Faculty Profile

Dr. John M. Greally, Ph.D., M.B.,B.Ch.

John M. Greally, Ph.D., M.B.,B.Ch.

Professor, Department of Genetics

Professor, Department of Medicine (Hematology)

Professor, Department of Pediatrics (Pediatric Genetic Medicine)

Faculty Advisor, Epigenetics Shared Facility, Department of Genetics

Director, Center for Epigenomics, Department of Genetics

Faculty Scholar for Epigenomics, Department of Genetics

Faculty Advisor, Computational Genomics Core, Department of Genetics

Director, Division of Computational Genetics, Department of Genetics

Areas of Research: Regulation of transcription, the influence of DNA sequence variation on transcriptional regulation, non-canonical nucleic acid structures, epigenetic models of mammalian phenotypes, data visualisation

Professional Interests

Our research is based on understanding models of genetic susceptibility to human disease, especially those affecting children.

Our main focus has been the study of transcriptional regulation, as a mediator of memory of prior events, whether developmental cues or environmental perturbations.

We study the normal physiology of transcriptional regulation in mammalian cells. The research is facilitated by Einstein's Center for Epigenomics, its Epigenomics Shared Facility and the Computational Epigenomics Group, where the development of the Wasp System software cyberecosystem is nurtured.

Our basic research involves the targeting mechanisms of DNA methylation, the role of non-canonical nucleic acid structures and the heritability of chromatin states. Our human disease research involves autism spectrum disorder, oncogenic viruses, and intrauterine effects on adult disease susceptibility.

We have been guided by our epigenomics studies to consider the broader possibility that mosaicism for cellular events is a much more common cause of human disease phenotypes than currently appreciated. We are therefore expanding our research interests to encompass genetic mosaicism, with an interest in isolated congenital malformations and covert chromosomal aneuploidy.

Selected Publications

Suzuki M, Liao W, Wos F, Johnston AD, DeGrazia J, Ishii J, Bloom T, Zody MC, Germer S, Greally JM. Whole-genome bisulfite sequencing with improved accuracy and cost. Genome Res. 2018 Aug 9. doi: 10.1101/gr.232587.117. [Epub ahead of print] PubMed PMID: 30093547.

Seoighe C, Tosh NJ, Greally JM. DNA methylation haplotypes as cancer markers. Nat Genet. 2018 Aug;50(8):1062-1063. doi: 10.1038/s41588-018-0185-x. PubMed PMID: 30054597.

Kong Y, Berko ER, Marcketta A, Maqbool SB, Simões-Pires CA, Kronn DF, Ye KQ, Suzuki M, Auton A, Greally JM. Detecting, quantifying, and discriminating the mechanism of mosaic chromosomal aneuploidies using MAD-seq. Genome Res. 2018 Jul;28(7):1039-1052. doi: 10.1101/gr.226282.117. Epub 2018 May 17. PubMed PMID:29773658; PubMed Central PMCID: PMC6028128.

Tozour JN, Delahaye F, Suzuki M, Praiss A, Zhao Y, Cai L, Heo HJ, Greally JM,  Hughes F. Intrauterine Hyperglycemia Is Associated with an Impaired Postnatal Response to Oxidative Damage. Stem Cells Dev. 2018 May 15;27(10):683-691. doi: 10.1089/scd.2017.0232. Epub 2018 Apr 26. PubMed PMID: 29598691; PubMed Central PMCID: PMC5962324.

Greally JM. A user's guide to the ambiguous word 'epigenetics'. Nat Rev Mol Cell Biol. 2018 Apr;19(4):207-208. doi: 10.1038/nrm.2017.135. Epub 2018 Jan 17. PubMed PMID: 29339796.

Lappalainen T, Greally JM. Associating cellular epigenetic models with human phenotypes. Nat Rev Genet. 2017 Jul;18(7):441-451. doi: 10.1038/nrg.2017.32. Epub 2017 May 30. Review. PubMed PMID: 28555657.

Rastogi D, Nico J, Johnston AD, Tobias TAM, Jorge Y, Macian F, Greally JM. CDC42-related genes are upregulated in helper T cells from obese asthmatic children. J Allergy Clin Immunol. 2017 May 4. pii: S0091-6749(17)30688-7. doi:10.1016/j.jaci.2017.04.016. [Epub ahead of print] PubMed PMID: 28479334; PubMed Central PMCID: PMC5671374.

Greally JM. Population Epigenetics. Curr Opin Syst Biol. 2017 Feb;1:84-89. doi: 10.1016/j.coisb.2017.01.004. Epub 2017 Jan 27. PubMed PMID: 28367533; PubMed Central PMCID: PMC5373102.

Wijetunga NA, Johnston AD, Maekawa R, Delahaye F, Ulahannan N, Kim K, Greally JM. SMITE: an R/Bioconductor package that identifies network modules by integrating genomic and epigenomic information. BMC Bioinformatics. 2017 Jan 18;18(1):41. doi: 10.1186/s12859-017-1477-3. PubMed PMID: 28100166; PubMed Central PMCID: PMC5242055.

