John M Greally

Summary

Affiliation: Albert Einstein College of Medicine
Country: USA

Publications

  1. ncbi request reprint A stain upon the silence: genes escaping X inactivation
    Carolyn J Brown
    Department of Medical Genetics, University of British Columbia, 6174 University Blvd, Vancouver, British Columbia, Canada V6T 1Z3
    Trends Genet 19:432-8. 2003
  2. pmc High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
    Mayumi Oda
    Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, USA
    Nucleic Acids Res 37:3829-39. 2009
  3. pmc CG dinucleotide clustering is a species-specific property of the genome
    Jacob L Glass
    Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA, Division of Hematology Oncology, University of Kentucky, Markey Cancer Center, 800 Rose Street, Lexington KY 40536, USA
    Nucleic Acids Res 35:6798-807. 2007
  4. pmc An integrative genomic and epigenomic approach for the study of transcriptional regulation
    Maria E Figueroa
    Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS ONE 3:e1882. 2008
  5. pmc Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica
    Radhika Das
    Department of Radiation Oncology, Duke University Medical Center, Box 3433, Durham, NC 27710, USA
    BMC Genomics 13:394. 2012
  6. pmc Genetic mapping of putative Chrna7 and Luzp2 neuronal transcriptional enhancers due to impact of a transgene-insertion and 6.8 Mb deletion in a mouse model of Prader-Willi and Angelman syndromes
    Mihaela Stefan
    Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Genomics 6:157. 2005
  7. pmc Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome
    John M Greally
    Department of Medicine Hematology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Ullmann 925, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 99:327-32. 2002
  8. ncbi request reprint An analytical pipeline for genomic representations used for cytosine methylation studies
    Reid F Thompson
    Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Bioinformatics 24:1161-7. 2008
  9. doi request reprint The Wasp System: an open source environment for managing and analyzing genomic data
    Andrew S McLellan
    Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
    Genomics 100:345-51. 2012
  10. pmc Comparative isoschizomer profiling of cytosine methylation: the HELP assay
    Batbayar Khulan
    Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Genome Res 16:1046-55. 2006

Detail Information

Publications61

  1. ncbi request reprint A stain upon the silence: genes escaping X inactivation
    Carolyn J Brown
    Department of Medical Genetics, University of British Columbia, 6174 University Blvd, Vancouver, British Columbia, Canada V6T 1Z3
    Trends Genet 19:432-8. 2003
    ..We discuss the impact of the evolutionary history of the X (and Y) chromosome, and the bioinformatic approaches that promise to provide new insights into the genomic architecture of genes or regions that escape X-chromosome inactivation...
  2. pmc High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers
    Mayumi Oda
    Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, USA
    Nucleic Acids Res 37:3829-39. 2009
    ....
  3. pmc CG dinucleotide clustering is a species-specific property of the genome
    Jacob L Glass
    Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA, Division of Hematology Oncology, University of Kentucky, Markey Cancer Center, 800 Rose Street, Lexington KY 40536, USA
    Nucleic Acids Res 35:6798-807. 2007
    ..Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters...
  4. pmc An integrative genomic and epigenomic approach for the study of transcriptional regulation
    Maria E Figueroa
    Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS ONE 3:e1882. 2008
    ..Integrative epigenomic studies are thus feasible using clinical samples and provide superior detection of aberrant transcriptional programming than single-platform microarray studies...
  5. pmc Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domestica
    Radhika Das
    Department of Radiation Oncology, Duke University Medical Center, Box 3433, Durham, NC 27710, USA
    BMC Genomics 13:394. 2012
    ..It is postulated to have evolved in placental mammals to modulate intrauterine resource allocation to the offspring. In this study, we determined the imprint status of metatherian orthologues of eutherian imprinted genes...
