    Colino-Sanguino, Yolanda / Clark, Susan J / Valdes-Mora, Fatima

    Trends in genetics : TIG

    2021  Volume 38, Issue 3, Page(s) 273–289

    Abstract: H2A.Z is a histone variant that provides specific structural and docking-side properties to the nucleosome, resulting in diverse and specialised molecular and cellular functions. In this review, we discuss the latest studies uncovering new functional ... ...

    Abstract H2A.Z is a histone variant that provides specific structural and docking-side properties to the nucleosome, resulting in diverse and specialised molecular and cellular functions. In this review, we discuss the latest studies uncovering new functional aspects of mammalian H2A.Z in gene transcription, including pausing and elongation of RNA polymerase II (RNAPII) and enhancer activity; DNA repair; DNA replication; and 3D chromatin structure. We also review the recently described role of H2A.Z in embryonic development, cell differentiation, neurodevelopment, and brain function. In conclusion, our cumulative knowledge of H2A.Z over the past 40 years, in combination with the implementation of novel molecular technologies, is unravelling an unexpected and complex role of histone variants in gene regulation and disease.
    MeSH term(s) Animals ; Chromatin/genetics ; Histones/genetics ; Mammals/genetics ; Nucleosomes/genetics ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism
    Chemical Substances Chromatin ; Histones ; Nucleosomes ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2021-10-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2021.10.003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Smoke-Induced Changes to the Epigenome Provide Fertile Ground for Oncogenic Mutation.

    Clark, Susan J / Molloy, Peter L

    Cancer cell

    2017  Volume 32, Issue 3, Page(s) 278–280

    Abstract: How genetic and epigenetic events synergize to generate the oncogenic state is not well understood. In this issue of Cancer Cell, Vaz et al. provide compelling evidence that exposure to chronic cigarette smoke causes progressive epigenetic alterations ... ...

    Abstract How genetic and epigenetic events synergize to generate the oncogenic state is not well understood. In this issue of Cancer Cell, Vaz et al. provide compelling evidence that exposure to chronic cigarette smoke causes progressive epigenetic alterations that prime for key genetic events to drive the development of lung cancer.
    MeSH term(s) Carcinogenesis ; Humans ; Lung ; Lung Neoplasms ; Mutation ; Smoke ; Nicotiana
    Chemical Substances Smoke
    Language English
    Publishing date 2017-09-11
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 2078448-X
    ISSN 1878-3686 ; 1535-6108
    ISSN (online) 1878-3686
    ISSN 1535-6108
    DOI 10.1016/j.ccell.2017.08.016
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Characterisation and reproducibility of the HumanMethylationEPIC v2.0 BeadChip for DNA methylation profiling.

    Peters, Timothy J / Meyer, Braydon / Ryan, Lauren / Achinger-Kawecka, Joanna / Song, Jenny / Campbell, Elyssa M / Qu, Wenjia / Nair, Shalima / Loi-Luu, Phuc / Stricker, Phillip / Lim, Elgene / Stirzaker, Clare / Clark, Susan J / Pidsley, Ruth

    BMC genomics

    2024  Volume 25, Issue 1, Page(s) 251

    Abstract: Background: The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost ... ...

    Abstract Background: The Illumina family of Infinium Methylation BeadChip microarrays has been widely used over the last 15 years for genome-wide DNA methylation profiling, including large-scale and population-based studies, due to their ease of use and cost effectiveness. Succeeding the popular HumanMethylationEPIC BeadChip (EPICv1), the recently released Infinium MethylationEPIC v2.0 BeadChip (EPICv2) claims to extend genomic coverage to more than 935,000 CpG sites. Here, we comprehensively characterise the reproducibility, reliability and annotation of the EPICv2 array, based on bioinformatic analysis of both manifest data and new EPICv2 data from diverse biological samples.
    Results: We find a high degree of reproducibility with EPICv1, evidenced by comparable sensitivity and precision from empirical cross-platform comparison incorporating whole genome bisulphite sequencing (WGBS), and high correlation between technical sample replicates, including between samples with DNA input levels below the manufacturer's recommendation. We provide a full assessment of probe content, evaluating genomic distribution and changes from previous array versions. We characterise EPICv2's new feature of replicated probes and provide recommendations as to the superior probes. In silico analysis of probe sequences demonstrates that probe cross-hybridisation remains a significant problem in EPICv2. By mapping the off-target sites at single nucleotide resolution and comparing with WGBS we show empirical evidence for preferential off-target binding.
    Conclusions: Overall, we find EPICv2 a worthy successor to the previous Infinium methylation microarrays, however some technical issues remain. To support optimal EPICv2 data analysis we provide an expanded version of the EPICv2 manifest to aid researchers in understanding probe design, data processing, choosing appropriate probes for analysis and for integration with methylation datasets from previous versions of the Infinium Methylation BeadChip.
    MeSH term(s) DNA Methylation ; Reproducibility of Results ; Computational Biology ; Data Analysis ; Sulfites
    Chemical Substances hydrogen sulfite (OJ9787WBLU) ; Sulfites
    Language English
    Publishing date 2024-03-06
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-024-10027-5
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  7. Article ; Online: Benchmark study comparing liftover tools for genome conversion of epigenome sequencing data.

    Luu, Phuc-Loi / Ong, Phuc-Thinh / Dinh, Thanh-Phuoc / Clark, Susan J

    NAR genomics and bioinformatics

    2020  Volume 2, Issue 3, Page(s) lqaa054

    Abstract: As reference genome assemblies are updated there is a need to convert epigenome sequence data from older genome assemblies to newer versions, to facilitate data integration and visualization on the same coordinate system. Conversion can be done by re- ... ...

