Matthew Simon

Kingston Lab

Assistant Professor at Yale University


About Matthew Simon

I study non-coding RNAs and their influence on chromatin structure. My approach to these problems was informed by my doctoral work in Kevan Shokat’s laboratory generating histones with site-specific methylation for the study of chromatin. My recent work includes the development of a biochemical means for mapping the direct DNA and protein targets of RNAs. The technique, Capture Hybridization Analysis of RNA Targets (CHART), is analogous to a chromatin-immunoprecipitation (ChIP) experiment for proteins and provides the foundation to ask diverse questions about the biology and function of newly discovered non-coding RNAs and how they relate to chromatin biology. In addition to the application of CHART, my plans include the development of complementary chemical techniques for answering fundamental questions about RNA and chromatin biology. In the 2012/2013 academic year, I will be starting as an Assistant Professor of Molecular Biophysics and Biochemistry at Yale University in the new Chemical Biology Institute on Yale's west campus.

  1. Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE. The genomic binding sites of a noncoding RNA. Proc. Natl. Acad. Sci. U.S.A. 2011 Dec 20; 108(51):20497-502.

  2. Canzio D, Chang EY, Shankar S, Kuchenbecker KM, Simon MD, Madhani HD, Narlikar GJ, Al-Sady B. Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly. Mol. Cell 2011 Jan 7; 41(1):67-81.

  3. 2010
  4. Simon MD. Installation of site-specific methylation into histones using methyl lysine analogs. Curr Protoc Mol Biol 2010 Apr; Chapter 21:Unit 21.18.1-10.

  5. Millet YA, Danna CH, Clay NK, Songnuan W, Simon MD, Werck-Reichhart D, Ausubel FM. Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns. Plant Cell 2010 Mar; 22(3):973-90.

  6. 2009
  7. Shen X, Kim W, Fujiwara Y, Simon MD, Liu Y, Mysliwiec MR, Yuan GC, Lee Y, Orkin SH. Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells. Cell 2009 Dec 24; 139(7):1303-14.

  8. Francis NJ, Follmer NE, Simon MD, Aghia G, Butler JD. Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro. Cell 2009 Apr 3; 137(1):110-22.

  9. Li B, Jackson J, Simon MD, Fleharty B, Gogol M, Seidel C, Workman JL, Shilatifard A. Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription. J. Biol. Chem. 2009 Mar 20; 284(12):7970-6.

  10. Hung T, Binda O, Champagne KS, Kuo AJ, Johnson K, Chang HY, Simon MD, Kutateladze TG, Gozani O. ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation. Mol. Cell 2009 Jan 30; 33(2):248-56.

  11. 2008
  12. Lu X, Simon MD, Chodaparambil JV, Hansen JC, Shokat KM, Luger K. The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure. Nat. Struct. Mol. Biol. 2008 Oct; 15(10):1122-4.

  13. 2007
  14. Simon MD, Chu F, Racki LR, de la Cruz CC, Burlingame AL, Panning B, Narlikar GJ, Shokat KM. The site-specific installation of methyl-lysine analogs into recombinant histones. Cell 2007 Mar 9; 128(5):1003-12.

  15. de la Cruz CC, Kirmizis A, Simon MD, Isono K, Koseki H, Panning B. The polycomb group protein SUZ12 regulates histone H3 lysine 9 methylation and HP1 alpha distribution. Chromosome Res. 2007; 15(3):299-314.

  16. 2006
  17. Simon MD, Feldman ME, Rauh D, Maris AE, Wemmer DE, Shokat KM. Structure and properties of a re-engineered homeodomain protein-DNA interface. ACS Chem. Biol. 2006 Dec 15; 1(12):755-60.

  18. 2004
  19. Simon MD, Shokat KM. Adaptability at a protein-DNA interface: re-engineering the engrailed homeodomain to recognize an unnatural nucleotide. J. Am. Chem. Soc. 2004 Jul 7; 126(26):8078-9.

  20. Sato K, Simon MD, Levin AM, Shokat KM, Weiss GA. Dissecting the Engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning. Chem. Biol. 2004 Jul; 11(7):1017-23.

  21. Simon MD, Sato K, Weiss GA, Shokat KM. A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Res. 2004; 32(12):3623-31.

  22. 2000
  23. Todd J. Zahn, Markus Eilers, Zhengmao Guo, Mohamad B. Ksebati, Matthew Simon, Jeffrey D. Scholten, Steven O. Smith and Richard A. Gibbs. Journal of the American Chemical Society. Evaluation of Isoprenoid Conformation in Solution and in the Active Site of Protein-Farnesyl Transferase Using Carbon-13 Labeling in Conjunction with Solution- and Solid-State NMR. 2000; 122(30):7153-7164.

  24. 1998
  25. Kurt Berlin, Rishi K. Jain, Matthew D. Simon, and Clemens Richert. Journal of Organic Chemistry. A Porphyrin Embedded in DNA. 1998; 63(5):1527-1535.

Back to top