Now showing items 1-20 of 29

    • 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 ...
    • 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 ...
    • 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 ...
    • Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq 

      Venteicher, Andrew S; Tirosh, Itay; Hebert, Christine; Yizhak, Keren; Neftel, Cyril Ralf Alexander; Filbin, Mariella Gruber; Hovestadt, Volker; Escalante, Leah; Shaw, McKenzie; Rodman, Christopher Jiahn-Leh; Gillespie, Shawn; Dionne, Danielle; Luo, Christina; Ravichandran, Hiranmayi; Mylvaganam, Ravindra; Mount, Christopher; Onozato, Maristela Lika; Nahed, Brian Vala; Wakimoto, Hiroaki; Curry, William Thomas; Iafrate, Anthony John; Rivera, Miguel Nicolas; Frosch, Matthew P.; Golub, Todd Robert; Brastianos, Priscilla Kalliope; Getz, Gad A; Patel, Anoop Premswaroop; Monje, Michelle; Cahill, Daniel P.; Rozenblatt-Rosen, Orit; Louis, David N.; Bernstein, Bradley E.; Regev, Aviv; Suvà, Mario (American Association for the Advancement of Science (AAAS), 2017)
    • Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo 

      Abdel-Wahab, Omar; Gao, Jie; Adli, Mazhar; Dey, Anwesha; Trimarchi, Thomas; Chung, Young Rock; Kuscu, Cem; Hricik, Todd; Ndiaye-Lobry, Delphine; LaFave, Lindsay M.; Koche, Richard; Shih, Alan H.; Guryanova, Olga A.; Kim, Eunhee; Li, Sheng; Pandey, Suveg; Shin, Joseph Y.; Telis, Leon; Liu, Jinfeng; Bhatt, Parva K.; Monette, Sebastien; Zhao, Xinyang; Mason, Christopher E.; Park, Christopher Y.; Bernstein, Bradley E.; Aifantis, Iannis; Levine, Ross L. (The Rockefeller University Press, 2013)
      Somatic Addition of Sex Combs Like 1 (ASXL1) mutations occur in 10–30% of patients with myeloid malignancies, most commonly in myelodysplastic syndromes (MDSs), and are associated with adverse outcome. Germline ASXL1 ...
    • Development and Validation of a T7 Based Linear Amplification for Genomic DNA 

      Liu, Chih Long; Schreiber, Stuart L.; Bernstein, Bradley E. (BioMed Central, 2003)
      Background: Genomic maps of transcription factor binding sites and histone modification patterns provide unique insight into the nature of gene regulatory networks and chromatin structure. These systematic studies use ...
    • DNA-Protein Interactions in High Definition 

      Mendenhall, Eric M; Bernstein, Bradley E. (BioMed Central, 2012)
      An elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors has been developed by Rhee and Pugh.
    • GC-rich sequence elements recruit PRC2 in mammalian ES cells 

      Mendenhall, Eric M; Koche, Richard Patrick; Truong, Thanh; Zhou, Vicky Weijie; Issac, Biju; Chi, Andrew S.; Ku, Manching; Bernstein, Bradley E. (Public Library of Science, 2010)
      Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression. In Drosophila, these repressors are recruited to sequence elements ...
    • Genetic and Epigenetic Fine-Mapping of Causal Autoimmune Disease Variants 

      Farh, Kyle Kai-How; Marson, Alexander; Zhu, Jiang; Kleinewietfeld, Markus; Housley, William J.; Beik, Samantha; Shoresh, Noam; Whitton, Holly; Ryan, Russell J.H.; Shishkin, Alexander A.; Hatan, Meital; Carrasco-Alfonso, Marlene J.; Mayer, Dita; Luckey, C. John; Patsopoulos, Nikolaos A.; De Jager, Philip L.; Kuchroo, Vijay K.; Epstein, Charles B; Daly, Mark J.; Hafler, David A.; Bernstein, Bradley E. (2014)
      Summary Genome-wide association studies have identified loci underlying human diseases, but the causal nucleotide changes and mechanisms remain largely unknown. Here we developed a fine-mapping algorithm to identify candidate ...
    • 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 ...
    • Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains 

      Rheinbay, Esther; Endoh, Mitsuhiro; Mikkelsen, Tarjei S.; Nusbaum, Chad; Xie, Xiaohui; Adli, Mazhar; Kasif, Simon; Ptaszek, Leon M.; Koseki, Haruhiko; van Steensel, Bas; Ku, Manching; Koche, Richard Patrick; Mendenhall, Eric M; Presser, Aviva; Chi, Andrew S.; Cowan, Chad A.; Lander, Eric Steven; Bernstein, Bradley E. (Public Library of Science, 2008)
      In embryonic stem (ES) cells, bivalent chromatin domains with overlapping repressive (H3 lysine 27 tri-methylation) and activating (H3 lysine 4 tri-methylation) histone modifications mark the promoters of more than 2,000 ...
    • Global Nucleosome Occupancy in Yeast 

      Bernstein, Bradley E.; Liu, Chih Long; Humphrey, Emily L; Perlstein, Ethan O; Schreiber, Stuart L. (BioMed Central, 2004)
      A genome-wide study of nucleosome occupancy at yeast promoters shows that promoters that regulate active genes, contain multiple conserved motifs, or contain Rap1 binding sites tend to be depleted of nucleosomes.
    • H2A.Z Landscapes and Dual Modifications in Pluripotent and Multipotent Stem Cells Underlie Complex Genome Regulatory Functions 

      Ku, Manching; Jaffe, Jacob D; Koche, Richard P; Rheinbay, Esther; Endoh, Mitsuhiro; Koseki, Haruhiko; Carr, Steven A; Bernstein, Bradley E (BioMed Central, 2012)
      Background: The histone variant H2A.Z has been implicated in nucleosome exchange, transcriptional activation and Polycomb repression. However, the relationships among these seemingly disparate functions remain obscure. ...
    • Heterodimeric JAK-STAT Activation as a Mechanism of Persistence to JAK2 Inhibitor Therapy 

      Koppikar, Priya; Bhagwat, Neha; Kilpivaara, Outi; Manshouri, Taghi; Adli, Mazhar; Hricik, Todd; Liu, Fan; Saunders, Lindsay M.; Mullally, Ann; Abdel-Wahab, Omar; Leung, Laura; Weinstein, Abby; Marubayashi, Sachie; Goel, Aviva; Gönen, Mithat; Estrov, Zeev; Ebert, Benjamin L.; Chiosis, Gabriela; Nimer, Stephen D.; Bernstein, Bradley E.; Verstovsek, Srdan; Levine, Ross L. (2012)
      The identification of somatic activating mutations in JAK21–4 and in the thrombopoietin receptor (MPL)5 in the majority of myeloproliferative neoplasm (MPN) patients led to the clinical development of JAK2 kinase inhibitors6,7. ...
    • High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics 

      Rotem, Assaf; Ram, Oren; Shoresh, Noam; Sperling, Ralph A.; Schnall-Levin, Michael; Zhang, Huidan; Basu, Anindita; Bernstein, Bradley E.; Weitz, David A. (Public Library of Science, 2015)
      The importance of single-cell level data is increasingly appreciated, and significant advances in this direction have been made in recent years. Common to these technologies is the need to physically segregate individual ...
    • Histone H2A Mono-Ubiquitination Is a Crucial Step to Mediate PRC1-Dependent Repression of Developmental Genes to Maintain ES Cell Identity 

      Endoh, Mitsuhiro; Endo, Takaho A.; Endoh, Tamie; Isono, Kyo-ichi; Sharif, Jafar; Ohara, Osamu; Toyoda, Tetsuro; Ito, Takashi; Eskeland, Ragnhild; Bickmore, Wendy A.; Koseki, Haruhiko; Vidal, Miguel; Bernstein, Bradley E. (Public Library of Science, 2012)
      Two distinct Polycomb complexes, PRC1 and PRC2, collaborate to maintain epigenetic repression of key developmental loci in embryonic stem cells (ESCs). PRC1 and PRC2 have histone modifying activities, catalyzing ...
    • Identification of promoter targets of enhancers by epigenetic knockdown using TAL DNA binding proteins 

      Mendenhall, Eric M; Williamson, Kaylyn Elise; Reyon, Deepak; Joung, Jae Keith; Bernstein, Bradley E. (BioMed Central, 2013)
    • In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites 

      Sander, Jeffry D.; Ramirez, Cherie L.; Linder, Samantha J.; Pattanayak, Vikram; Shoresh, Noam; Ku, Manching; Foden, Jennifer A.; Reyon, Deepak; Bernstein, Bradley E.; Liu, David R.; Joung, J. Keith (Oxford University Press, 2013)
      Gene-editing nucleases enable targeted modification of DNA sequences in living cells, thereby facilitating efficient knockout and precise editing of endogenous loci. Engineered nucleases also have the potential to introduce ...
    • Insulator dysfunction and oncogene activation in IDH mutant gliomas 

      Flavahan, William A.; Drier, Yotam; Liau, Brian B.; Gillespie, Shawn M.; Venteicher, Andrew S.; Stemmer-Rachamimov, Anat O.; Suvà, Mario L.; Bernstein, Bradley E. (2015)
      Gain-of-function IDH mutations are initiating events that define major clinical and prognostic classes of gliomas1,2. Mutant IDH protein produces a novel onco-metabolite, 2-hydroxyglutarate (2-HG), that interferes with ...
    • Integrative analysis of 111 reference human epigenomes 

      Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Kheradpour, Pouya; Zhang, Zhizhuo; Heravi-Moussavi, Alireza; Liu, Yaping; Amin, Viren; Ziller, Michael J; Whitaker, John W; Schultz, Matthew D; Sandstrom, Richard S; Eaton, Matthew L; Wu, Yi-Chieh; Wang, Jianrong; Ward, Lucas D; Sarkar, Abhishek; Quon, Gerald; Pfenning, Andreas; Wang, Xinchen; Claussnitzer, Melina; Coarfa, Cristian; Harris, R Alan; Shoresh, Noam; Epstein, Charles B; Gjoneska, Elizabeta; Leung, Danny; Xie, Wei; Hawkins, R David; Lister, Ryan; Hong, Chibo; Gascard, Philippe; Mungall, Andrew J; Moore, Richard; Chuah, Eric; Tam, Angela; Canfield, Theresa K; Hansen, R Scott; Kaul, Rajinder; Sabo, Peter J; Bansal, Mukul S; Carles, Annaick; Dixon, Jesse R; Farh, Kai-How; Feizi, Soheil; Karlic, Rosa; Kim, Ah-Ram; Kulkarni, Ashwinikumar; Li, Daofeng; Lowdon, Rebecca; Mercer, Tim R; Neph, Shane J; Onuchic, Vitor; Polak, Paz; Rajagopal, Nisha; Ray, Pradipta; Sallari, Richard C; Siebenthall, Kyle T; Sinnott-Armstrong, Nicholas; Stevens, Michael; Thurman, Robert E; Wu, Jie; Zhang, Bo; Zhou, Xin; Beaudet, Arthur E; Boyer, Laurie A; De Jager, Philip; Farnham, Peggy J; Fisher, Susan J; Haussler, David; Jones, Steven; Li, Wei; Marra, Marco; McManus, Michael T; Sunyaev, Shamil; Thomson, James A; Tlsty, Thea D; Tsai, Li-Huei; Wang, Wei; Waterland, Robert A; Zhang, Michael; Chadwick, Lisa H; Bernstein, Bradley E; Costello, Joseph F; Ecker, Joseph R; Hirst, Martin; Meissner, Alexander; Milosavljevic, Aleksandar; Ren, Bing; Stamatoyannopoulos, John A; Wang, Ting; Kellis, Manolis (2015)
      The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but a similar reference has lacked for epigenomic studies. To address this need, the NIH Roadmap ...