Alexander Meissner

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. doi request reprint Epigenetic modifications in pluripotent and differentiated cells
    Alexander Meissner
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:1079-88. 2010
  2. pmc Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
    Hongcang Gu
    Broad Institute, Cambridge, Massachusetts, USA
    Nat Methods 7:133-6. 2010
  3. pmc Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
    Michael J Ziller
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
    PLoS Genet 7:e1002389. 2011
  4. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
  5. pmc Dissecting direct reprogramming through integrative genomic analysis
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:49-55. 2008
  6. pmc Charting a dynamic DNA methylation landscape of the human genome
    Michael J Ziller
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 500:477-81. 2013
  7. pmc Reprogramming factor expression initiates widespread targeted chromatin remodeling
    Richard P Koche
    Broad Institute, Cambridge, MA 02142, USA
    Cell Stem Cell 8:96-105. 2011
  8. pmc DNA methylation dynamics during in vivo differentiation of blood and skin stem cells
    Christoph Bock
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:633-47. 2012
  9. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
  10. doi request reprint Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    Hongcang Gu
    Broad Institute, Cambridge, Massachusetts, USA
    Nat Protoc 6:468-81. 2011

Detail Information

Publications44

  1. doi request reprint Epigenetic modifications in pluripotent and differentiated cells
    Alexander Meissner
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:1079-88. 2010
    ..Although iPS cells appear molecularly and functionally similar to embryonic stem cells, more genome-wide studies are needed to define the extent and functions of epigenetic remodeling during reprogramming...
  2. pmc Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution
    Hongcang Gu
    Broad Institute, Cambridge, Massachusetts, USA
    Nat Methods 7:133-6. 2010
    ..Thirty nanograms of DNA was sufficient for genome-scale analysis and our protocol worked well on formalin-fixed, paraffin-embedded samples...
  3. pmc Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
    Michael J Ziller
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
    PLoS Genet 7:e1002389. 2011
    ..In summary these results contribute further to our understanding of cytosine methylation patterns in human cells using a large representative sample set...
  4. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
    ..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...
  5. pmc Dissecting direct reprogramming through integrative genomic analysis
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:49-55. 2008
    ..We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process...
  6. pmc Charting a dynamic DNA methylation landscape of the human genome
    Michael J Ziller
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 500:477-81. 2013
    ..Therefore, our selected DMRs can serve as a starting point to guide new, more effective reduced representation approaches to capture the most informative fraction of CpGs, as well as further pinpoint putative regulatory elements. ..
  7. pmc Reprogramming factor expression initiates widespread targeted chromatin remodeling
    Richard P Koche
    Broad Institute, Cambridge, MA 02142, USA
    Cell Stem Cell 8:96-105. 2011
    ..Our data provide evidence for an early, organized, and population-wide epigenetic response to ectopic reprogramming factors that clarify the temporal order through which somatic identity is reset during reprogramming...
  8. pmc DNA methylation dynamics during in vivo differentiation of blood and skin stem cells
    Christoph Bock
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:633-47. 2012
    ..In summary, these results demonstrate that in vivo differentiation of adult stem cells is associated with small but informative changes in the genomic distribution of DNA methylation...
  9. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations...
  10. doi request reprint Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling
    Hongcang Gu
    Broad Institute, Cambridge, Massachusetts, USA
    Nat Protoc 6:468-81. 2011
    ..The entire process of RRBS library construction takes ∼9 d...
  11. pmc High-throughput bisulfite sequencing in mammalian genomes
    Zachary D Smith
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
    Methods 48:226-32. 2009
    ..Contemporary sequencing and array-based technologies are compared against sample throughput and coverage, highlighting the variety of options available to investigate methylation on the genome-scale...
  12. pmc A unique regulatory phase of DNA methylation in the early mammalian embryo
    Zachary D Smith
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 484:339-44. 2012
    ..Our data provide a genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic, before returning to the canonical somatic pattern...
  13. ncbi request reprint DNA methylation: roles in mammalian development
    Zachary D Smith
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Nat Rev Genet 14:204-20. 2013
    ....
  14. pmc Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    Casey A Gifford
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 153:1149-63. 2013
    ....
  15. ncbi request reprint In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state
    Marius Wernig
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nature 448:318-24. 2007
    ..Our results show that the biological potency and epigenetic state of in-vitro-reprogrammed induced pluripotent stem cells are indistinguishable from those of ES cells...
  16. ncbi request reprint Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin
    Jacob Hanna
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Science 318:1920-3. 2007
    ..The problems associated with using retroviruses and oncogenes for reprogramming need to be resolved before iPS cells can be considered for human therapy...
  17. pmc Quantitative comparison of genome-wide DNA methylation mapping technologies
    Christoph Bock
    Broad Institute, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:1106-14. 2010
    ..We highlight strengths and weaknesses of the four methods and give practical recommendations for the design of epigenomic case-control studies...
  18. pmc Genome-wide chromatin state transitions associated with developmental and environmental cues
    Jiang Zhu
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 152:642-54. 2013
    ..We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming...
  19. pmc Mouse ooplasm confers context-specific reprogramming capacity
    Michelle M Chan
    Broad Institute of MIT, Cambridge, Massachusetts, USA
    Nat Genet 44:978-80. 2012
    ..We identify specific targets for DNA demethylation after nuclear transfer, such as germline-associated promoters, as well as unique limitations that include certain repetitive element classes...
  20. pmc lincRNAs act in the circuitry controlling pluripotency and differentiation
