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Showing 1–13 of 13 results
Advanced filters: Author: Lee E. Edsall Clear advanced filters

  • Eosinophils exist as a functionally heterogeneous population. Whether the heterogeneity is driven by cell-intrinsic or extrinsic factors is underexplored. Here, by leveraging single-cell transcriptomic data and epigenomic analysis, the authors propose that local environmental cues define the gene expression program of murine esophageal eosinophils and identify AP-1 family members, including ATF3, as key regulators of gene expression.

    • Jennifer M. Felton
    • Lee E. Edsall
    • Marc E. Rothenberg
    ResearchOpen Access
    Nature Communications
    Volume: 16, P: 1-20

  • A genomic map of nearly 300,000 potential cis-regulatory sequences determined from diverse mouse tissues and cell types reveals active promoters, enhancers and CCCTC-binding factor sites encompassing 11% of the mouse genome and significantly expands annotation of mammalian regulatory sequences.

    • Yin Shen
    • Feng Yue
    • Bing Ren
    Research
    Nature
    Volume: 488, P: 116-120

  • DNA cytosine methylation has essential roles in a number of cellular processes. Here, the first genome-wide, single-base-resolution maps of methylated cytosines in a mammalian genome — from both human embryonic stem cells and fetal fibroblasts — are presented, along with analyses of the transcriptome, histone modifications, and sites of DNA–protein interaction for several regulatory factors. The results reveal key differences in methylation patterns between the two genomes.

    • Ryan Lister
    • Mattia Pelizzola
    • Joseph R. Ecker
    Research
    Nature
    Volume: 462, P: 315-322

  • The Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types; these data were compared with those from human to confirm substantial conservation in the newly annotated potential functional sequences and to reveal pronounced divergence of other sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.

    • Feng Yue
    • Yong Cheng
    • Bing Ren
    ResearchOpen Access
    Nature
    Volume: 515, P: 355-364

  • This study describes the integrative analysis of 111 reference human epigenomes, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression; the results annotate candidate regulatory elements in diverse tissues and cell types, their candidate regulators, and the set of human traits for which they show genetic variant enrichment, providing a resource for interpreting the molecular basis of human disease.

    • Anshul Kundaje
    • Wouter Meuleman
    • Manolis Kellis
    ResearchOpen Access
    Nature
    Volume: 518, P: 317-330

  • As part of the Epigenome Roadmap project, this study uses a chromosome-spanning haplotype reconstruction strategy to construct haplotype-resolved epigenomic maps for a diverse set of human tissues; the maps reveal extensive allelic biases in chromatin state and transcription, which vary across individuals due to genetic backgrounds.

    • Danny Leung
    • Inkyung Jung
    • Bing Ren
    ResearchOpen Access
    Nature
    Volume: 518, P: 350-354

  • A novel approach to analyse high-depth Hi-C data provides a comprehensive chromatin interaction map at approximately 5–10 kb resolution in human fibroblasts; this reveals that TNF-α-responsive enhancers are already in contact with target promoters before signalling and that this chromatin looping is a strong predictor of gene induction.

    • Fulai Jin
    • Yan Li
    • Bing Ren
    Research
    Nature
    Volume: 503, P: 290-294

  • Andrew Singleton and colleagues report a large-scale meta-analysis of genome-wide association data in Parkinson's disease using over 13,000 cases and 95,000 controls plus additional samples for replication. They identify 6 new risk loci and replicate 28 independent risk variants for Parkinson's disease across 24 loci.

    • Mike A Nalls
    • Nathan Pankratz
    • Andrew B Singleton
    Research
    Nature Genetics
    Volume: 46, P: 989-993