Epigenomics Core

The aim of the Epigenomics Core is to facilitate the research programs of investigators by providing shared resources to study epigenetic modifications across the entire genome, including DNA methylation, histone modification and DNA-protein interactions.

This shared facility is part of Einstein’s Center for Epigenomics. The Center's goal is to make it easy to perform studies of the epigenome, opening up this field of research for non-specialists. The Center supports a wide spectrum of research interests, but has as a major goal the support of studies of the role of epigenomic dysregulation in human disease.

Selected Publications

• Thompson RF, Suzuki M, Lau KW, Greally JM. A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics. 2009. doi:10.1093/bioinformatics/btp382 [PMID: 19561019].
  
• Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, Green RD, Melnick A, Hatchwell E, Bouhassira EE, Verma A, Suzuki M, Greally JM. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 2009;37(12):3829-39.
  
• Figueroa ME, Melnick A, Greally JM. Genome-wide determination of DNA methylation by Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemias. Methods Mol Biol. 2009;538:395-407.
  
• Figueroa ME, Wouters BJ, Skrabanek L, Glass J, Li Y, Erpelinck-Verschueren CA, Langerak AW, Löwenberg B, Fazzari M, Greally JM, Valk PJ, Melnick A, Delwel R. Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features. Blood. 2009;113(12):2795-804.
  
• Oda M, Greally JM. The HELP assay. Methods Mol Biol. 2009;507:77-87.
  
• Thompson RF, Reimers M, Khulan B, Gissot M, Richmond TA, Chen Q, Zheng X, Kim K, Greally JM. An analytical pipeline for genomic representations used for cytosine methylation studies. Bioinformatics. 2008;24(9):1161-7.
  
• Gissot M, Choi SW, Thompson RF, Greally JM, Kim K. Toxoplasma gondii and Cryptosporidium parvum lack detectable DNA cytosine methylation. Eukaryot Cell. 2008;7(3):537-40.
  
• Greally JM. Genomics: Encyclopaedia of humble DNA. Nature 2007;14;447(7146):782-3.
  
• Glass JL, Thompson RF, Khulan B, Figueroa ME, Olivier EN, Oakley EJ, Van Zant G, Bouhassira EE, Melnick A, Golden A, Fazzari MJ, Greally JM. CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Res. 2007;35(20):6798-807.
  
• Gissot M, Kelly KA, Ajioka JW, Greally JM, Kim K. Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii. PLoS Pathog. 2007;3(6):e77.
  
• Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006;16(8):1046-55.
  
• Fazzari MJ and Greally JM. Epigenomics: beyond CpG islands. Nature Rev. Genet. 2004;5:446-455.