DNA is methylated on cytosine in the context of CpG dinucleotide in mammalian cells. The absence of such methylation in CpG-rich promoter regions known as “CpG islands” is a hallmark of transcriptional activity. In contrast, CpGs in intergenic and intronic regions are frequently heavily methylated. Such methylation likely serves to maintain the ‘parasitic’ transposable elements in these regions on a transcriptionally inert state.
Although the mammalian “de novo” DNA methyltransferases Dnmt3A and Dnmt3B were cloned several years ago, very little is known about the mechanism by which specific regions of the genome are targeted for methylation by these enzymes. As CpG islands are typically a kilobase or longer in length, it is likely that some attribute of chromatin structure, rather than transcription factor binding per se, protects these regions from de novo methylation. Whatever the nature of this protective affect, it clearly breaks down in cancer cells, in which the CpG island promoters of tumor suppressor genes are frequently aberrantly methylated.
Recently, a number of factors have been described that catalyze the post-translational addition or removal of specific moieties, such as acetyl or methyl groups, to/from specific residues on the core nucleosomal histones. A subset of these ‘histone-modifying enzymes’, including histone acetyltransferases and histone H3 lysine 4 (H3K4) methyltransferases, are required for transcription. Intriguingly, histones associated with the promoter regions of actively transcribing genes are marked by a unique combination of covalent modifications. Such modifications may serve to protect promoters from DNA methylation. Conversely, the presence of repressive histone marks, such as H3K9me3 and H3K27me3, in promoter regions, may silence genes in concert with or independent of DNA methylation.
Research in the lab is directed towards understanding the interplay between transcription, DNA methylation and histone modifications in the mouse both in early development and in the germline, using several approaches, including RNA interference and genetic knockouts in combination with ex vivo biochemical analyses of chromatin structure and function, such as chromatin immunoprecipitation (ChIP) DNaseI hypersensitivity and bisulphite sequencing. Integration of genome-wide analyses of the roles specific histone modifying enzymes and DNA methyltransferases using next generation (Illumina) sequencing (ChIP-seq, meDIP and RNA-seq) provides a powerful approach to dissect the roles of specific epigenetic marks in the regulation of genes, retroelements and chimaeric transcripts. We also employ a novel Cre/lox-based genomic targeting system to create synthetic domains of histone modifications and to introduce regulatory elements at defined genomic sites in mESCs for further analysis.
Ongoing projects include: 1) Characterization of the molecular basis of proviral silencing in the germline and early in embryonic development versus in somatic cells; 2) the “heritability” of covalent histone modifications through mitosis; 3) The role of H3K9 “writers” (methyltransferases) and “readers” in transcriptional regulation in mESCs and 4) the role of chimaeric LTR-genic transcripts in cancers of the hematopoietic system.
Peter J. Thompson, Vered Dulberg, Kyung-Mee Moon, Leonard J. Foster, Carol Chen, Mohammad M. Karimiand Matthew C. Lorincz hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells. In Press, PLoS Genetics (Dec, 2014)
Julie Brind’Amour, Matthew Hudson, Sheng Liu, Carol Chen, Mohammad M Karimi and Matthew C Lorincz Ultra-low-input native ChIP-seq for genome-wide profiling of rare cell populations.In Press, Nature Communications, (Dec, 2014)
Jichang Wang, Gangcai Xie, Avazeh T. Ghanbarian, Manvedra Singh, Attila Szvetnik, Wei Chen, Matthew C. Lorincz, Zoltan Ivics, Laurence D. Hurst, Zsuzsanna Izsvák. Primate-specific endogenous retrovirus driven transcription defines naïve-like stem cells. Nature 516, 405-409, 17 Dec (2014)
Sheng Liu, Julie Brind’Amour, Mohammad Mehdi Karimi, Kenjiro Shirane, Aaron Bogutz, Louis Lefebvre, Hiroyuki Sasaki, Yoichi Shinkai, Matthew C Lorincz. Setdb1 is required for persistence of H3K9me3 and repression of endogenous retroviruses in mouse primordial germ cells. Genes & Development 28:2041–2055 Sept (2014)
Danny Leung, Tingting Du, Ulrich Wagner, Wei Xie, Ah Young Lee, Preeti Goyal, Yujing Li, Keith E. Szulwach, Peng Jin, Matthew C. Lorincz, and Bing Ren. Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1. Proc Natl Acad Sci USA. 22 Apr (2014)
Hamid Younesy, Torsten Moller, Alireza Heravi-Moussavi, Jeffrey B. Cheng, Joseph F. Costello, Matthew C. Lorincz, Mohammad M. Karimi,and Steven J.M. Jones. ALEA: a toolbox for allele-specific epigenomics analysis. Bioinformatics. 21 Jan (2014)
Kathryn Blaschke, Kevin T. Kabata, Mohammad M. Karimi, Jorge A. Zepeda-Martinez, Preeti Goyal, Sahasransu Mahaptra, Angela Tam, Diana J. Laird, Martin Hirst, Anjana Rao, Matthew C. Lorincz, and Miguel Ramalho-Santos. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature, 500, 222-226. 8 August (2013)
H. Younesy, C.B. Nielsen, T. Moller, O. Alder, R. Cullum, M.C. Lorincz, M.M. Karimi, and S.J.M. Jones. An Interactive Analysis and Exploration Tool for Epigenomic Data. Computer Graphics Forum (Proceedings of EuroVis 2013), 32(3), (2013).
