Array

Lorincz Lab Publications

Google Scholar link to Lorincz Lab Publications

2016

Peter Thompson, Todd S. Macfarlan, Matthew C. Lorincz. Long Terminal Repeats: From Parasitic Elements to Building Blocks of the Transcriptional Regulatory Repertoire Molecular Cell, 62(5) 766-776 (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.
Activation of Endogenous Retroviruses in Dnmt1-/- ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA.
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 HP1β-dimerization establishes a plastic state of condensed chromatin.
Nature Communications, 7, 11310, 1-16 (March, 2016)

2015

Hamid Younesy, Torsten Möller, Matthew C Lorincz, Mohammad M Karimi, Steven JM Jones VisRseq: R-based visual framework for analysis of sequencing data BMC Bioinformatics 2015, 16(Suppl 11):S2

Bin Xia Yang, Chadi EL Farran, Hong Chao Guo,Tao Yu, Hai Tong Fang,Hao Fei Wang, Sharon Schlesinger, Yu Fen, Samantha Seah, Germaine Goh, Suat Peng Neo, Yinghui Li, Matthew C. Lorincz*, Vinay Tergaonkar, Tit-Meng Lim, Lingyi Chen, Jayantha Gunaratne, James J. Collins, Stephen Goff, George Daley, Hu Li, Frederic Bard, and Yuin-Han Loh Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells Cell,  2015, 163, 1–16, September 24

 

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, 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 Jan 21;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. (2014).2015 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 DataComputer 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)

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