Advanced search

Filter By:

Journal Check one or more journals to show results from those journals only.

Choose more journals

Article type Check one or more article types to show results from those article types only.
Subject Check one or more subjects to show results from those subjects only.
Date Choose a date option to show results from those dates only.

Custom date range

Clear all filters
Sort by:
Showing 1–20 of 20 results
Advanced filters: Author: Ozren Bogdanovic Clear advanced filters

  • Ozren Bogdanović, Ryan Lister, José Luis Gómez-Skarmeta, Michiel Vermeulen and colleagues report widespread DNA demethylation at developmental enhancers during the phylotypic period in zebrafish, Xenopus and mouse embryos. Their findings suggest a conserved role for Tet proteins and active DNA demethylation in the regulation of phylotypic enhancers.

    • Ozren Bogdanović
    • Arne H Smits
    • Ryan Lister
    Research
    Nature Genetics
    Volume: 48, P: 417-426

  • Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva, and accurately resolves medically-relevant repetitive genes.

    • Hasindu Gamaarachchi
    • Igor Stevanovski
    • Ira W. Deveson
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-14

  • Genomic, epigenomic and transcriptomic data derived from the Mediterranean amphioxus (Branchiostoma lanceolatum) provide insights into the evolution of the genomic regulatory landscape of chordates.

    • Ferdinand Marlétaz
    • Panos N. Firbas
    • Manuel Irimia
    ResearchOpen Access
    Nature
    Volume: 564, P: 64-70

  • Identifying genes associated with SNPs in non-coding regions is difficult as the SNPs are often located far from the promoters they impact. Cross-species comparison of sites occupied by the insulating protein CTCF reveals conserved boundaries between genes often associated with disease. Multiple sclerosis–associated SNPs occur in the GFI1-EVI5 genomic region near several constitutively bound CTCF sites, enabling the authors to propose GFI1 as the gene linked to MS instead of the previously suggested EVI5.

    • David Martin
    • Cristina Pantoja
    • José Luis Gómez-Skarmeta
    Research
    Nature Structural & Molecular Biology
    Volume: 18, P: 708-714

  • DNA methylation plays a major role in establishing cell identity, but the dynamics of DNA methylation patterns are highly variable across species. Here, the authors discover extensive DNA methylation reprogramming during embryonic development of the sea lamprey, a jawless fish with a distinctive, highly disordered methylome.

    • Allegra Angeloni
    • Skye Fissette
    • Ozren Bogdanovic
    ResearchOpen Access
    Nature Communications
    Volume: 15, P: 1-14

  • Germ cells are the means of transferring genetic information to the next generation. Here the authors characterise the DNA methylomes of zebrafish primordial germ cells and find that, unlike mammals, the zebrafish germ cells do not undergo genome-wide DNA demethylation but rather retain paternal DNA methylation patterns

    • Ksenia Skvortsova
    • Katsiaryna Tarbashevich
    • Ozren Bogdanovic
    ResearchOpen Access
    Nature Communications
    Volume: 10, P: 1-13

  • On 16 September 2020, when the news of José Luis Gómez-Skarmeta’s untimely passing broke, the scientific community was left in dismay.

    • Ozren Bogdanovic
    • Manuel Irimia
    Comments & Opinion
    Nature Genetics
    Volume: 52, P: 1267-1268

  • This Review discusses noncanonical DNA methylation (mCH) in animal genomes and highlights the remaining need to clarify whether mCH represents a conserved regulatory layer or a lineage-specific epigenetic feature with distinct biological roles.

    • Thirsa Brethouwer
    • Alex de Mendoza
    • Ozren Bogdanovic
    Reviews
    Nature Genetics
    Volume: 57, P: 2395-2407

  • By studying brain DNA methylation across 13 distantly related animals, the authors show that non-CpG DNA methylation, which plays a regulatory role in cognition, is restricted to vertebrates and was assembled at the origin of the vertebrate lineage as a result of the ancestral vertebrate whole-genome duplication.

    • Alex de Mendoza
    • Daniel Poppe
    • Ryan Lister
    Research
    Nature Ecology & Evolution
    Volume: 5, P: 369-378

  • Whereas vertebrate genomes are highly methylated at CpG positions, invertebrate genomes are typically sparsely methylated. Here, the authors report a highly methylated genome in a marine sponge and show striking similarities with vertebrates.

    • Alex de Mendoza
    • William L. Hatleberg
    • Ryan Lister
    Research
    Nature Ecology & Evolution
    Volume: 3, P: 1464-1473

  • The gene regulatory network controlling the bifurcation of common progenitors into the neural retina and retinal-pigmented epithelium programs remains poorly understood. Here the authors study transcriptome dynamics and chromatin accessibility during this process in zebrafish, revealing network redundancy, as well as context-dependent and sequential transcription factor activity.

    • Lorena Buono
    • Jorge Corbacho
    • Juan-Ramón Martínez-Morales
    ResearchOpen Access
    Nature Communications
    Volume: 12, P: 1-16

  • Histone modifying enzymes are required for cell differentiation and lineage commitment during embryonic development. By a comprehensive set of epigenome reference maps of Xenopusembryos, the authors show that H3K4me3 and H3K27me3 exert an extended maternal control well into post-gastrulation development.

    • Saartje Hontelez
    • Ila van Kruijsbergen
    • Gert Jan C. Veenstra
    ResearchOpen Access
    Nature Communications
    Volume: 6, P: 1-13

  • The two homoeologous subgenomes in the allotetraploid frog Xenopus laevis evolved asymmetrically; one often retained the ancestral state, whereas the other experienced gene loss, deletion, rearrangement and reduced gene expression.

    • Adam M. Session
    • Yoshinobu Uno
    • Daniel S. Rokhsar
    ResearchOpen Access
    Nature
    Volume: 538, P: 336-343

  • Epigenetic profiling of germline and zygotic genomes has revealed that a fraction of mammalian genomes do not undergo epigenetic reprogramming during early development, highlighting the importance of epigenetic inheritance in animals. Inheritance of histone modifications, tRNA fragments and microRNAs can affect gene regulation in the offspring; however, in mammals, epigenetic inheritance rarely operates beyond two generations.

    • Ksenia Skvortsova
    • Nicola Iovino
    • Ozren Bogdanović
    Reviews
    Nature Reviews Molecular Cell Biology
    Volume: 19, P: 774-790