  6. pmc Genetic mapping of putative Chrna7 and Luzp2 neuronal transcriptional enhancers due to impact of a transgene-insertion and 6.8 Mb deletion in a mouse model of Prader-Willi and Angelman syndromes
    Mihaela Stefan
    Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Genomics 6:157. 2005
    ..In this study, we define the deletion endpoints and examine the impact on expression of flanking genes...
  7. pmc Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome
    John M Greally
    Department of Medicine Hematology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Ullmann 925, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 99:327-32. 2002
    ..Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival...
  8. ncbi request reprint An analytical pipeline for genomic representations used for cytosine methylation studies
    Reid F Thompson
    Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Bioinformatics 24:1161-7. 2008
    ..Here we describe all of the components of the pipeline, which can also be applied to data derived from other assays based on genomic representations...
  9. doi request reprint The Wasp System: an open source environment for managing and analyzing genomic data
    Andrew S McLellan
    Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
    Genomics 100:345-51. 2012
    ..Here we describe the current implementation and development of the Wasp System and the roadmap for its community development...
  10. pmc Comparative isoschizomer profiling of cytosine methylation: the HELP assay
    Batbayar Khulan
    Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Genome Res 16:1046-55. 2006
    ..The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome...
  11. pmc Tissue-specific dysregulation of DNA methylation in aging
    Reid F Thompson
    Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
    Aging Cell 9:506-18. 2010
    ..We conclude that different patterns of epigenetic dysregulation occur in each tissue over time and may cause some of the physiological changes associated with normal aging...
  12. pmc Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome
    Masako Suzuki
    Department of Genetics Computational Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Genome Res 21:1833-40. 2011
    ....
  13. ncbi request reprint Methylome profiling reveals distinct alterations in phenotypic and mutational subgroups of myeloproliferative neoplasms
    Sangeeta Nischal
    Albert Einstein College of Medicine, Bronx, New York Mayo Clinic, Rochester, MN, USA
    Cancer Res 73:1076-85. 2013
    ..These results show epigenetic differences between PMF and polycythemia vera/essential thrombocytosis and reveal methylomic signatures of ASXL1 and TET2 mutations...
  14. pmc Genome-wide hydroxymethylation tested using the HELP-GT assay shows redistribution in cancer
    Sanchari Bhattacharyya
    Cancer Center, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA, Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA, Department of Pathology, Johns Hopkins School of Medicine, 1550 Orleans Street, Baltimore MD 21231, USA, Department of Medicine, University of Chicago, 5841 S Maryland Avenue, Chicago, IL 60637, USA and Department of Medicine, Hematology and Medical Oncology, Mount Sinai School of Medicine, 1470 Madison Avenue, New York, NY 10029, USA
    Nucleic Acids Res 41:e157. 2013
    ..Redistribution of 5-hmC seen in cancer highlights the importance of determination of this modification in conjugation with conventional methylome analysis. ..
  15. doi request reprint Genome-wide determination of DNA methylation by Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemias
    Maria E Figueroa
    Department of Medicine and Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Ullmann 911, Bronx, NY 10461, USA
    Methods Mol Biol 538:395-407. 2009
    ..The HELP assay allows methylation levels throughout the genome to be accurately determined so that the epigenetic state of leukemia cells can be identified, compared, and contrasted...
  16. doi request reprint The HELP assay
    Mayumi Oda
    Departments of Medicine Hematology and Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
    Methods Mol Biol 507:77-87. 2009
    ....
  17. doi request reprint DNA methylation changes in murine breast adenocarcinomas allow the identification of candidate genes for human breast carcinogenesis
    Deanna Acosta
    Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461, USA
    Mamm Genome 22:249-59. 2011
    ..Based on these studies, we present a model in which comparative epigenetic techniques can be used to identify novel candidate genes important for human breast tumorigenesis, in both primary and metastatic tumors...
  18. ncbi request reprint CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains
    Jacob L Glass
    Department of Genetics Computational Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
    Mamm Genome 20:633-43. 2009
    ..We conclude that CG dinucleotide periodicity helps to explain some but not all of the relative sequence specificity of mutations of Dnmt3a or Dnmt3L in the establishment of germline cytosine methylation patterns...
