Article

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

Broad Institute, Cambridge, MA 02142, USA.
Cell (Impact Factor: 33.12). 02/2011; 144(3):439-52. DOI: 10.1016/j.cell.2010.12.032
Source: PubMed

ABSTRACT The developmental potential of human pluripotent stem cells suggests that they can produce disease-relevant cell types for biomedical research. However, substantial variation has been reported among pluripotent cell lines, which could affect their utility and clinical safety. Such cell-line-specific differences must be better understood before one can confidently use embryonic stem (ES) or induced pluripotent stem (iPS) cells in translational research. Toward this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have measured the in vitro differentiation propensity of these cell lines. This resource enabled us to assess the epigenetic and transcriptional similarity of ES and iPS cells and to predict the differentiation efficiency of individual cell lines. The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines.

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Available from: Mackenzie W Amoroso, Jul 28, 2015
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    • "Furthermore, by sequencing and combining dozens of low-input methylomes from the same sample (e.g., one-cell, four-cell, or 20-cell pools), it will be possible to create composite methylomes that provide excellent genomewide coverage based on relatively few cells and include an inherent assessment of variation. Essentially, composite methylomes redefine the concept of reference epigenome corridors (Bock et al., 2011) in the context of individual samples, thus providing a new type of reference methylome map that can account for tissue heterogeneity and cell-to-cell variation. "
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    ABSTRACT: Methods for single-cell genome and transcriptome sequencing have contributed to our understanding of cellular heterogeneity, whereas methods for single-cell epigenomics are much less established. Here, we describe a whole-genome bisulfite sequencing (WGBS) assay that enables DNA methylation mapping in very small cell populations (μWGBS) and single cells (scWGBS). Our assay is optimized for profiling many samples at low coverage, and we describe a bioinformatic method that analyzes collections of single-cell methylomes to infer cell-state dynamics. Using these technological advances, we studied epigenomic cell-state dynamics in three in vitro models of cellular differentiation and pluripotency, where we observed characteristic patterns of epigenome remodeling and cell-to-cell heterogeneity. The described method enables single-cell analysis of DNA methylation in a broad range of biological systems, including embryonic development, stem cell differentiation, and cancer. It can also be used to establish composite methylomes that account for cell-to-cell heterogeneity in complex tissue samples. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
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    • "However, in other published studies, either methylation data was generated using antibody pulldown techniques (e.g., MeDIP, which does not provide base-resolution information), or a limited number of CpG sites were investigated [2] [9] [16] [18]. Reduced representation bisulfite sequencing (RRBS) is a cost-efficient alternative to WGBS and has been shown to generate reproducible methylomes by several groups [5] [10] [17] [21]. RRBS has been widely used for genome-wide methylation profiling of human and mouse genomes, but has not been applied to zebrafish genome. "
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    ABSTRACT: Zebrafish (Danio rerio) is a vertebrate model organism that is widely used for studying a plethora of biological questions, including developmental processes, effects of external cues on phenotype, and human disease modeling. DNA methylation is an important epigenetic mechanism that contributes to gene regulation, and is prevalent in all vertebrates. Reduced representation bisulfite sequencing (RRBS) is a cost-effective technique to generate genome-wide DNA methylation maps and has been used in mammalian genomes (e.g., human, mouse and rat) but not in zebrafish. High-resolution DNA methylation data in zebrafish are limited: increased availability of such data will enable us to model and better understand the roles, causes and consequences of changes in DNA methylation. Here we present five high-resolution DNA methylation maps for wild-type zebrafish brain (two pooled male and two pooled female methylomes) and liver. These data were generated using the RRBS technique (includes 1.43 million CpG sites of zebrafish genome) on the Illumina HiSeq platform. Alignment to the reference genome was performed using the Zv9 genome assembly. To our knowledge, these datasets are the only RRBS datasets and base-resolution DNA methylation data available at this time for zebrafish brain and liver. These datasets could serve as a resource for future studies to document the functional role of DNA methylation in zebrafish. In addition, these datasets could be used as controls while performing analysis on treated samples.
    12/2014; 2(December 2014):342–344. DOI:10.1016/j.gdata.2014.10.008
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    • "Human transcriptome datasets without replicates were from GSE12583 (Aasen et al., 2008), GSE16654 (Chin et al., 2009), GSE9832 (Park et al., 2008), GSE14711 (Soldner et al., 2009), and GSE9561 (Takahashi et al., 2007). Human transcriptome datasets with biological replicates used in this study were those from GSE25970 (Bock et al., 2011), the super series of GSE26451 and GSE26453 (Munoz et al., 2011), GSE13828 (Ebert et al., 2008), GSE9865 (Lowry et al., 2008), GSE12390 (Maherali et al., 2008), GSE14982 (Sun et al., 2009), and GSE15148 (Yu et al., 2009). "
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    ABSTRACT: The Disposable Soma Theory holds that genetic integrity will be maintained at more pristine levels in germ cells than in somatic cells because of the unique role germ cells play in perpetuating the species. We tested the hypothesis that the same concept applies to pluripotent cells compared to differentiated cells. Analyses of transcriptome and cistrome databases, along with canonical pathway analysis and chromatin immunoprecipitation confirmed differential expression of DNA repair and cell death genes in embryonic stem cells and induced pluripotent stem cells relative to fibroblasts, and predict extensive direct and indirect interactions between the pluripotency and genetic integrity gene networks in pluripotent cells. These data suggest that enhanced maintenance of genetic integrity is fundamentally linked to the epigenetic state of pluripotency at the genomic level. In addition, these findings demonstrate how a small number of key pluripotency factors can regulate large numbers of downstream genes in a pathway-specific manner.
    Stem Cell Research 11/2014; 13(3). DOI:10.1016/j.scr.2014.09.006 · 3.91 Impact Factor
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