Greally JM, Drake AJ. The Current State of Epigenetic Research in Humans: Promise and Reality. JAMA Pediatr. 2017 Feb 1;171(2):103-104. doi: 10.1001/jamapediatrics.2016.3508. PubMed PMID: 27918756.

Wijetunga NA, Pascual M, Tozour J, Delahaye F, Alani M, Adeyeye M, Wolkoff AW, Verma A, Greally JM. A pre-neoplastic epigenetic field defect in HCV-infected liver at transcription factor binding sites and polycomb targets. Oncogene. 2017 Apr 6;36(14):2030-2044. doi: 10.1038/onc.2016.340. Epub 2016 Oct 10. PubMed PMID:27721404; PubMed Central PMCID: PMC5383522.

Wijetunga NA, Ben-Dayan M, Tozour J, Burk RD, Schlecht NF, Einstein MH, Greally JM. A polycomb-mediated epigenetic field defect precedes invasive cervical carcinoma. Oncotarget. 2016 Sep 20;7(38):62133-62143. doi:10.18632/oncotarget.11390. PubMed PMID: 27557505; PubMed Central PMCID:PMC5308716.

Henikoff S, Greally JM. Epigenetics, cellular memory and gene regulation. Curr Biol. 2016 Jul 25;26(14):R644-8. doi: 10.1016/j.cub.2016.06.011. PubMed PMID: 27458904.

Birney E, Smith GD, Greally JM. Epigenome-wide Association Studies and the Interpretation of Disease -Omics. PLoS Genet. 2016 Jun 23;12(6):e1006105. doi:10.1371/journal.pgen.1006105. eCollection 2016 Jun. Review. PubMed PMID:27336614; PubMed Central PMCID: PMC4919098.

Nadel J, Athanasiadou R, Lemetre C, Wijetunga NA, Ó Broin P, Sato H, Zhang Z, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM. RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships. Epigenetics Chromatin. 2015 Nov 16;8:46. doi: 10.1186/s13072-015-0040-6. eCollection 2015. PubMed PMID: 26579211; PubMed Central PMCID: PMC4647656.

Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM. Post-conversion targeted capture of modified cytosines in mammalian and plant genomes. Nucleic Acids Res. 2015 Jul 13;43(12):e81. doi: 10.1093/nar/gkv244. Epub 2015 Mar 26. PubMed PMID: 25813045; PubMed Central PMCID: PMC4499119.

Wijetunga NA, Delahaye F, Zhao YM, Golden A, Mar JC, Einstein FH, Greally JM. The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences. Nat Commun. 2014 Oct 20;5:5195. doi:10.1038/ncomms6195. PubMed PMID: 25327398; PubMed Central PMCID: PMC4300104.

Delahaye F, Wijetunga NA, Heo HJ, Tozour JN, Zhao YM, Greally JM, Einstein FH. Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth. Nat Commun. 2014 Oct 10;5:5187. doi: 10.1038/ncomms6187. PubMed PMID:25300954; PubMed Central PMCID: PMC4197137.

Berko ER, Suzuki M, Beren F, Lemetre C, Alaimo CM, Calder RB, Ballaban-Gil K, Gounder B, Kampf K, Kirschen J, Maqbool SB, Momin Z, Reynolds DM, Russo N, Shulman L, Stasiek E, Tozour J, Valicenti-McDermott M, Wang S, Abrahams BS, Hargitai J, Inbar D, Zhang Z, Buxbaum JD, Molholm S, Foxe JJ, Marion RW, Auton A, Greally JM. Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS Genet. 2014 May 29;10(5):e1004402. doi:

10.1371/journal.pgen.1004402. eCollection 2014. PubMed PMID: 24875834; PubMed Central PMCID: PMC4038484.

Greally JM, Jacobs MN. In vitro and in vivo testing methods of epigenomic endpoints for evaluating endocrine disruptors. ALTEX. 2013;30(4):445-71. Review. PubMed PMID: 24173168.

Rastogi D, Suzuki M, Greally JM. Differential epigenome-wide DNA methylation patterns in childhood obesity-associated asthma. Sci Rep. 2013;3:2164. doi:10.1038/srep02164. PubMed PMID: 23857381; PubMed Central PMCID: PMC3712321.

McLellan AS, Dubin RA, Jing Q, Broin PÓ, Moskowitz D, Suzuki M, Calder RB, Hargitai J, Golden A, Greally JM. The Wasp System: an open source environment for managing and analyzing genomic data. Genomics. 2012 Dec;100(6):345-51. doi:10.1016/j.ygeno.2012.08.005. Epub 2012 Aug 27. PubMed PMID: 22944616.

Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q, Sandstrom R, Fazzari MJ, Hansen RS, Stamatoyannopoulos JA, McLellan AS, Greally JM. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res. 2011 Nov;21(11):1833-40. doi: 10.1101/gr.116509.110. Epub 2011 Sep 28. PubMed PMID: 21957152; PubMed Central PMCID: PMC3205568.


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Research Information

In the News

The New York Times interviews Dr. John Greally about epigenetics and whether humans can inherit trauma.

The Atlantic speaks with Dr. John Greally about the “fake news” story that swirled around an astronaut’s DNA.

More media coverage