  19. pmc MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation
    Maria E Figueroa
    Department of Medicine Hematology Oncology Division, Weill Cornell Medical College, New York, NY 10065, USA
    Blood 114:3448-58. 2009
    ..This trial was registered at www.clinicaltrials.gov as J0443...
  20. ncbi request reprint The Einstein Genome Gateway using WASP - a high throughput multi-layered life sciences portal for XSEDE
    Aaron Golden
    Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Stud Health Technol Inform 175:182-91. 2012
    ..In this paper we discuss the existing WASP system, its proposed middleware role, and its planned interaction with XSEDE to form the Einstein Genome Gateway...
  21. pmc Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats
    Reid F Thompson
    Departments of Genetics Computational Genetics, Albert Einstein College of Medicine, Bronx, New York, New York 10461, USA
    J Biol Chem 285:15111-8. 2010
    ..These results demonstrate that epigenetic dysregulation is a strong candidate for propagating the cellular memory of intrauterine events, causing changes in expression of nearby genes and long term susceptibility to type 2 diabetes...
  22. pmc Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas
    Jose M Polo
    Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 104:3207-12. 2007
    ..More broadly, these data show how genome-wide identification of direct target genes can identify tumors dependent on oncogenic transcription factors and amenable to targeted therapeutics...
  23. pmc DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma
    Rita Shaknovich
    Division of Hematology Oncology, Department of Medicine, Weill Cornell Medical College, New York, NY, USA
    Blood 116:e81-9. 2010
    ..This reduced gene set was an accurate predictor of ABC and GCB subtypes. Collectively, the data suggest that epigenetic patterning contributes to the ABC and GCB DLBCL phenotypes and could serve as useful biomarker...
  24. pmc Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterations
    Britta Will
    Albert Einstein College of Medicine, Bronx, NY, USA
    Blood 120:2076-86. 2012
    ..This study demonstrates that stem and progenitor cells in MDS are characterized by stage-specific expansions and contain epigenetic and genetic alterations...
  25. pmc Optimized design and data analysis of tag-based cytosine methylation assays
    Masako Suzuki
    Department of Genetics Computational Genetics, Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
    Genome Biol 11:R36. 2010
    ..8 million loci in the human genome. This HELP-tagging assay is not sensitive to sequence polymorphism or base composition and allows exploration of both CG-rich and depleted genomic contexts...
  26. pmc Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7q
    Li Zhou
    Albert Einstein College of Medicine, Bronx, New York 10461, USA
    J Biol Chem 286:25211-23. 2011
    ..These findings reveal widespread novel epigenetic alterations in myelodysplastic leukocytes and implicate DOCK4 as a pathogenic gene located on the 7q chromosomal region...
  27. pmc Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features
    Maria E Figueroa
    Department of Medicine Hematology Oncology Division, Weill Cornell Medical College, New York, NY 10021, USA
    Blood 113:2795-804. 2009
    ..Biologically, CEBPA-silenced leukemias presented with a decreased response to myeloid growth factors in vitro...
  28. ncbi request reprint Epigenomics: beyond CpG islands
    Melissa J Fazzari
    Department of Epidemiology and Social Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Nat Rev Genet 5:446-55. 2004
  29. doi request reprint Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assays
    Qiang Jing
    Departments of Genetics Computational Genetics and Center for Epigenomics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, USA
    Methods Mol Biol 815:79-87. 2012
    ..HELP-tagging analysis results are supplied in standard file formats (BED and WIG) that can be readily examined on the UCSC genome browser...
  30. ncbi request reprint Introduction to epigenomics and epigenome-wide analysis
    Melissa J Fazzari
    Division of Biostatistics, Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
    Methods Mol Biol 620:243-65. 2010
    ..We will conclude this chapter by identifying issues in building methylation-based models for prediction and potential directions of further statistical research in epigenetics...
