62. Boddu P., Gupta A., Roy R., De La Peña Avalos B., Olazabal-Herrero A., Neuenkirchen N., Zimmer, J.T., Chandhok N.S., King D., Nannya Y., Ogawa S., Lin H., Simon M.D., Dray E., Kupfer G., Verma A., Neugebauer K., Pillai M. (2024) Transcription elongation defect links oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Molecular Cell, doi:https://doi.org/10.1016/j.molcel.2024.02.032. (Pubmed)
61. Pintado-Urbanc A.P. and Simon M.D. (2023) RNA function, synthesis, and probing. In Hang H.R. (Edit.), Pratt M.R. (Edit.), Prescher J.A. (Edit.), Advanced Chemical Biology: Chemical Dissection and Reprogramming of Biological Systems. (pp. 55-74). Weinheim Germany: Wiley-VCH.
60. Gao Y., Zimmer J.T., Vasic R., Liu C., Gbyli R., Zheng S., Patel A., Liu W., Qi Z., Li Y., Nelakanti R., Song Y., Biancon G., Xiao A.Z., Slavoff S., Kibbey R.G., Flavell R.A., Simon M.D., Tebaldi T., Li H., Halene S. (2023) ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control. Cell Reports, doi:https://doi.org/10.1016/j.celrep.2023.113163. (Pubmed)
59. Lu-Culligan W.J., Connor L.J., Xie Y., Ekundayo B.E., Rose B.T., Machyna M., Pintado-Urbanc A., Zimmer J.T., Vock I.W., Bhanu N.V., King M.C., Garcia B.A., Bleichert F., Simon M.D. (2023) Acetyl-methyllysine marks chromatin at active transcription start sites. Nature, doi: https://doi.org/10.1038/s41586-023-06565-9. (Pubmed)
58. Patel S., Sexton A.N., Strine M.S., Wilen C.B., Simon M.D., Pyle A.M. (2023). Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq. Nature Communications, doi: 10.1038/s41467-023-38623-1 (Pubmed)
57. Zimmer J.T., Vock I.W., Schofield J.A., Kiefer L., Moon M.H., Simon M.D. (2023). Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry. bioRxiv, doi: https://doi.org/10.1101/2023.05.24.542133 (Pubmed)
56. Vock I.W. and Simon M.D. (2023). bakR: Uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling. RNA, doi: 10.1261/rna.079451.122 (Pubmed)
55. Courvan M.C.S., Niederer R.O., Vock I.W., Kiefer L., Gilbert W.V., and Simon M.D. (2022) Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry. Nucleic Acids Res, doi: 10.1093/nar/gkac693 (Pubmed)
54. Swartzel J.C., Bond M.J., Pintado-Urbanc A.P., Daftary M., Krone M.W., Douglas T., Carder E.J., Zimmer J.T., Maeda T., Simon M.D., and Crews C.M. (2022). Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC. ACS Chem Biol, doi: 10.1021/acschembio.2c00145 (Pubmed)
53. Winkler L., Jimenez M., Zimmer J.T., Williams A., Simon M.D., and Dimitrova N. (2022). Functional elements of the cis-regulatory lincRNA-p21. Cell Reports, 39(3):110687. doi: 10.1016/j.celrep.2022.110687 (Pubmed)
52. Biancon G., Joshi P., Zimmer J.T., Hunck T., Gao Y., Lessard M.D., Courchaine E., Barentine A.E.S., Machyna M., Botti V., Qin A., Gbyli R., Patel A., Song Y., Kiefer L., Viero G., Neuenkirchen N., Lin H., Bewersdorf J., Simon M.D., Neugebauer K. M., Tebaldi T., Halene S. (2022). Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Mol Cell, 82(6), 1107-1122.e7. doi: 10.1016/j.molcel.2022.02.025 (Pubmed)
51. Zimmer J.T., Rosa-Mercado N.A., Canzio D., Steitz J.A., and Simon M.D. (2021). STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. Mol Cell, 81(21), 4398-4412. doi: 10.1016/j.molcel.2021.08.01 (Pubmed)
