Bradley E Bernstein

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc GC-rich sequence elements recruit PRC2 in mammalian ES cells
    Eric M Mendenhall
    Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 6:e1001244. 2010
  2. pmc Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
    Manching Ku
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
    PLoS Genet 4:e1000242. 2008
  3. 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
  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 Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
    Oren Ram
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 147:1628-39. 2011
  7. ncbi request reprint A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 125:315-26. 2006
  8. 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
  9. pmc Digital transcriptome profiling from attomole-level RNA samples
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Genome Res 20:519-25. 2010
  10. 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

Detail Information

Publications50

  1. pmc GC-rich sequence elements recruit PRC2 in mammalian ES cells
    Eric M Mendenhall
    Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 6:e1001244. 2010
    ....
  2. pmc Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
    Manching Ku
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
    PLoS Genet 4:e1000242. 2008
    ..We propose that large CpG islands depleted of activating motifs confer epigenetic memory by recruiting the full repertoire of Polycomb complexes in pluripotent cells...
  3. 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
    ....
  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 Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
    Oren Ram
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 147:1628-39. 2011
    ..Our work provides a multiplex method that substantially enhances the ability to monitor CR binding, presents a large resource of CR maps, and reveals common principles for combinatorial CR function...
  7. ncbi request reprint A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 125:315-26. 2006
    ..These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency...
  8. 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...
  9. pmc Digital transcriptome profiling from attomole-level RNA samples
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Genome Res 20:519-25. 2010
    ....
  10. 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...
  11. 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...
  12. 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. ..
  13. pmc Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses
    Ido Amit
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 326:257-63. 2009
    ..This study establishes a broadly applicable, comprehensive, and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells...
  14. pmc Global nucleosome occupancy in yeast
    Bradley E Bernstein
    Department of Chemistry and Chemical Biology, Bauer Center for Genomics Research, and Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Genome Biol 5:R62. 2004
    ..We systematically evaluated nucleosome occupancy in yeast promoters by immunoprecipitating nucleosomal DNA and quantifying enrichment by microarrays...
  15. pmc A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
    Manuel Garber
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:810-22. 2012
    ....
  16. pmc Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network
    Aviva Presser Aiden
    Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Cell Stem Cell 6:591-602. 2010
    ..We suggest that Wilms cells share a transcriptional and epigenetic landscape with a normal renal stem cell, which is inherently susceptible to transformation and may represent a cell of origin for this disease...
  17. ncbi request reprint Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
    Anoop P Patel
    Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA Broad Institute of Harvard and Massachusetts Institute of Techonology MIT, Cambridge, MA 02142, USA Howard Hughes Medical Institute Chevy Chase, MD 20815, USA
    Science 344:1396-401. 2014
    ..Thus, we reveal previously unappreciated heterogeneity in diverse regulatory programs central to glioblastoma biology, prognosis, and therapy. ..
  18. pmc An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia
    Birgit Knoechel
    1 Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA 2 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3 Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA 4 Division of Hematology Oncology, Boston Children s Hospital and Harvard Medical School, Boston, Massachusetts, USA 5
    Nat Genet 46:364-70. 2014
    ..Our findings establish a role for epigenetic heterogeneity in leukemia resistance that may be addressed by incorporating epigenetic modulators in combination therapy. ..
  19. 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
    ....
  20. pmc Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    Ahmad M Khalil
    The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:11667-72. 2009
    ..We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression...
  21. doi request reprint Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq
    Mazhar Adli
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Protoc 6:1656-68. 2011
    ..In terms of the numbers of cells required, the method provides two to three orders of magnitude of improvement over the conventional ChIP-seq method and the entire procedure can be completed within 4 d...
  22. pmc Mapping and analysis of chromatin state dynamics in nine human cell types
    Jason Ernst
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 473:43-9. 2011
    ..Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease...
  23. 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...
  24. ncbi request reprint Genome-wide analysis of histone modifications by ChIP-on-chip
    Dana J Huebert
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Methods 40:365-9. 2006
    ..The resulting maps provide insight into the functions of, and relationships between, different modifications. Here, we provide validated ChIP-on-chip methods for analyzing histone modification patterns at genome-scale in mammalian cells...
  25. ncbi request reprint The mammalian epigenome
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 128:669-81. 2007
    ..Here we review current research efforts, with an emphasis on large-scale studies, emerging technologies, and challenges ahead...
  26. pmc Locus-specific editing of histone modifications at endogenous enhancers
    Eric M Mendenhall
    1 Howard Hughes Medical Institute, Chevy Chase, Maryland, USA 2 Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA 3 Broad Institute of Harvard and MIT, Cambridge Massachusetts, USA 4 Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, USA 5
    Nat Biotechnol 31:1133-6. 2013
    ..Our study demonstrates the potential of epigenome editing tools to characterize an important class of functional genomic elements. ..
  27. ncbi request reprint Genomic views of chromatin
