Now showing items 1-20 of 48

    • Age- and Pregnancy-Associated DNA Methylation Changes in Mammary Epithelial Cells 

      Huh, Sung Jin; Clement, Kendell; Jee, David; Merlini, Alessandra; Choudhury, Sibgat; Maruyama, Reo; Yoo, Ronnie; Chytil, Anna; Boyle, Patrick; Ran, Fei Ann; Moses, Harold L.; Barcellos-Hoff, Mary Helen; Jackson-Grusby, Laurie; Meissner, Alexander; Polyak, Kornelia (Elsevier, 2015)
      Summary Postnatal mammary gland development and differentiation occur during puberty and pregnancy. To explore the role of DNA methylation in these processes, we determined the genome-wide DNA methylation and gene expression ...
    • Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci 

      De Jager, Philip Lawrence; Srivastava, Gyan; Lunnon, Katie; Burgess, Jeremy; Schalkwyk, Leonard C; Yu, Lei; Eaton, Matthew L; Keenan, Brendan T; Ernst, Jason; McCabe, Cristin; Tang, Anna; Raj, Towfique; Replogle, Joseph; Brodeur, Wendy; Gabriel, Stacey; Chai, High S; Younkin, Curtis; Younkin, Steven G; Zou, Fanggeng; Szyf, Moshe; Epstein, Charles B; Schneider, Julie A; Bernstein, Bradley E.; Meissner, Alexander; Ertekin-Taner, Nilufer; Chibnik, Lori; Kellis, Manolis; Mill, Jonathan; Bennett, David A (Nature Publishing Group, 2014)
      We used a collection of 708 prospectively collected autopsied brains to assess the methylation state of the brain's DNA in relation to Alzheimer's disease (AD). We found that the level of methylation at 71 of the 415,848 ...
    • Analysing human neural stem cell ontogeny by consecutive isolation of Notch active neural progenitors 

      Edri, Reuven; Yaffe, Yakey; Ziller, Michael J.; Mutukula, Naresh; Volkman, Rotem; David, Eyal; Jacob-Hirsch, Jasmine; Malcov, Hagar; Levy, Carmit; Rechavi, Gideon; Gat-Viks, Irit; Meissner, Alexander; Elkabetz, Yechiel (Nature Pub. Group, 2015)
      Decoding heterogeneity of pluripotent stem cell (PSC)-derived neural progeny is fundamental for revealing the origin of diverse progenitors, for defining their lineages, and for identifying fate determinants driving ...
    • Broader Implications of Defining Standards for the Pluripotency of iPSCs 

      Daley, George Quentin; Lensch, Mathew William; Jaenisch, Rudolf; Meissner, Alexander; Plath, Kathrin; Yamanaka, Shinya (Elsevier BV, 2009)
      We read with great interest the excellent review by Maherali and Hochedlinger (2008) that recommends standards for characterization of pluripotent stem cell lines, especially the many new lines being generated using ...
    • Charting a dynamic DNA methylation landscape of the human genome 

      Ziller, Michael J.; Gu, Hongcang; Müller, Fabian; Donaghey, Julie; Tsai, Linus T.-Y.; Kohlbacher, Oliver; De Jager, Phil L.; Rosen, Evan D.; Bennett, David A.; Bernstein, Bradley E.; Gnirke, Andreas; Meissner, Alexander (2013)
      DNA methylation is a defining feature of mammalian cellular identity and essential for normal development1,2. Most cell types, except germ cells and pre-implantation embryos3–5, display relatively stable DNA methylation ...
    • A comparison of non-integrating reprogramming methods 

      Schlaeger, Thorsten M.; Daheron, Laurence Marie; Brickler, Thomas R; Entwisle, Samuel; Chan, Karrie; Cianci, Amelia; DeVine, Alexander; Ettenger, Andrew; Fitzgerald, Kelly; Godfrey, Michelle; Gupta, Dipti; McPherson, Jade; Malwadkar, Prerana; Gupta, Manav; Bell, Blair; Doi, Akiko; Jung, Namyoung; Li, Xin; Lynes, Maureen M.; Brookes, Emily; Cherry, Anne B C; Demirbas, Didem; Tsankov, Alexander; Zon, Leonard Ira; Rubin, Lee; Feinberg, Andrew P; Meissner, Alexander; Cowan, Chad A.; Daley, George Quentin (Nature Publishing Group, 2014)
      Human induced pluripotent stem cells (hiPSCs1, 2, 3) are useful in disease modeling and drug discovery, and they promise to provide a new generation of cell-based therapeutics. To date there has been no systematic evaluation ...
    • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications 

