Publications

2017

Wolf G, Rebollo R, Karimi MM, Ewing AD, Kamada R, Wu W, Wu B, Bachu M, Ozato K, Faulkner GJ, Mager DL, Lorincz MC, Macfarlan.
On the role of H3.3 in retroviral silencing.
Nature. (2017) 548(7665):E1-E3.

Mager DL & Lorincz MC.
Epigenetic modifier drugs trigger widespread transcription of endogenous retroviruses.
Nature Genetics.
(2017) 49, 974-975. doi:10.1038/ng.3902

 

2016

Sharif J, Endo TA, Nakayama M, Karimi MM, Shimada M, Katsuyama K, Goyal P, Brind'Amour J, Sun MA, Sun Z, Ishikura T, Mizutani-Koseki Y, Ohara O, Shinkai Y, Nakanishi M, Xie H, Lorincz MC, Koseki H.
Activation of Endogenous Retroviruses in Dnmt1(-/-) ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA.
Cell Stem Cell. (2016) Jul 7;19(1):81-94. doi: 10.1016/j.stem.2016.03.013.

Thompson PJ, Macfarlan TS, Lorincz MC.
Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire.
Mol Cell. (2016) Jun 2;62(5):766-76. doi: 10.1016/j.molcel.2016.03.029.

Hiragami-Hamada K, Soeroes S, Nikolov M, Wilkins B, Kreuz S, Chen C, De La Rosa-Velázquez 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 HP1β dimerization establishes a plastic state of condensed chromatin.
Nat Commun. (2016) Apr 19;7:11310. doi: 10.1038/ncomms11310.

 

2015

Yang BX, El Farran CA, Guo HC, Yu T, Fang HT, Wang HF, Schlesinger S, Seah YF, Goh GY, Neo SP, Li Y, Lorincz MC, Tergaonkar V, Lim TM, Chen L, Gunaratne J, Collins JJ, Goff SP, Daley GQ, Li H, Bard FA, Loh YH.
Systematic identification of factors for provirus silencing in embryonic stem cells.
Cell. (2015) Sep 24;163(1):230-45. doi: 10.1016/j.cell.2015.08.037.

Younesy H, Möller T, Lorincz MC, Karimi MM, Jones SJ.
VisRseq: R-based visual framework for analysis of sequencing data.
BMC Bioinformatics. (2015) 16 Suppl 11:S2. doi: 10.1186/1471-2105-16-S11-S2.

Peter J. Thompson*, Vered Dulberg*, Kyung-Mee Moon, Leonard J. Foster, Carol Chen*, Mohammad M. Karimi*, & Matthew C. Lorincz*.
hnRNP K coordinates transcriptional silencing by SETDB1 in embryonic stem cells.
PLoS Genetics. (2015) 11(1), e1004933. http://doi.org/10.1371/journal.pgen.1004933

Julie Brind'Amour, Sheng Liu, Matthew Hudson, Carol Chen, Mohammad M. Karimi, and Matthew C. Lorincz.
An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations.
Nat Commun. (2015) 6:6033. http://doi.org/10.1038/ncomms7033

 

2014

Wang, J., Xie, G., Singh, M., Ghanbarian, A. T., Raskó, T., Szvetnik, A., Rasko, T., Szvetnik, A., Huiqiang, C., Besser, D., Prigione, A., Fuchs, N.V., Schumann, G.G., Chen, W., Lorincz*, M.C., Zoltan, I., Hurst, L.D., and Izsvak, Z.
Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.
Nature. (2014) 516(7531), 405–409. http://doi.org/10.1038/nature13804

Sheng Liu*, Julie Brind'Amour*, Mohammad M. Karimi*, Kenjiro Shirane, Aaron Bogutz, Louis Lefebvre, Hiroyuki Sasaki, Yoichi Shinkai, Matthew C. Lorincz*.
Setdb1 is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells.  
Genes Dev. (2014) 15 Sep; 28(18):2041-55.

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)

 

2013

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 2013 Aug; 21(8):1536-50. doi: 10.1038/mt.2013.131.

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 2013 Jun 4;6(1):15.

 

2012

Vicki E. Maltby, Benjamin J.E. Martin, Julie Brind’Amour*, Adam T. Chruscicki, Kristina McBurney, Julia M. Schulze, Ian J. Johnson, Mark Hills. Thomas Hentrich, Michael S. Kobor , Matthew C. Lorincz*, and LeAnn Howe.
Histone H3K4 Demethylation is Negatively Regulated by Histone H3 Acetylation in S. cerevisiae.
Proc Natl Acad Sci USA 109(45): 18505-10 (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).

 

2011

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
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)


D.C. Leung*, 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)

 

2010

Toshiyuki Matsui, Danny Leung*, Hiroki Miyashita, Hitoshi Miyachi, Hiroshi Kimura, Makoto Tachibana, Matthew C. Lorincz* and Yoichi Shinkai.
Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET.
Nature, 464, 927-931. 8 April (2010)

 

2009

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 Sciences. 34:158-61 (2009)

 

2008

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)

 

2007

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)

 

2006

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)