Bradley E Bernstein

Summary

Affiliation: Massachusetts General Hospital
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. pmc Digital transcriptome profiling from attomole-level RNA samples
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Genome Res 20:519-25. 2010

Research Grants

Detail Information

Publications40

  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. pmc Digital transcriptome profiling from attomole-level RNA samples
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Genome Res 20:519-25. 2010
    ....
  11. 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...
  12. 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...
  13. doi request reprint 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
    ....
  14. 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...
  15. 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...
  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. 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
    ....
  18. 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...
  19. 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...
  20. 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...
  21. 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...
  22. 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...
  23. 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...
  24. 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
  25. 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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...
  30. doi request reprint 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. ..
  31. 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...
  32. ncbi request reprint Global approaches to chromatin
    Bradley E Bernstein
    Department of Chemistry and Chemical Biology, Bauer Center for Genomics Research and the Howard Hughes Medical Institute, Harvard University, 02138, Cambridge, MA, USA
    Chem Biol 9:1167-73. 2002
  33. pmc Methylation of histone H3 Lys 4 in coding regions of active genes
    Bradley E Bernstein
    Department of Chemistry and Chemical Biology and The Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 99:8695-700. 2002
    ..In the context of recent studies showing that Lys 4 methylation precludes histone deacetylase recruitment, we conclude that Set1 facilitates transcription, in part, by protecting active coding regions from deacetylation...
  34. 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...
  35. 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
    ....
  36. ncbi request reprint A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma
    Esther Rheinbay
    Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
    Cancer Cell 21:329-31. 2012
    ..The findings extend discoveries of chromatin regulator inactivation and gain-of-function mutations by documenting alteration of a modifiable histone residue in human cancer...
  37. ncbi request reprint Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes
    Melissa M Steward
    Department of Biochemistry, Saint Louis University School of Medicine, 1402 South Grand Blvd, St Louis, Missouri 63104, USA
    Nat Struct Mol Biol 13:852-4. 2006
    ..These findings offer insight into the molecular role of ASH2L, and by extension that of WDR5, in proper H3K4 trimethylation...
  38. ncbi request reprint Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin
    Helena Santos-Rosa
    Wellcome Trust Cancer Research UK Institute and Department of Pathology, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
    Mol Cell 12:1325-32. 2003
    ..These results indicate that K4 H3 methylation and Isw1p ATPase activity are intimately linked in regulating transcription of certain genes in yeast...
  39. ncbi request reprint Active genes are tri-methylated at K4 of histone H3
    Helena Santos-Rosa
    Wellcome Trust Cancer Research UK Institute and Department of Pathology, Tennis Court Road, Cambridge, CB2 1QR, UK
    Nature 419:407-11. 2002
    ..These findings establish the concept of methyl status as a determinant for gene activity and thus extend considerably the complexity of histone modifications...

Research Grants5

  1. Biochemical and genomic studies of histone deacetylases
    BRADLEY BERNSTEIN; Fiscal Year: 2005
    ..This project should yield valuable insight into the mechanisms that underlie gene regulation and will prepare the applicant for a career as an independent investigator. ..
  2. High-throughput sequencing of chromatin regulatory elements
    BRADLEY BERNSTEIN; Fiscal Year: 2007
    ..All data collected in the context of the proposed project will be made available pre-publication to the greater scientific community once reliability has been confirmed. ..