Genomes and Genes
John M Greally
Affiliation: Albert Einstein College of Medicine
- A stain upon the silence: genes escaping X inactivationCarolyn 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...
- Convergent and divergent evolution of genomic imprinting in the marsupial Monodelphis domesticaRadhika 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...
- 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 syndromesMihaela 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...
- Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genomeJohn 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...
- An integrative genomic and epigenomic approach for the study of transcriptional regulationMaria 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...
- The Wasp System: an open source environment for managing and analyzing genomic dataAndrew 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...
- Methylome profiling reveals distinct alterations in phenotypic and mutational subgroups of myeloproliferative neoplasmsSangeeta Nischal
Authors Affiliations Albert Einstein College of Medicine, Bronx, New York Mayo Clinic, Rochester, Minnesota Johns Hopkins School of Medicine, Baltimore, Maryland Cleveland Clinic, Cleveland, Ohio and Weill Cornell Medical School, New York, New York
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. Cancer Res; 73(3); 1076-85. ©2012 AACR...
- An analytical pipeline for genomic representations used for cytosine methylation studiesReid 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...
- Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genomeMasako Suzuki
Department of Genetics Computational Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
Genome Res 21:1833-40. 2011....
- High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbersMayumi Oda
Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, USA
Nucleic Acids Res 37:3829-39. 2009....
- Genome-wide determination of DNA methylation by Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemiasMaria 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...
- Tissue-specific dysregulation of DNA methylation in agingReid 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...
- The HELP assayMayumi Oda
Departments of Medicine Hematology and Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
Methods Mol Biol 507:77-87. 2009....
- The Einstein Genome Gateway using WASP - a high throughput multi-layered life sciences portal for XSEDEAaron 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...
- Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of ratsReid 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...
- Automated computational analysis of genome-wide DNA methylation profiling data from HELP-tagging assaysQiang 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...
- CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domainsJacob 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...
- Cytosine methylation dysregulation in neonates following intrauterine growth restrictionFrancine 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....
- Introduction to epigenomics and epigenome-wide analysisMelissa 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...
- The Einstein Center for Epigenomics: studying the role of epigenomic dysregulation in human diseaseAndrew 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...
- Experimental approaches to the study of epigenomic dysregulation in ageingReid 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...
- 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...
- Optimized design and data analysis of tag-based cytosine methylation assaysMasako 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...
- DNA methylation changes in murine breast adenocarcinomas allow the identification of candidate genes for human breast carcinogenesisDeanna 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...
- Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylationMathieu 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...
- Genome-wide DNA methylation analysis using massively parallel sequencing technologiesMasako 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...
- Stem and progenitor cells in myelodysplastic syndromes show aberrant stage-specific expansion and harbor genetic and epigenetic alterationsBritta 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...
- Comparative isoschizomer profiling of cytosine methylation: the HELP assayBatbayar 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...
- A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometryReid 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...
- DNA methylation alterations in multiple myeloma as a model for epigenetic changes in cancerAmy 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...
- Repressor element-1 silencing transcription factor (REST)-dependent epigenetic remodeling is critical to ischemia-induced neuronal deathKyung 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....
- Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7qLi 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...
- Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondiiMathieu 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...
- CG dinucleotide clustering is a species-specific property of the genomeJacob 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...
- Epigenomics: beyond CpG islandsMelissa 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
- Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomasJose 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...
- Phase II trial of the histone deacetylase inhibitor romidepsin in patients with recurrent/metastatic head and neck cancerMissak 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...
- Differential epigenome-wide DNA methylation patterns in childhood obesity-associated asthmaDeepa 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. ..
- Mammalian linker-histone subtypes differentially affect gene expression in vivoRaouf 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....
- Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequencesTarjei 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...
- Genomics: Encyclopaedia of humble DNAJohn M Greally
Nature 447:782-3. 2007
- Epigenetics: perceptive enzymesAnne C Ferguson-Smith
Nature 449:148-9. 2007
- Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarityHideki 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...
- Genome-wide and locus-specific DNA hypomethylation in G9a deficient mouse embryonic stem cellsKohta 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...
- A new class of tissue-specifically methylated regions involving entire CpG islands in the mouseMasako 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...
- The potential role of epigenomic dysregulation in complex human diseaseEli Hatchwell
Department of Pathology, SUNY at Stony Brook, HSC T8, Room 053, Stony Brook, NY 11794 8088, USA
Trends Genet 23:588-95. 2007....
- Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell linesEloisi 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...
- 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-3Lynda 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...
- Homez, a homeobox leucine zipper gene specific to the vertebrate lineageDashzeveg 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...
- Spectral imaging and flourescence microscopy systemJohn 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. ..
- Massively-parallel sequencing technology for the epigenomeJohn 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. ..
- Massively-parallel sequencing technology for the epigenomeJohn 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. ..
- Epigenomic influences of diet on intestinal neoplasiaJohn 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. ..
- Genomic analysis of mammalian imprinted lociJohn Greally; Fiscal Year: 2007....
- Genome-wide cytosine methylation analysisJohn 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. ..
- In vivo imaging of X inactivationMatthew Levy; Fiscal Year: 2010....