50. Luo Y., Schofield J.A., Na Z., Hann T., Simon M.D., and Slavoff S.A. (2021). Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Cell Chem Biol, 28(4), 463-474.e7. doi: 10.1016/j.chembiol.2020.12.003 (Pubmed)
49. Rosa-Mercado N.A., Zimmer J.T., Apostolidi M., Rinehart J., Simon M.D., and Steitz J.A. (2021). Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. Mol Cell. doi: 10.1016/j.molcel.2020.12.002. (Pubmed)
48. Wei J, Alfajaro MM, DeWeirdt PC, Hanna RE, Lu-Culligan WJ, Cai WL, Strine MS, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Ravindra NG, Gasque V, de Miguel FJ, Patil A, Chen H, Oguntuyo KY, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach BD, Politi K, van Dijk D, Kadoch C, Simon MD, Yan Q, Doench JG, Wilen CB. (2020). Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell. Oct 20:S0092-8674(20)31392-1. doi: 10.1016/j.cell.2020.10.028. (Pubmed)
47. Na Z., Luo Y., Schofield J.A., Smelyansky S., Khitun A., Muthukumar S., Valkov E., Simon M.D., and Slavoff S.A. (2020). The NBDY Microprotein Regulates Cellular RNA Decapping. Biochemistry, 59(42), 4131-4142. doi: 10.1021/acs.biochem.0c00672. (Pubmed)
46. Luo, Y., Schofield, J., Simon, M.D. and Slavoff, S.A. (2020). Global profiling of cellular substrates of human Dcp2. Biochemistry. 59(43), 4176-4188. doi: 10.1021/acs.biochem.0c00069 (Pubmed)
45. Machyna M., Kiefer, L. and Simon M.D. (2020). Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. Nat Struct Mol Biol 27, 297-304 (Pubmed)
44. Olivero C.E., Martínez-Terroba E., Zimmer J., Liao C., Tesfaye E., Hooshdaran N., Schofield J.A., Bendor J., Fang D., Simon M.D., Zamudio J.R., and Dimitrova N. (2020). p53 Activates the Long Noncoding RNA Pvt1b to Inhibit Myc and Suppress Tumorigenesis. Mol Cell. 77(4):761-774.e8. doi: 10.1016/j.molcel.2019.12.014 (Pubmed)
43. Simon, M.D. and Machyna, M. (2019) Principles and Practices of Hybridization Capture Experiments to Study Long Noncoding RNAs That Act on Chromatin. In Cech, T. (Edit.), Steitz, J.A. (Edit.), Atkins, J.F. (Edit.), RNA Worlds: New Tools for Deep Exploration. (pp. 221-235). Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
42. Smith, T.S., Zoltek, M.A. and Simon, M.D. (2019) Reengineering a tRNA methyltransferase to covalently capture new RNA substrates. JACS. doi: 10.1021/jacs.9b08529. (Pubmed)
41. Kiefer, L. and Simon, M.D. (2019) Stella’s Role in Oocyte DNA Methylation Suggests Additional Activities of DNMT1. Biochemistry. doi: 10.1021/acs.biochem.9b00146. (Pubmed)
40. Canzio, D. Nwakeze, C.L., Horta, A., Rajkumar, S.M., Coffey, E.L., Duffy, E.E., Duffié, R., Monahan, K., O’Keeffe, S., Simon, M.D., Lomvardas, S., Maniatis, T. (2019) Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice. Cell. doi: 10.1016/j.cell.2019.03.008. (Pubmed)
39. Wang, P.Y., Sexton, A.N., Culligan, W.J. and Simon, M.D. (2018) Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA. doi: 10.1261/rna.067561.118. (Pubmed)
38. Duffy, E.E., Schofield, J.A. and Simon, M.D. (2018) Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. