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Showing 1–12 of 12 results
Advanced filters: Author: Burak H. Alver Clear advanced filters

  • Nucleosome positioning and chromatin accessibility are important contributors to the regulation of gene expression. Here the authors describe a method that allows the simultaneous measurement of nucleosome occupancy and chromatin accessibility in the same assay, revealing new features of chromatin organization linked to gene regulation.

    • Jakub Mieczkowski
    • April Cook
    • Michael Y. Tolstorukov
    ResearchOpen Access
    Nature Communications
    Volume: 7, P: 1-11

  • This paper describes the ‘4DN Data Portal’ that hosts data generated by the 4D Nucleome network, including Hi-C and other chromatin conformation capture assays, as well as various sequencing-based and imaging-based assays. Raw data have been uniformly processed to increase comparability and the portal is implemented with visualization tools to browse the data without download.

    • Sarah B. Reiff
    • Andrew J. Schroeder
    • Peter J. Park
    ResearchOpen Access
    Nature Communications
    Volume: 13, P: 1-11

  • Changes in chromatin structure impact gene expression programs by modulating accessibility to the transcription machinery. Here, West et al. explore differences in nucleosome occupancy between mammalian pluripotent and somatic cells and uncover regulatory regions likely to play key roles in determining cell identity.

    • Jason A. West
    • April Cook
    • Robert E. Kingston
    ResearchOpen Access
    Nature Communications
    Volume: 5, P: 1-12

  • Charles Roberts, Peter Park, Bradley Bernstein and colleagues examine the consequences of SMARCB1 loss on enhancer landscapes in human rhabdoid tumors. They show that SMARCB1 is essential for the integrity and abundance of SWI/SNF complexes and facilitates their targeting to appropriate enhancers.

    • Xiaofeng Wang
    • Ryan S Lee
    • Charles W M Roberts
    Research
    Nature Genetics
    Volume: 49, P: 289-295

  • Large-scale biobanks have become a font of data that have led to discoveries across many fields of research. Here, the authors provide an overview of the Estonian Biobank, highlighting its value for research and towards personalized medicine.

    • Lili Milani
    • Maris Alver
    • Andres Metspalu
    ReviewsOpen Access
    Nature Communications
    Volume: 16, P: 1-13

  • Uniform processing and detailed annotation of human, worm and fly RNA-sequencing data reveal ancient, conserved features of the transcriptome, shared co-expression modules (many enriched in developmental genes), matched expression patterns across development and similar extent of non-canonical, non-coding transcription; furthermore, the data are used to create a single, universal model to predict gene-expression levels for all three organisms from chromatin features at the promoter.

    • Mark B. Gerstein
    • Joel Rozowsky
    • Robert Waterston
    ResearchOpen Access
    Nature
    Volume: 512, P: 445-448

  • A large collection of new modENCODE and ENCODE genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human are analysed; this reveals many conserved features of chromatin organization among the three organisms, as well as notable differences in the composition and locations of repressive chromatin.

    • Joshua W. K. Ho
    • Youngsook L. Jung
    • Peter J. Park
    ResearchOpen Access
    Nature
    Volume: 512, P: 449-452

  • Charles Roberts and colleagues show that deletion of Arid1a from mouse intestinal epithelium results in invasive adenocarcinomas resembling human colorectal cancer. They further show that ARID1A loss impairs SWI/SNF targeting and enhancer-mediated gene regulation.

    • Radhika Mathur
    • Burak H Alver
    • Charles W M Roberts
    Research
    Nature Genetics
    Volume: 49, P: 296-302