  31. pmc Cytosine methylation dysregulation in neonates following intrauterine growth restriction
    Francine Einstein
    Department of Obstetrics, Gynecology and Women s Health, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS ONE 5:e8887. 2010
    ....
  32. pmc Repressor element-1 silencing transcription factor (REST)-dependent epigenetic remodeling is critical to ischemia-induced neuronal death
    Kyung Min Noh
    Dominick P Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA
    Proc Natl Acad Sci U S A 109:E962-71. 2012
    ....
  33. pmc Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii
    Mathieu Gissot
    Department of Medicine Infectious Diseases, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS Pathog 3:e77. 2007
    ..In addition, with its compact genome, genetic tractability, and discrete life cycle stages, T. gondii provides an important new model to study the evolutionarily conserved components of the histone code...
  34. pmc DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia
    Maria E Figueroa
    Department of Medicine, Hematology Oncology Division, Weill Cornell Medical College, New York, NY 10065, USA
    Cancer Cell 17:13-27. 2010
    ..We report a 15 gene methylation classifier predictive of overall survival in an independent patient cohort (p < 0.001, adjusted for known covariates)...
  35. doi request reprint The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human disease
    Andrew S McLellan
    Price Center for Genetics and Translational Medicine, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
    Epigenomics 1:33-8. 2009
    ..As a result, several avenues of research are now expanding, with cancer epigenomics being complemented by studies of the epigenomics of infectious disease and a neuroepigenomics program...
  36. pmc DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP)
    Masako Suzuki
    Center for Epigenomics and Division of Computational Genetics, Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, USA
    Methods 52:218-22. 2010
    ..Here we describe the assay, its relative strengths and weaknesses, and the transition of the assay from a microarray to massively-parallel sequencing-based foundation...
  37. pmc Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylation
    Mathieu Gissot
    Albert Einstein College of Medicine, Ullmann 1225, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Eukaryot Cell 7:537-40. 2008
    ..To assess the presence of cytosine methylation of Toxoplasma gondii and Cryptosporidium parvum DNA, we used mass spectrometry analysis and confirmed that these organisms lack detectable methylcytosine in their DNA...
  38. pmc Experimental approaches to the study of epigenomic dysregulation in ageing
    Reid F Thompson
    Department of Genetics and Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Exp Gerontol 45:255-68. 2010
    ..We describe how such experiments are currently performed, their limitations technically and analytically and their application to ageing research...
  39. pmc Unusual characteristics of the DNA binding domain of epigenetic regulatory protein MeCP2 determine its binding specificity
    Sergei Khrapunov
    Department of Biochemistry and Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461, United States
    Biochemistry 53:3379-91. 2014
    ..The significance of these results in the context of neuronal function and development and MeCP2-related developmental disorders such as Rett syndrome is discussed. ..
  40. pmc Differential epigenome-wide DNA methylation patterns in childhood obesity-associated asthma
    Deepa Rastogi
    Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
    Sci Rep 3:2164. 2013
    ..These findings suggest that dysregulated DNA methylation is associated with non-atopic inflammation observed in pediatric obesity-associated asthma. ..
  41. pmc Lack of evidence for green tea polyphenols as DNA methylation inhibitors in murine prostate
    Shannon R Morey Kinney
    Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, New York, USA
    Cancer Prev Res (Phila) 2:1065-75. 2009
    ..These data indicate that oral administration of GTPs does not affect normal or cancer-specific DNA methylation in the murine prostate...
  42. doi request reprint Genome-wide DNA methylation analysis using massively parallel sequencing technologies
    Masako Suzuki
    Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Semin Hematol 50:70-7. 2013
    ..We will also describe recently discovered DNA modifications, and the protocols to detect these modifications...
  43. pmc A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
    Reid F Thompson
    Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    Bioinformatics 25:2164-70. 2009
    ..The tools in this package include bisulphite conversion efficiency calculation, sequence polymorphism flagging and visualization tools that combine multiple experimental replicates and create tracks for genome browser viewing...
