Genome-scale DNA methylation maps of pluripotent and differentiated cells
Alexander Meissner,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Hongcang Gu,Marius Wernig,Jacob H. Hanna,Andrey Sivachenko,Xiaolan Zhang,Bradley E. Bernstein,Bradley E. Bernstein,Chad Nusbaum,David B. Jaffe,Andreas Gnirke,Rudolf Jaenisch,Eric S. Lander +14 more
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TLDR
Low-throughput reduced representation bisulphite sequencing is established as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.Abstract:
DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.read more
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Identification of 13 Key Genes Correlated With Progression and Prognosis in Hepatocellular Carcinoma by Weighted Gene Co-expression Network Analysis.
Yang Gu,Jun Li,Deliang Guo,Baiyang Chen,Pengpeng Liu,Yusha Xiao,Kang Yang,Zhisu Liu,Quanyan Liu +8 more
TL;DR: 13 hub genes correlated with the progression and prognosis of HCC were discovered by WGCNA in this study, and these hub genes may contribute to the tumorigenesis and tumor progression of H CC.
Book ChapterDOI
Genome-wide analysis of DNA methylation in low cell numbers by reduced representation bisulfite sequencing.
TL;DR: A protocol for Reduced Representation Bisulfite Sequencing applicable to low amounts of starting material and offering the advantages of absolute DNA methylation quantification and single nucleotide resolution while covering mainly CpG islands is presented.
Journal ArticleDOI
Induction of Vascular Progenitor Cells From Endothelial Cells Stimulates Coronary Collateral Growth
Liya Yin,Vahagn Ohanyan,Yuh Fen Pung,Angelo L DeLucia,Erin Bailey,Molly Enrick,Kelly Stevanov,Christopher Kolz,Giacinta Guarini,William M. Chilian +9 more
TL;DR: iVPCs, generated by partially reprogramming ECs, are an ideal cell type for cell-based therapy designed to stimulate coronary collateral growth and demonstrate better in vitro angiogenic potential than native ECs.
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Highly parallel SNP genotyping reveals high-resolution landscape of mono-allelic Ube3a expression associated with locus-wide antisense transcription
TL;DR: The present study shows that brain-specific maternal expression of Ube3a is restricted to the second half part of the locus, but is absent from the first half part, and highlights the importance of locus-wide competition between sense and antisense transcripts.
Journal ArticleDOI
Genome-wide DNA methylation patterns and transcription analysis in sheep muscle.
Christine Couldrey,Rudiger Brauning,Jeremy Bracegirdle,Paul S. MacLean,Harold V. Henderson,John C. McEwan +5 more
TL;DR: In this paper, the authors used reduced representation bisulfite sequencing (RRBS) to investigate DNA methylation in sheep Longissimus dorsi muscles and compared the results with methylomes from other species.
References
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A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells
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