Sylvie Rival-Gervier, Mandy Y.M. Lo, Shahryar Khattak, Peter Pasceri, Matthew C. Lorincz, and James Ellis. Kinetics and Epigenetics of Retroviral Silencing in Mouse Embryonic Stem Cells Defined by Deletion of the D4Z4 Element. Mol Ther Aug; 21(8):1536-50. doi: 10.1038/mt.2013.131 (2013)
Irina A. Maksakova, Peter J. Thompson, Preeti Goyal, Steven J.M. Jones, Prim B. Singh, Mohammad M. Karimi, and Lorincz C. Matthew. Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. Epigenetics & Chromatin Jun 4;6(1):15 (2013)
Maltby V, Martin B, Brind’Amour J, Chruscicki A, McBurney K, Schulze J, Johnson I, Hills M, Hentrich T, Kobor M, Lorincz M, Howe, L. Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae. PNAS, USA 109:45 18505-18510, (2012)
Danny C. Leung and Matthew C. Lorincz. Silencing of endogenous retroviruses: when and why do histone marks predominate? Trends in Biochemical Sciences (Cover article) 37:4, 127-133 (2012).
Rita Rebollo, Mohammad M. Karimi, Misha Bilenky, Liane Gagnier, Katharine Miceli-Royer, Ying Zhang, Preeti Goyal, Thomas M. Keane, Steven Jones, Martin Hirst, Matthew C. Lorincz* and Dixie L. Mager* (*corresponding authors). Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms PLoS Genetics 7(9): e1002301 (2011)
Irina A. Maksakova, Preeti Goyal, Jörn Bullwinke, Jeremy P. Brown, Misha Bilenky, Dixie L. Mager, Prim B. Singh and Matthew C. Lorincz. H3K9me3 binding proteins are dispensable for SETDB1/H3K9me3-dependent retroviral silencing. Epigenetics & Chromatin, 4:12 doi:10.1186/1756-8935-4-12 (2011)
Karimi, M. M., P. Goyal, I. A. Maksakova, M. Bilenky, D. Leung, J. X. Tang, Y. Shinkai, D. L. Mager, S. Jones, M. Hirst, and M. C. Lorincz. DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs. Cell Stem Cell 8:676-87 (2011)
Leung, D. C., K. B. Dong, I. A. Maksakova, P. Goyal, R. Appanah, S. Lee, M. Tachibana, Y. Shinkai, B. Lehnertz, D. L. Mager, F. Rossi, and M. C. Lorincz. Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing. PNAS, USA 108:5718-23 (2011)
Toshiyuki Matsui, Danny Leung, Hiroki Miyashita, Hitoshi Miyachi, Hiroshi Kimura, Makoto Tachibana, Matthew C. Lorincz* and Yoichi Shinkai* (*corresponding authors). Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature, 464, 927-931 8 April (2010)
Margaret Rush, Ruth Appanah, Sandra Lee, Lucia L. Lam, Preeti Goyal, Matthew C. Lorincz. Targeting of EZH2 to a defined genomic site is sufficient for recruitment of DNMT3a but not de novo DNA methylation. Epigenetics, 4:6 1-11 (2009)
Michael S. Kobor and Matthew C. Lorincz. H2A.Z and DNA methylation: a mutually exclusive relationship. Trends in Biochemical Science. 34:158-61 (2009)
Kevin B. Dong, Irina A. Maksakova, Fabio Mohn, Danny Leung, Ruth Appanah, Sandra Lee, Hao W. Yang, Lucia L. Lam, Dixie L. Mager, Dirk Schübeler, Makoto Tachibana, Yoichi Shinkai and Matthew C. Lorincz. DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity. EMBO J., 27:2691-701 (2008)
M. C. Lorincz and D. Schübeler. RNA polymerase II: Just Stopping By. Cell, 130: 16-18 (2007)
Appanah, R., D. R. Dickerson, P. Goyal, M. Groudine and M. C. Lorincz.
An Unmethylated 3′ Unmethylated 3′ Promoter-Proximal Region Is Required for Efficient Transcription Initiation. PLoS Genetics. 3.2: e27 doi:10.1371/journal.pgen.0030027 (2007)
Laura B. Sontag, M. C. Lorincz and E. Georg Luebeck. Dynamics, stability and inheritance of somatic DNA methylation imprints. Journal of Theoretical Biology, 242:4, 890-899 (2006)