Research Topics
Genomes and Genes | Bradley E BernsteinSummaryAffiliation: Massachusetts General Hospital Country: USA Publications
Research Grants
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Detail Information
Publications
Genomic views of chromatinDana 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...
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...- A bivalent chromatin structure marks key developmental genes in embryonic stem cellsBradley 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... - The mammalian epigenomeBradley 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... 
Global nucleosome occupancy in yeastBradley 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...- Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domainsManching 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... - Dissecting direct reprogramming through integrative genomic analysisTarjei 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... - Genome-scale DNA methylation maps of pluripotent and differentiated cellsAlexander 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... - Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cellsOren 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... - In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like stateMarius 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... - Reprogramming factor expression initiates widespread targeted chromatin remodelingRichard 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... - Digital transcriptome profiling from attomole-level RNA samplesFatih Ozsolak
Helicos BioSciences Corporation, Cambridge, MA 02139, USA
Genome Res 20:519-25. 2010.... - Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responsesIdo 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... - Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental networkAviva 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... - Genomic maps and comparative analysis of histone modifications in human and mouseBradley 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... - Rpd3p relocation mediates a transcriptional response to rapamycin in yeastEmily 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... - Genome-wide maps of chromatin state in pluripotent and lineage-committed cellsTarjei 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... - Mapping and analysis of chromatin state dynamics in nine human cell typesJason 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... - Genome-wide analysis of histone modifications by ChIP-on-chipDana 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... - Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNAAlon 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... - Initial genome sequencing and analysis of multiple myelomaMichael 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... - The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modificationsBradley E Bernstein
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
Methods Enzymol 376:349-60. 2004 - Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammalsMitchell 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... 
Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seqMazhar 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...- Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expressionAhmad 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... - Development and validation of a T7 based linear amplification for genomic DNAChih 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... - A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammalsManuel Garber
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Mol Cell 47:810-22. 2012.... - Chromatin state maps: new technologies, new insightsEric 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... - Global approaches to chromatinBradley 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 - Methylation of histone H3 Lys 4 in coding regions of active genesBradley 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... - Signaling network model of chromatinStuart 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... - The NIH Roadmap Epigenomics Mapping ConsortiumBradley E Bernstein
Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
Nat Biotechnol 28:1045-8. 2010.... - A tell-tail sign of chromatin: histone mutations drive pediatric glioblastomaEsther 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... - Active genes are tri-methylated at K4 of histone H3Helena 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... - Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatinHelena 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... - Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexesMelissa 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... - Moving AHEAD with an international human epigenome projectPeter A Jones
Nature 454:711-5. 2008
Research Grants
- Biochemical and genomic studies of histone deacetylasesBRADLEY 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. ..
- High-throughput sequencing of chromatin regulatory elementsBRADLEY 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. ..