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 (CGIs) is a hallmark of transcriptional activity. In contrast, CpGs in intergenic and intronic regions are frequently heavily methylated. Such methylation likely serves to maintain transposable elements in these regions in 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 CGIs are frequently aberrantly methylated, coincident with hypomethylation of the rest of the genome.
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, including H3K4 methylation, which may serve to protect promoters from DNA methylation. Conversely, the presence of repressive histone marks, such as H3K9me3 and H3K36me3, in promoter regions and gene bodies, respectively, may promote methylation of associated DNA.
Research in the lab is directed towards understanding the interplay between transcription, DNA methylation and histone modifications in early development and in the germline, using the mouse as a model system. We employ CRISPR/Cas9 and conventional genetic knockouts of chromatin factors or regulatory regions with genome-wide analyses of chromatin structure and function to dissect the roles of specific epigenetic marks in the regulation of genes, retroelements and chimaeric transcripts. These studies are made possible by low-cell input methods for whole genome analysis of chromatin marks (ULI-ChIP-seq), DNA methylation (PBAT) and transcription (RNAseq), and in house pipelines developed to integrate the analyses of these epigenomic datasets at an allele-specific level.
Ongoing projects include: 1) dissecting the interplay between the histone modifications H3K36me2 and H3K27me3, deposited by NSD1 and EZH2, respectively, in early embryonic development to define the molecular basis of the related overgrowth disorders Sotos and Weaver Syndromes; 2) characterizing the “heritability” of covalent histone modifications and DNA methylation through fertilization using F1 hybrid mice and allele-specific analyses; 3) characterizing the role of H3K9 “writers” (methyltransferases) and “readers” in transcriptional regulation and 4) characterizing the role of LTR-initiated transcripts in the establishment of imprinting in oocytes.
Hiragami-Hamada K, Soeroes S, Nikolov M, Wilkins B, Kreuz S, Chen C, La Rosa-Velazquez De IA, Zenn HM, Kost N, Pohl W, Chernev A, Schwarzer D, Jenuwein T, Lorincz M, Zimmermann B, Walla PJ, Neumann H, Baubec T, Urlaub H & Fischle W Dynamic and flexible H3K9me3 bridging via HP1beta dimerization establishes a plastic state of condensed chromatin. Nat Commun 7: 11310 (2016).
Younesy, H., Nielsen CB, Lorincz MC, Jones SJ, Karimi MM, Möller T. ChAsE: chromatin analysis and exploration tool. Bioinformatics btw382 (2016). doi:10.1093/bioinformatics/btw382.
Peter J. Thompson, Todd S. Macfarlan, and Matthew C. Lorincz. Long terminal repeats: from parasitic elements to building blocks for the transcriptional regulatory repertoire Molecular Cell, 62(5), 666-676 (June, 2016).
Jafar Sharif, Takaho Endo, Manabu Nakayama, Mohammad Karimi, Midori Shimada, Kayoko Katsuyama, Preeti Goyal, Julie Brind’Amour, Ming-An Sun, Zhixiong Sun, Tomoyuki Ishikura, Yoko Mizutani-Koseki, Osamu Ohara, Yoichi Shinkai, Makoto Nakanishi, Hehuang Xie, Matthew C. Lorincz,* & Haruhiko Koseki* (* Corresponding authors). Protracted NP95 binding to hemimethylated DNA disrupts SETDB1-mediated proviral silencing. Cell Stem Cell, 19, 1-14 (July, 2016).
Kyoko Hiragami-Hamada, Szabolcs Soeroes, Tuncay Baubec, Miroslav Nikolov, Bryan Wilkins, Sarah Kreuz, Carol Chen, Inti De La Rosa-Velázquez , Hans M Zenn, Nils Kost, Wiebke Pohl, Aleksandar Chernev, Dirk Schwarzer, Thomas Jenuwein, Matthew Lorincz, Bastian Zimmermann, Peter Walla, Heinz Neumann, Henning Urlaub, Wolfgang Fischle. Dynamic and flexible bridging of H3K9me3 via HP1beta-dimerization establishes a plastic state of condensed chromatin. Nature Communications, 7, 11310, 1-16 (March, 2015).
Bin Xia Yang, Chadi El Farran, Hong Chao Guo, Hai Tong Fang, Hao Fei Wan, Tao Yu, Sharon Schlesinger, Hong Trang Nguyen, Germaine Yen Lin Goh, Yu Fen Samantha Seah, Tit-Meng Lim, Lingyi Chen, Matthew C. Lorincz, James J. Collins, Stephen P. Goff, George Q. Daley, Hu Li, Frederic A. Bard, Yuin-Han Loh. Systematic Identification of Factors Crucial for Provirus Silencing in Embryonic Stem Cells. Cell, 163(1) (Sept. 2015).
*H Younesy, T Möller, MC Lorincz, MM Karimi, SJM Jones VisRseq: R-based visual framework for analysis of sequencing data. BMC bioinformatics 16 (Suppl 11), S2 2015
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 An ultra-low-input native ChIP-seq for genome-wide profiling of rare cell populations. 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).