  44. doi request reprint DNA methylation alterations in multiple myeloma as a model for epigenetic changes in cancer
    Amy Sharma
    Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Wiley Interdiscip Rev Syst Biol Med 2:654-69. 2010
    ..We have thus focused on DNA methylation changes in the pathogenesis of multiple myeloma, which promises to become an excellent model for systems biological studies of epigenomic dysregulation in human disease...
  45. doi request reprint Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell lines
    Eloisi C Lopes
    Department of Molecular Pharmacology and Chemistry, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    Cancer Res 68:7258-63. 2008
    ..Because Kaiso inactivation sensitized colon cancer cell lines to chemotherapy, it is possible that therapeutic targeting of Kaiso could improve the efficacy of current treatment regimens...
  46. pmc Mammalian linker-histone subtypes differentially affect gene expression in vivo
    Raouf Alami
    Department of Medicine, Division of Hematology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Proc Natl Acad Sci U S A 100:5920-5. 2003
    ....
  47. pmc Distinct factors control histone variant H3.3 localization at specific genomic regions
    Aaron D Goldberg
    Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
    Cell 140:678-91. 2010
    ..3 at telomeres and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells...
  48. ncbi request reprint In vitro and in vivo testing methods of epigenomic endpoints for evaluating endocrine disruptors
    John M Greally
    Center for Epigenomics, Albert Einstein College of Medicine, Bronx, NY, USA
    ALTEX 30:445-71. 2013
    ..Follow-up studies should include both an epigenetic as well as a genomic component to differentiate between the contributions of potentially compensatory mechanisms. ..
  49. pmc Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder
    Esther R Berko
    Center for Epigenomics and Department of Genetics Division of Computational Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
    PLoS Genet 10:e1004402. 2014
    ..The results indicate that epigenetic dysregulatory mechanisms may complement and interact with DNA mutations in the pathogenesis of the disorder...
  50. pmc Comparative sequence and x-inactivation analyses of a domain of escape in human xp11.2 and the conserved segment in mouse
    Karen D Tsuchiya
    Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
    Genome Res 14:1275-84. 2004
    ..Our findings indicate that genomic context, as well as gene-specific regulatory elements, interact to determine expression of a gene from the inactive X-chromosome...
  51. pmc Phase II trial of the histone deacetylase inhibitor romidepsin in patients with recurrent/metastatic head and neck cancer
    Missak Haigentz
    Division of Oncology, Department of Medicine, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY 10467, USA
    Oral Oncol 48:1281-8. 2012
    ..Inhibition of histone deacetylases (HDACs) represents a novel therapeutic approach warranting additional investigation in solid tumors...
  52. ncbi request reprint A new class of tissue-specifically methylated regions involving entire CpG islands in the mouse
    Masako Suzuki
    Laboratory of Cellular Biochemistry, Veterinary Medical Sciences Animal Resource Sciences, The University of Tokyo, Tokyo 113 8657, Japan
    Genes Cells 12:1305-14. 2007
    ..T-DMRs at CpG islands are functionally important gene regulatory elements that may now be categorized into two classes: T-DMRs involving a subregion of the CpG island and those that occupy the whole CpG island...
  53. ncbi request reprint The potential role of epigenomic dysregulation in complex human disease
    Eli Hatchwell
    Department of Pathology, SUNY at Stony Brook, HSC T8, Room 053, Stony Brook, NY 11794 8088, USA
    Trends Genet 23:588-95. 2007
    ....
  54. ncbi request reprint Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity
    Hideki Sakamoto
    Cellular Biochemistry, Animal Resource Sciences Veterinary Medical Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113 8657, Japan
    Genes Cells 12:1123-32. 2007
    ..The finding indicates the power of NotI methylation profiles in evaluating the relatedness of different cell types...
