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Showing 1–11 of 11 results
Advanced filters: Author: Jessica Antosiewicz-Bourget Clear advanced filters

  • By generating maps of histone modifications at promoters and enhancers in several different human cell lines, it has been possible to determine that although modification patterns at promoters are largely invariant between cell types, the patterns at most enhancers are specific to a single cell type and correlate well with cell-type-specific gene expression.

    • Nathaniel D. Heintzman
    • Gary C. Hon
    • Bing Ren
    Research
    Nature
    Volume: 459, P: 108-112

  • Reprogramming of somatic cells to induced pluripotent stem (iPS) cells that can be differentiated into many cell types has great potential for personalized therapy. This study finds that 22 human iPS cell lines that were reprogrammed using five different methods contain protein coding point mutations. Some mutations were pre existing in the somatic cells, others were new mutations that occurred during and after reprogramming. Therefore, it will be important to ensure iPS cell safety before clinical use.

    • Athurva Gore
    • Zhe Li
    • Kun Zhang
    Research
    Nature
    Volume: 471, P: 63-67

  • A defined and simplified culture system for the derivation and growth of human induced pluripotent stem cells is reported. It permits increased efficiency of human reprogramming with an episomal approach. Also in this issue, Okita et al. describe methods for more efficient episomal reprogramming of human cells.

    • Guokai Chen
    • Daniel R Gulbranson
    • James A Thomson
    Research
    Nature Methods
    Volume: 8, P: 424-429

  • 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

  • Although technically feasible, whole-genome analysis of cytosine methylation using bisulfite sequencing remains prohibitively expensive for large eukaryotic genomes. Deng et al. use 30,000 nondegenerate padlock probes to capture ∼66,000 bisulfite-converted sites in human CpG islands and compare their methylation in fibroblasts, embryonic stem cells and induced pluripotent stem cells.

    • Jie Deng
    • Robert Shoemaker
    • Kun Zhang
    Research
    Nature Biotechnology
    Volume: 27, P: 353-360

  • Reprogramming of somatic cells to induce pluripotent cellular properties that closely resemble those of embryonic stem (ES) cells has important therapeutic potential. The first whole genome single-base resolution profiling of the DNA methylomes of several human ES cell, induced pluripotent stem cell (iPSC) and somatic progenitor lines shows that iPSCs are fundamentally distinct from ES cells, insofar as they manifest common, quantifiable epigenomic differences. These 'hotspots of aberrant reprogramming' might be potentially useful as diagnostic markers for incomplete iPSC reprogramming, for the characterization of the efficacy of different reprogramming techniques, and for screening the potential propagation of altered methylation states into derivative differentiated cells.

    • Ryan Lister
    • Mattia Pelizzola
    • Joseph R. Ecker
    Research
    Nature
    Volume: 471, P: 68-73

  • An analysis of genome-wide chromatin interactions during human embryonic stem cell differentiation reveals changes in chromatic organization and simultaneously identifies allele-resolved chromatin structure and differences in gene expression during differentiation.

    • Jesse R. Dixon
    • Inkyung Jung
    • Bing Ren
    ResearchOpen Access
    Nature
    Volume: 518, P: 331-336

  • 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