    Abstract As reference genome assemblies are updated there is a need to convert epigenome sequence data from older genome assemblies to newer versions, to facilitate data integration and visualization on the same coordinate system. Conversion can be done by re-alignment of the original sequence data to the new assembly or by converting the coordinates of the data between assemblies using a mapping file, an approach referred to as 'liftover'. Compared to re-alignment approaches, liftover is a more rapid and cost-effective solution. Here, we benchmark six liftover tools commonly used for conversion between genome assemblies by coordinates, including
    Language English
    Publishing date 2020-08-06
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqaa054
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Target-Specific Profiling of RNA m

    Sibbritt, Tennille / Schumann, Ulrike / Shafik, Andrew / Guarnacci, Marco / Clark, Susan J / Preiss, Thomas

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

    2021  Volume 2404, Page(s) 375–392

    Abstract: Mapping the position and quantifying the level of 5-methylcytosine ( ... ...

    Abstract Mapping the position and quantifying the level of 5-methylcytosine (m
    MeSH term(s) 5-Methylcytosine ; High-Throughput Nucleotide Sequencing ; Methylation ; RNA/genetics ; Sequence Analysis, DNA
    Chemical Substances RNA (63231-63-0) ; 5-Methylcytosine (6R795CQT4H)
    Language English
    Publishing date 2021-10-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1851-6_21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: UHRF1 ubiquitin ligase activity supports the maintenance of low-density CpG methylation.

    Tiedemann, Rochelle L / Hrit, Joel / Du, Qian / Wiseman, Ashley K / Eden, Hope E / Dickson, Bradley M / Kong, Xiangqian / Chomiak, Alison A / Vaughan, Robert M / Hebert, Jakob M / David, Yael / Zhou, Wanding / Baylin, Stephen B / Jones, Peter A / Clark, Susan J / Rothbart, Scott B

    bioRxiv : the preprint server for biology

    2024  

    Abstract: The RING E3 ubiquitin ligase UHRF1 is an established cofactor for DNA methylation inheritance. Nucleosomal engagement through histone and DNA interactions directs UHRF1 ubiquitin ligase activity toward lysines on histone H3 tails, creating binding sites ... ...

    Abstract The RING E3 ubiquitin ligase UHRF1 is an established cofactor for DNA methylation inheritance. Nucleosomal engagement through histone and DNA interactions directs UHRF1 ubiquitin ligase activity toward lysines on histone H3 tails, creating binding sites for DNMT1 through ubiquitin interacting motifs (UIM1 and UIM2). Here, we profile contributions of UHRF1 and DNMT1 to genome-wide DNA methylation inheritance and dissect specific roles for ubiquitin signaling in this process. We reveal DNA methylation maintenance at low-density CpGs is vulnerable to disruption of UHRF1 ubiquitin ligase activity and DNMT1 ubiquitin reading activity through UIM1. Hypomethylation of low-density CpGs in this manner induces formation of partially methylated domains (PMD), a methylation signature observed across human cancers. Furthermore, disrupting DNMT1 UIM2 function abolishes DNA methylation maintenance. Collectively, we show DNMT1-dependent DNA methylation inheritance is a ubiquitin-regulated process and suggest a disrupted UHRF1-DNMT1 ubiquitin signaling axis contributes to the development of PMDs in human cancers.
    Language English
    Publishing date 2024-02-16
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.02.13.580169
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Disruption of the 3D cancer genome blueprint.

    Achinger-Kawecka, Joanna / Clark, Susan J

    Epigenomics

    2017  Volume 9, Issue 1, Page(s) 47–55

    Abstract: Recent advances in chromosome conformation capture technologies are improving the current appreciation of how 3D genome architecture affects its function in different cell types and disease. Long-range chromatin interactions are organized into ... ...

    Abstract Recent advances in chromosome conformation capture technologies are improving the current appreciation of how 3D genome architecture affects its function in different cell types and disease. Long-range chromatin interactions are organized into topologically associated domains, which are known to play a role in constraining gene expression patterns. However, in cancer cells there are alterations in the 3D genome structure, which impacts on gene regulation. Disruption of topologically associated domains architecture can result in alterations in chromatin interactions that bring new regulatory elements and genes together, leading to altered expression of oncogenes and tumor suppressor genes. Here, we discuss the impact of genetic and epigenetic changes in cancer and how this affects the spatial organization of chromatin. Understanding how disruptions to the 3D architecture contribute to the cancer genome will provide novel insights into the principles of epigenetic gene regulation in cancer and mechanisms responsible for cancer associated mutations and rearrangements.
    MeSH term(s) Animals ; CCCTC-Binding Factor ; Chromatin Assembly and Disassembly ; Epigenesis, Genetic ; Gene Expression Regulation, Neoplastic ; Genome, Human ; Humans ; Neoplasms/genetics ; Repressor Proteins/genetics ; Repressor Proteins/metabolism
    Chemical Substances CCCTC-Binding Factor ; CTCF protein, human ; Repressor Proteins
    Language English
    Publishing date 2017-01
    Publishing country England
    Document type Journal Article ; Review
    ISSN 1750-192X
    ISSN (online) 1750-192X
    DOI 10.2217/epi-2016-0111
    Database MEDical Literature Analysis and Retrieval System OnLINE

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