      Harris, R Alan; Wang, Ting; Coarfa, Cristian; Nagarajan, Raman P; Hong, Chibo; Downey, Sara L; Johnson, Brett E; Fouse, Shaun D; Delaney, Allen; Zhao, Yongjun; Olshen, Adam; Ballinger, Tracy; Zhou, Xin; Forsberg, Kevin J; Gu, Junchen; Echipare, Lorigail; O, Henriette; Lister, Ryan; Pelizzola, Mattia; Xi, Yuanxin; Epstein, Charles B; Bernstein, Bradley E.; Hawkins, R David; Ren, Bing; Chung, Wen-Yu; Gu, Hongcang; Bock, Christoph; Gnirke, Andreas; Zhang, Michael Q; Haussler, David; Ecker, Joseph R; Li, Wei; Farnham, Peggy J; Waterland, Robert A; Meissner, Alexander; Marra, Marco A; Hirst, Martin; Milosavljevic, Aleksandar; Costello, Joseph F (Nature Publishing Group, 2010)
      Sequencing-based DNA methylation profiling methods are comprehensive and, as accuracy and affordability improve, will increasingly supplant microarrays for genome-scale analyses. Here, four sequencing-based methodologies ...
    • Coverage recommendations for methylation analysis by whole genome bisulfite sequencing 

      Ziller, Michael J.; Hansen, Kasper D.; Meissner, Alexander; Aryee, Martin J. (2014)
      Whole genome bisulfite sequencing (WGBS) allows genome-wide DNA methylation profiling but the associated high sequencing costs continue to limit its widespread application. We utilized several high coverage reference data ...
    • Discovery and In Vivo Characterization of Long Noncoding RNAs 

      Liapis, Stephen Constantine (2016-05-17)
      The noncoding genome, or the portion of the genome that does not encode for proteins, encompasses >95% of the human genome. It has been found that the majority of disease-associated genetic variants identified by genome-wide ...
    • DNA methylation dynamics of the human preimplantation embryo 

      Smith, Zachary D.; Chan, Michelle M.; Humm, Kathryn C.; Karnik, Rahul; Mekhoubad, Shila; Regev, Aviv; Eggan, Kevin; Meissner, Alexander (2014)
      In mammals, cytosine methylation is predominantly restricted to CpG dinucleotides and stably distributed across the genome, with local, cell type-specific regulation directed by DNA binding factors1-3. This comparatively ...
    • DNA methylation signatures link prenatal famine exposure to growth and metabolism 

      Tobi, Elmar W.; Goeman, Jelle J.; Monajemi, Ramin; Gu, Hongcang; Putter, Hein; Zhang, Yanju; Slieker, Roderick C.; Stok, Arthur P.; Thijssen, Peter E.; Müller, Fabian; van Zwet, Erik W.; Bock, Christoph; Meissner, Alexander; Lumey, L. H.; Eline Slagboom, P.; Heijmans, Bastiaan T. (Nature Pub. Group, 2014)
      Periconceptional diet may persistently influence DNA methylation levels with phenotypic consequences. However, a comprehensive assessment of the characteristics of prenatal malnutrition-associated differentially methylated ...
    • Epigenetic Hierarchy Governing Nestin Expression 

      Han, Dong Wook; Do, Jeong Tae; Arauzo-Bravo, Marcos J.; Lee, Sung Ho; Meissner, Alexander; Lee, Hoon Taek; Jaenisch, Rudolf; Scholer, Hans R. (Wiley-Blackwell, 2009)
      Nestin is an intermediate filament protein expressed specifically in neural stem cells and progenitor cells of the central nervous system. DNA demethylation and histone modifications are two types of epigenetic modifications ...
    • Epigenomic Profiling of Young and Aged HSCs Reveals Concerted Changes during Aging that Reinforce Self-Renewal 