    Dana J Huebert
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Curr Opin Genet Dev 15:476-81. 2005
    ..In parallel, state-of-the-art imaging techniques are being used to investigate higher-order chromatin organization, and are beginning to bridge our understanding of chromatin biology with that of chromosome structure...
  28. pmc Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors
    Mazhar Adli
    Howard Hughes Medical Institute, Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Nat Methods 7:615-8. 2010
    ..We used the technique to characterize mouse hematopoietic progenitors and thereby gain insight into their developmental program...
  29. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 458:223-7. 2009
    ..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes...
  30. pmc Initial genome sequencing and analysis of multiple myeloma
    Michael A Chapman
    The Eli and Edythe L Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02412, USA
    Nature 471:467-72. 2011
    ..These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge...
  31. pmc Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA
    Alon Goren
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 7:47-9. 2010
    ..This method is compatible with just 50 pg of DNA and should thus facilitate charting chromatin maps from limited cell populations...
  32. 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...
  33. pmc Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth
    Bo Zhao
    Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:14902-7. 2011
    ..The primed RBL program likely supports antigen-induced proliferation...
  34. ncbi request reprint Genomic maps and comparative analysis of histone modifications in human and mouse
    Bradley E Bernstein
    Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Cell 120:169-81. 2005
    ..This suggests that the DNA elements that direct the methylation represent only a small fraction of the region or lie at some distance from the site...
  35. pmc Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins
    Morgan L Maeder
    1 Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA 2 Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA 3 Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA 4
    Nat Biotechnol 31:1137-42. 2013
    ....
  36. pmc Chromatin state maps: new technologies, new insights
    Eric M Mendenhall
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Curr Opin Genet Dev 18:109-15. 2008
    ..Chromatin state maps thus provide a rich resource for understanding chromatin at a 'systems level', and a starting point for mechanistic studies aimed at defining epigenetic controls that underlie development...
  37. ncbi request reprint The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications
    Bradley E Bernstein
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Methods Enzymol 376:349-60. 2004
  38. doi request reprint Charting histone modifications and the functional organization of mammalian genomes
    Vicky W Zhou
    Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
    Nat Rev Genet 12:7-18. 2011
    ..Here we review a selection of recent studies that have probed histone modifications and successive layers of chromatin structure in mammalian genomes, the patterns that have been identified and future directions for research...
  39. pmc The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism
    Carlos Sebastian
    The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
    Cell 151:1185-99. 2012
    ..Our studies reveal SIRT6 to be a potent tumor suppressor acting to suppress cancer metabolism...
  40. pmc Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells
    Mario L Suvà
    Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA Electronic address
    Cell 157:580-94. 2014
    ..Our study establishes the epigenetic basis of a developmental hierarchy in GBM, provides detailed insight into underlying gene regulatory programs, and suggests attendant therapeutic strategies. PAPERCLIP:..
  41. ncbi request reprint Rpd3p relocation mediates a transcriptional response to rapamycin in yeast
    Emily L Humphrey
    Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, MA 02138, USA
    Chem Biol 11:295-9. 2004
    ..Rather, the comprehensive analysis presented here strongly supports a model in which recruitment of Rpd3p to gene promoters is a regulated step in the control of gene repression...
  42. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
    ..MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available...
  43. pmc In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites
    Jeffry D Sander
    Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Pathology, Harvard Medical School, Boston, MA 02115, USA, Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 01238, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA and Howard Hughes Medical Institute, Chevy Chase, MD 02815, USA
    Nucleic Acids Res 41:e181. 2013
    ..Our improved method should enable more comprehensive profiling of ZFN specificities. ..
  44. pmc Large-scale discovery and validation of functional elements in the human genome
    Bradley E Bernstein
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Genome Biol 6:312. 2005
    ..A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004...
  45. pmc DNA-protein interactions in high definition
    Eric M Mendenhall
    Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
    Genome Biol 13:139. 2012
    ..An elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors has been developed by Rhee and Pugh...
  46. ncbi request reprint Signaling network model of chromatin
    Stuart L Schreiber
    Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Cell 111:771-8. 2002
    ..This view provides insight into chromatin function and epigenetic inheritance...
  47. pmc EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas
    Russell J H Ryan
    Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
    PLoS ONE 6:e28585. 2011
    ..Our work may be helpful in the selection of lymphoma patients for future trials of pharmacologic agents targeting EZH2 and EZH2-regulated pathways...
  48. pmc Development and validation of a T7 based linear amplification for genomic DNA
    Chih Long Liu
    Department of Chemistry and Chemical Biology, and Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
    BMC Genomics 4:19. 2003
    ..These protocols have yet to be applied to the analysis of genomic DNA due to the lack of a suitable tag such as the polyA tail...
  49. pmc Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning
    Kevin A Peterson
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genes Dev 26:2802-16. 2012
    ....
  50. pmc Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells
    Hongfang Wang
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:14908-13. 2011
    ..Thus, there is a conserved network of cis-regulatory factors that interacts with Notch1 to regulate gene expression in TLL cells, as well as unique classes of divergent RBPJ-only sites that also likely regulate transcription...