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 477:295-300. 2011
    ..Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state...
  21. doi request reprint Pluripotency factors in embryonic stem cells regulate differentiation into germ layers
    Matt Thomson
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 145:875-89. 2011
    ..Our study provides a framework for understanding how complex transcription factor networks control cell fate decisions in progenitor cells...
  22. doi request reprint Induced pluripotent stem cells: current progress and potential for regenerative medicine
    Giovanni Amabile
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
    Trends Mol Med 15:59-68. 2009
    ..The approach of generating patient-specific pluripotent cells will undoubtedly transform regenerative medicine in many ways...
  23. pmc Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines
    Christoph Bock
    Broad Institute, Cambridge, MA 02142, USA
    Cell 144:439-52. 2011
    ..The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines...
  24. doi request reprint Somatic cell nuclear transfer and derivation of embryonic stem cells in the mouse
    Styliani Markoulaki
    The Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Methods 45:101-14. 2008
    ....
  25. pmc Suppression of intestinal neoplasia by deletion of Dnmt3b
    Haijiang Lin
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02141, USA
    Mol Cell Biol 26:2976-83. 2006
    ....
  26. doi request reprint Derivation and manipulation of murine embryonic stem cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
    Methods Mol Biol 482:3-19. 2009
    ..In this chapter, we will describe the derivation and propagation of murine ES cells. This is followed by a description of targeting ES cells and a protocol for the generation of mice by diploid and tetraploid blastocyst injections...
  27. pmc Epigenomics and chromatin dynamics
    Veronika Akopian
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
    Genome Biol 13:313. 2012
    ..A report of the 'Joint Keystone Symposium on Epigenomics and Chromatin Dynamics', Keystone, Colorado, 17-22 January 2012...
  28. pmc Epigenetic obstacles encountered by transcription factors: reprogramming against all odds
    Casey A Gifford
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
    Curr Opin Genet Dev 22:409-15. 2012
    ..Several recent studies have begun to provide mechanistic insights that will eventually lead to a more rational design and improved understanding of nuclear reprogramming...
  29. pmc Erosion of dosage compensation impacts human iPSC disease modeling
    Shila Mekhoubad
    The Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
    Cell Stem Cell 10:595-609. 2012
    ..However, our finding that most genes subject to XCI are derepressed by this erosion of XCI suggests that it should be a significant consideration when selecting hiPSC lines for modeling any disease...
  30. pmc A model for genetic and epigenetic regulatory networks identifies rare pathways for transcription factor induced pluripotency
    Maxim N Artyomov
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
    PLoS Comput Biol 6:e1000785. 2010
    ..Further experimental tests of predictions emerging from our model should lead to fundamental advances in our understanding of how cellular identity is maintained and transformed...
  31. ncbi request reprint Recommendations for the design and analysis of epigenome-wide association studies
    Karin B Michels
    1 Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics and Gynecology, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts, USA 2 Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
    Nat Methods 10:949-55. 2013
    ....
  32. pmc Transcription factor-mediated epigenetic reprogramming
    Camille Sindhu
    Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
    J Biol Chem 287:30922-31. 2012
    ..In this minireview, we summarize many of the classic examples and a large number of recent studies that have taken advantage of TF-mediated reprogramming to produce cell types of biomedical relevance...
  33. pmc Dynamic single-cell imaging of direct reprogramming reveals an early specifying event
    Zachary D Smith
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:521-6. 2010
    ..These data contribute to the theoretical modeling of reprogramming and suggest that certain parts of the reprogramming process follow defined rather than stochastic steps...
  34. pmc Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis
    Alexander Meissner
    Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, MA 02142, USA
    Nucleic Acids Res 33:5868-77. 2005
    ..Near-complete bisulfite conversion and largely unbiased representation of RRBS libraries suggest that random shotgun bisulfite sequencing can be scaled to a genome-wide approach...
  35. ncbi request reprint Generation of nuclear transfer-derived pluripotent ES cells from cloned Cdx2-deficient blastocysts
    Alexander Meissner
    Whitehead Institute and Department of Biology, Massachusetts Institute of Technology, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 439:212-5. 2006
    ..Cloned blastocysts were morphologically abnormal, lacked functional trophoblast and failed to implant into the uterus. However, they efficiently generated pluripotent embryonic stem cells when explanted into culture...
  36. ncbi request reprint Mammalian nuclear transfer
    Alexander Meissner
    Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Dev Dyn 235:2460-9. 2006
    ..In the long term, nuclear transfer or alternative strategies aim to generate customized pluripotent cells, which would be invaluable to medical research and therapy...
  37. pmc The NIH Roadmap Epigenomics Mapping Consortium
    Bradley E Bernstein
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:1045-8. 2010
    ....
  38. pmc Sprouty-2 regulates oncogenic K-ras in lung development and tumorigenesis
    Alice T Shaw
    Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston 02114, USA
    Genes Dev 21:694-707. 2007
    ..These findings indicate that in the lung, Sprouty-2 plays a critical role in the regulation of oncogenic K-ras, and implicate counter-regulatory mechanisms in the pathogenesis of Ras-based disease...
  39. pmc RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
    Yuanxin Xi
    Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
    Bioinformatics 28:430-2. 2012
    ..In summary, RRBSMAP removes bioinformatic hurdles and reduces the computational burden of large-scale epigenome association studies performed with RRBS...
  40. pmc Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature
    Huansheng Xu
    Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
    Cell Res 22:142-54. 2012
    ....
  41. doi request reprint Epigenetic regulation of pluripotency
    Eleni M Tomazou
    Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, Massachusettes, 02138, USA
    Adv Exp Med Biol 695:26-40. 2010
    ..This chapter provides an overview of epigenetic regulation in embryonic stem cells. We present a brief introduction into epigenetic mechanisms and focus on their role in pluripotent cells...