      Sun, Deqiang; Luo, Min; Jeong, Mira; Rodriguez, Benjamin; Xia, Zheng; Hannah, Rebecca; Wang, Hui; Le, Thuc; Faull, Kym F.; Chen, Rui; Gu, Hongcang; Bock, Christoph; Meissner, Alexander; Göttgens, Berthold; Darlington, Gretchen J.; Li, Wei; Goodell, Margaret A. (Elsevier BV, 2014)
      To investigate the cell-intrinsic aging mechanisms that erode the function of somatic stem cells during aging, we have conducted a comprehensive integrated genomic analysis of young and aged cells. We profiled the ...
    • Epigenomics and Chromatin Dynamics 

      Akopian, Veronika; Chan, Michelle; Clement, Kendell; Galonska, Christina; Gifford, Casey; Lehtola, Elizabeth; Liao, Jing; Samavarchi-Tehrani, Payman; Sindhu, Camille; Smith, Zachary D; Tsankov, Alexander; Webster, Jamie Orme; Zhang, Yingying; Ziller, Michael Johannes; Meissner, Alexander (BioMed Central, 2012)
      A report of the 'Joint Keystone Symposium on Epigenomics and Chromatin Dynamics', Keystone, Colorado, 17-22 January 2012. This year's Joint Keystone Symposium on Epigenomics and Chromatin Dynamics was one of the largest ...
    • Erosion of Dosage Compensation Impacts Human iPSC Disease Modeling 

      Mekhoubad, Shila; Bock, Christoph; de Boer, A. Sophie; Kiskinis, Evangelos; Meissner, Alexander; Eggan, Kevin Carl (Elsevier BV, 2012)
      Although distinct human induced pluripotent stem cell (hiPSC) lines can display considerable epigenetic variation, it has been unclear whether such variability impacts their utility for disease modeling. Here, we show that ...
    • G1 arrest and differentiation can occur independently of Rb family function 

      Wirt, S. E.; Adler, A. S.; Gebala, V.; Weimann, J. M.; Schaffer, B. E.; Saddic, L. A.; Viatour, P.; Vogel, H.; Chang, H. Y.; Meissner, Alexander; Sage, J. (Rockefeller University Press, 2010)
      The ability of progenitor cells to exit the cell cycle is essential for proper embryonic development and homeostasis, but the mechanisms governing cell cycle exit are still not fully understood. Here, we tested the requirement ...
    • Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling 

      Boyle, Patrick; Clement, Kendell; Gu, Hongcang; Smith, Zachary D; Ziller, Michael Johannes; Fostel, Jennifer L; Holmes, Laurie; Meldrim, Jim; Kelley, Fontina; Gnirke, Andreas; Meissner, Alexander (BioMed Central, 2012)
      Sequencing-based approaches have led to new insights about DNA methylation. While many different techniques for genome-scale mapping of DNA methylation have been employed, throughput has been a key limitation for most. To ...
    • Genome-Scale DNA Methylation Analysis in Distinct Pluripotent Stem Cells 

      Webster, Jamie Orme (2014-06-06)
      Mouse embryonic stem cells (ESCs) and embryonic germ cells (EGCs) are both pluripotent cell types derived from distinct developmental stages. Despite sharing many characteristics, some differences have been reported between ...
    • Genome-Scale DNA Methylation Mapping of Clinical Samples at Single-Nucleotide Resolution 

      Gu, Hongcang; Bock, Christoph; Mikkelsen, Tarjei S; Jäger, Natalie; Smith, Zachary D; Tomazou, Eleni; Gnirke, Andreas; Lander, Eric Steven; Meissner, Alexander (Nature Publishing Group, 2010)
      Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical ...
    • Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues 

      Zhu, Jiang; Adli, Mazhar; Zou, James Y.; Verstappen, Griet; Coyne, Michael J.; Zhang, Xiaolan; Durham, Timothy; Miri, Mohammad; Deshpande, Vikram; De Jager, Philip L.; Bennett, David A.; Houmard, Joseph A.; Muoio, Deborah M.; Onder, Tamer T.; Camahort, Raymond; Cowan, Chad A.; Meissner, Alexander; Epstein, Charles B.; Shoresh, Noam; Bernstein, Bradley E. (Elsevier BV, 2013)
      Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin ...