LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 74

Search options

  1. Book: TET proteins and DNA demethylation

    Bogdanovic, Ozren / Vermeulen, Michiel

    methods and protocols

    (Methods in molecular biology ; 2272 ; Springer protocols)

    2021  

    Author's details edited by Ozren Bogdanovic, Michiel Vermeulen
    Series title Methods in molecular biology ; 2272
    Springer protocols
    Collection
    Keywords DNA-protein interactions
    Subject code 572.786
    Language English
    Size x, 320 Seiten, Illustrationen, 26 cm
    Publisher Humana Press
    Publishing place New York, NY
    Publishing country United States
    Document type Book
    HBZ-ID HT020940467
    ISBN 978-1-0716-1293-4 ; 9781071612941 ; 1-0716-1293-X ; 1071612948
    Database Catalogue ZB MED Medicine, Health

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Shelf markLoan statusLocation
    Zs A 7042 -2272- verfügbar in Königswinter Königswinter

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: Generation and Molecular Characterization of Transient tet1/2/3 Zebrafish Knockouts.

    Ross, Samuel E / Bogdanovic, Ozren

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

    2021  Volume 2272, Page(s) 281–318

    Abstract: 5-methylcytosine (5mC) is a gene-regulatory mark associated with transcriptional repression. 5mC can be erased through the catalytic action of Ten-eleven translocation (TET) methylcytosine dioxygenases (TET1, TET2, TET3), which oxidize 5mC resulting in ... ...

    Abstract 5-methylcytosine (5mC) is a gene-regulatory mark associated with transcriptional repression. 5mC can be erased through the catalytic action of Ten-eleven translocation (TET) methylcytosine dioxygenases (TET1, TET2, TET3), which oxidize 5mC resulting in its removal from the genome. In vertebrates, TET enzymes facilitate DNA demethylation of regulatory regions linked to genes involved in developmental processes. Consequently, TET ablation leads to severe morphological defects and developmental arrest. Here we describe a system that can facilitate the study of relationships between TET enzymes, 5mC, and embryo development. We provide detailed descriptions for the generation of F0 zebrafish tet1/2/3 knockouts using CRISPR/Cas9 technology and elaborate on the strategies to assess the impact of TET loss by reduced representation bisulfite sequencing (RRBS).
    MeSH term(s) Animals ; Animals, Genetically Modified/genetics ; Animals, Genetically Modified/growth & development ; Animals, Genetically Modified/metabolism ; DNA Methylation ; Dioxygenases/genetics ; Dioxygenases/metabolism ; Gene Expression Regulation, Developmental ; Zebrafish/genetics ; Zebrafish/growth & development ; Zebrafish/metabolism ; Zebrafish Proteins/genetics ; Zebrafish Proteins/metabolism
    Chemical Substances Zebrafish Proteins ; TET2 protein, zebrafish (EC 1.-) ; TET3 protein, zebrafish (EC 1.-) ; Tet1 protein, zebrafish (EC 1.-) ; Dioxygenases (EC 1.13.11.-)
    Language English
    Publishing date 2021-05-19
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1294-1_17
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: TAB-seq and ACE-seq Data Processing for Genome-Wide DNA hydroxymethylation Profiling.

    Skvortsova, Ksenia / Bogdanovic, Ozren

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

    2021  Volume 2272, Page(s) 163–178

    Abstract: 5-Methylcytosine (5mC) is one of the most abundant and well-studied chemical DNA modifications of vertebrate genomes. 5mC plays an essential role in genome regulation including: silencing of retroelements, X chromosome inactivation, and heterochromatin ... ...

    Abstract 5-Methylcytosine (5mC) is one of the most abundant and well-studied chemical DNA modifications of vertebrate genomes. 5mC plays an essential role in genome regulation including: silencing of retroelements, X chromosome inactivation, and heterochromatin stability. Furthermore, 5mC shapes the activity of cis-regulatory elements crucial for cell fate determination. TET enzymes can oxidize 5mC to form 5-hydroxymethylcytosine (5hmC), thereby adding an additional layer of complexity to the DNA methylation landscape dynamics. The advent of techniques enabling genome-wide 5hmC profiling provided critical insights into its genomic distribution, scope, and function. These methods include immunoprecipitation, chemical labeling and capture-based approaches, as well as single-nucleotide 5hmC profiling techniques such as TET-assisted bisulfite sequencing (TAB-seq) and APOBEC-coupled epigenetic sequencing (ACE-seq). Here we provide a detailed protocol for computational analysis required for the genomic alignment of TAB-seq and ACE-seq data, 5hmC calling, and statistical analysis.
    MeSH term(s) 5-Methylcytosine/analogs & derivatives ; 5-Methylcytosine/chemistry ; Computational Biology/methods ; DNA/analysis ; DNA/chemistry ; DNA/genetics ; DNA Methylation ; Epigenesis, Genetic ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Humans ; Mixed Function Oxygenases/metabolism ; Oxidation-Reduction ; Proto-Oncogene Proteins/metabolism ; Sulfites/chemistry
    Chemical Substances Proto-Oncogene Proteins ; Sulfites ; 5-hydroxymethylcytosine (1123-95-1) ; 5-Methylcytosine (6R795CQT4H) ; DNA (9007-49-2) ; Mixed Function Oxygenases (EC 1.-) ; TET1 protein, human (EC 1.-) ; hydrogen sulfite (OJ9787WBLU)
    Language English
    Publishing date 2021-05-19
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1294-1_9
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Correction to: TET Proteins and DNA Demethylation.

    Bogdanovic, Ozren / Vermeulen, Michiel

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

    2021  Volume 2272, Page(s) C1

    Language English
    Publishing date 2021-07-23
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-1294-1_18
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Sequence determinants, function, and evolution of CpG islands.

    Angeloni, Allegra / Bogdanovic, Ozren

    Biochemical Society transactions

    2021  Volume 49, Issue 3, Page(s) 1109–1119

    Abstract: In vertebrates, cytosine-guanine (CpG) dinucleotides are predominantly methylated, with ∼80% of all CpG sites containing 5-methylcytosine (5mC), a repressive mark associated with long-term gene silencing. The exceptions to such a globally hypermethylated ...

    Abstract In vertebrates, cytosine-guanine (CpG) dinucleotides are predominantly methylated, with ∼80% of all CpG sites containing 5-methylcytosine (5mC), a repressive mark associated with long-term gene silencing. The exceptions to such a globally hypermethylated state are CpG-rich DNA sequences called CpG islands (CGIs), which are mostly hypomethylated relative to the bulk genome. CGIs overlap promoters from the earliest vertebrates to humans, indicating a concerted evolutionary drive compatible with CGI retention. CGIs are characterised by DNA sequence features that include DNA hypomethylation, elevated CpG and GC content and the presence of transcription factor binding sites. These sequence characteristics are congruous with the recruitment of transcription factors and chromatin modifying enzymes, and transcriptional activation in general. CGIs colocalize with sites of transcriptional initiation in hypermethylated vertebrate genomes, however, a growing body of evidence indicates that CGIs might exert their gene regulatory function in other genomic contexts. In this review, we discuss the diverse regulatory features of CGIs, their functional readout, and the evolutionary implications associated with CGI retention in vertebrates and possibly in invertebrates.
    MeSH term(s) Animals ; Binding Sites/genetics ; Chromatin/genetics ; Chromatin/metabolism ; CpG Islands/genetics ; DNA Methylation ; Gene Expression Regulation ; Genome/genetics ; Humans ; Promoter Regions, Genetic/genetics ; Transcription Factors/metabolism
    Chemical Substances Chromatin ; Transcription Factors
    Language English
    Publishing date 2021-06-22
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 184237-7
    ISSN 1470-8752 ; 0300-5127
    ISSN (online) 1470-8752
    ISSN 0300-5127
    DOI 10.1042/BST20200695
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 944: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article ; Online: Tet proteins: master regulators of vertebrate body plan formation?

    Bogdanović, Ozren

    Epigenomics

    2016  Volume 9, Issue 2, Page(s) 93–96

    MeSH term(s) Animals ; Body Patterning/genetics ; DNA Methylation ; Dioxygenases/genetics ; Gene Expression Regulation, Developmental ; Humans ; Vertebrates/embryology ; Vertebrates/genetics
    Chemical Substances Dioxygenases (EC 1.13.11.-)
    Language English
    Publishing date 2016-12-02
    Publishing country England
    Document type Editorial ; Research Support, Non-U.S. Gov't
    ISSN 1750-192X
    ISSN (online) 1750-192X
    DOI 10.2217/epi-2016-0164
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Nanopore Sequencing and Data Analysis for Base-Resolution Genome-Wide 5-Methylcytosine Profiling.

    Angeloni, Allegra / Ferguson, James / Bogdanovic, Ozren

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

    2022  Volume 2458, Page(s) 75–94

    Abstract: Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling; however, the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such ...

    Abstract Whole-genome bisulfite sequencing (WGBS) is currently the gold standard for DNA methylation (5-methylcytosine, 5mC) profiling; however, the destructive nature of sodium bisulfite results in DNA fragmentation and subsequent biases in sequencing data. Such issues have led to the development of bisulfite-free methods for 5mC detection. Nanopore sequencing is a long read nondestructive approach that directly analyzes DNA and RNA fragments in real time. Recently, computational tools have been developed that enable base-resolution detection of 5mC from Oxford Nanopore sequencing data. In this chapter, we provide a detailed protocol for preparation, sequencing, read assembly, and analysis of genome-wide 5mC using Nanopore sequencing technologies.
    MeSH term(s) 5-Methylcytosine/analysis ; DNA Methylation ; Data Analysis ; High-Throughput Nucleotide Sequencing/methods ; Nanopore Sequencing ; Sequence Analysis, DNA/methods ; Sulfites
    Chemical Substances Sulfites ; 5-Methylcytosine (6R795CQT4H)
    Language English
    Publishing date 2022-03-10
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2140-0_5
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article ; Online: Invertebrate epigenomics: the brave new world of the spineless.

    Bogdanović, Ozren

    Briefings in functional genomics

    2014  Volume 13, Issue 3, Page(s) 189–190

    MeSH term(s) Animals ; Biological Evolution ; Epigenomics ; Invertebrates/genetics ; Phenotype ; Phylogeny
    Language English
    Publishing date 2014-05
    Publishing country England
    Document type Editorial ; Introductory Journal Article
    ZDB-ID 2540916-5
    ISSN 2041-2657 ; 2041-2649 ; 2041-2647
    ISSN (online) 2041-2657
    ISSN 2041-2649 ; 2041-2647
    DOI 10.1093/bfgp/elu008
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 6076: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article ; Online: Enhancer DNA methylation: implications for gene regulation.

    Angeloni, Allegra / Bogdanovic, Ozren

    Essays in biochemistry

    2019  Volume 63, Issue 6, Page(s) 707–715

    Abstract: DNA methylation involves the addition of a methyl group to the fifth carbon of the pyrimidine cytosine ring (5-methylcytosine, 5mC). 5mC is widespread in vertebrate genomes where it is predominantly found within CpG dinucleotides. In mammals, 5mC ... ...

    Abstract DNA methylation involves the addition of a methyl group to the fifth carbon of the pyrimidine cytosine ring (5-methylcytosine, 5mC). 5mC is widespread in vertebrate genomes where it is predominantly found within CpG dinucleotides. In mammals, 5mC participates in long-term silencing processes such as X-chromosome inactivation, genomic imprinting, somatic silencing of germline genes, and silencing of repetitive DNA elements. The evidence for 5mC as a dynamic gene-regulatory mechanism is mostly limited to specific examples, and is far from being completely understood. Recent work from diverse model systems suggests that 5mC might not always act as a dominant repressive mechanism and that hypermethylated promoters and enhancers can be permissive to transcription in vivo and in vitro. In this review, we discuss the links between 5mC and enhancer activity, and evaluate the role of this biochemical mechanism in various biological contexts.
    MeSH term(s) Animals ; DNA/metabolism ; DNA Methylation/physiology ; Epigenesis, Genetic/physiology ; Gene Expression Regulation/physiology ; Humans
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2019-09-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 1744-1358 ; 0071-1365
    ISSN (online) 1744-1358
    ISSN 0071-1365
    DOI 10.1042/EBC20190030
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article: Developmental Accumulation of Gene Body and Transposon Non-CpG Methylation in the Zebrafish Brain.

    Ross, Samuel E / Hesselson, Daniel / Bogdanovic, Ozren

    Frontiers in cell and developmental biology

    2021  Volume 9, Page(s) 643603

    Abstract: DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes; however, non-CG methylation (mCH) is also detectable in vertebrate tissues, most notably in the nervous system. In mammals it is well established that mCH is targeted to CAC ... ...

    Abstract DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes; however, non-CG methylation (mCH) is also detectable in vertebrate tissues, most notably in the nervous system. In mammals it is well established that mCH is targeted to CAC trinucleotides by DNMT3A during nervous system development where it is enriched in gene bodies and associated with transcriptional repression. Nevertheless, the conservation of developmental mCH accumulation and its deposition by DNMT3A is largely unexplored and has yet to be functionally demonstrated in other vertebrates. In this study, by analyzing DNA methylomes and transcriptomes of zebrafish brains, we identified enrichment of mCH at CAC trinucleotides (mCAC) at defined transposon motifs as well as in developmentally downregulated genes associated with developmental and neural functions. We further generated and analyzed DNA methylomes and transcriptomes of developing zebrafish larvae and demonstrated that, like in mammals, mCH accumulates during post-embryonic brain development. Finally, by employing CRISPR/Cas9 technology, we unraveled a conserved role for Dnmt3a enzymes in developmental mCAC deposition. Overall, this work demonstrates the evolutionary conservation of developmental mCH dynamics and highlights the potential of zebrafish as a model to study mCH regulation and function during normal and perturbed development.
    Language English
    Publishing date 2021-03-04
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2737824-X
    ISSN 2296-634X
    ISSN 2296-634X
    DOI 10.3389/fcell.2021.643603
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top