  55. ncbi request reprint Epigenetics: perceptive enzymes
    Anne C Ferguson-Smith
    Nature 449:148-9. 2007
  56. ncbi request reprint Genomics: Encyclopaedia of humble DNA
    John M Greally
    Nature 447:782-3. 2007
  57. ncbi request reprint Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  58. ncbi request reprint Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cells
    Kohta Ikegami
    Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences and Veterinary Medical Sciences, The University of Tokyo, Tokyo 113 8657, Japan
    Genes Cells 12:1-11. 2007
    ..Chromatin immunoprecipitation (ChIP) confirmed these loci to be targets of G9a, with decreased H3-K9 and/or -K27 dimethylation in the G9a(-/-) cells. These data indicate that G9a site-selectively contributes to DNA methylation...
  59. pmc Homez, a homeobox leucine zipper gene specific to the vertebrate lineage
    Dashzeveg Bayarsaihan
    Department of Molecular, Cellular, and Developmental Biology, Yale University, 266 Whitney Avenue, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 100:10358-63. 2003
    ..We apply a duplication-degeneration-complementation model to explain how this family of genes has evolved...
  60. ncbi request reprint Identification of a candidate regulatory region in the human CD8 gene complex by colocalization of DNase I hypersensitive sites and matrix attachment regions which bind SATB1 and GATA-3
    Lynda J Kieffer
    Department of Laboratory Medicine and Department of Genetics and Section of Immunobiology, Yale University, New Haven, CT 06520, USA
    J Immunol 168:3915-22. 2002
    ..This clustering of DNase HS sites and MARs capable of binding SATB1 and GATA-3 at the 3' end of the CD8B gene suggests that this region is an epigenetic regulator of CD8 expression...

Research Grants12

  1. Massively-parallel sequencing technology for the epigenome
    John Greally; Fiscal Year: 2007
    ..As sequencing technology continues to advance, the insights gained from this project will allow their adoption for epigenomic identification of functional elements. ..
  2. Massively-parallel sequencing technology for the epigenome
    John Greally; Fiscal Year: 2009
    ..As sequencing technology continues to advance, the insights gained from this project will allow their adoption for epigenomic identification of functional elements. ..
  3. Genome-wide cytosine methylation analysis
    John Greally; Fiscal Year: 2005
    ..We will make the developed assay broadly available to this institution's Cancer Center researchers through our fluorescence in situ hybridisation (FISH) core facility, for which the P.I. is scientific director. ..
  4. Massively-parallel sequencing technology for the epigenome
    John Greally; Fiscal Year: 2008
    ..As sequencing technology continues to advance, the insights gained from this project will allow their adoption for epigenomic identification of functional elements. ..
  5. Genomic analysis of mammalian imprinted loci
    John Greally; Fiscal Year: 2008
    ....
  6. Epigenomic influences of diet on intestinal neoplasia
    John Greally; Fiscal Year: 2008
    ..The study will be the first genome-wide study of cytosine methylation to see whether diet-induced changes represent an intermediate stage in the development of cancer. [unreadable] [unreadable] [unreadable] [unreadable]..
  7. Spectral imaging and flourescence microscopy system
    John Greally; Fiscal Year: 2003
    ..The College, for its part, is supporting\ this application with a strong commitment to both facilities and to the infrastructure required for the equipment and the FISH facility. ..
  8. Epigenomic influences of diet on intestinal neoplasia
    John Greally; Fiscal Year: 2007
    ..The study will be the first genome-wide study of cytosine methylation to see whether diet-induced changes represent an intermediate stage in the development of cancer. [unreadable] [unreadable] [unreadable] [unreadable]..
  9. Genomic analysis of mammalian imprinted loci
    John Greally; Fiscal Year: 2007
    ....
  10. Genomic analysis of mammalian imprinted loci
    John Greally; Fiscal Year: 2006
    ....
  11. Genomic analysis of mammalian imprinted loci
    John Greally; Fiscal Year: 2005
    ....
  12. In vivo imaging of X inactivation
    Matthew Levy; Fiscal Year: 2010
    ....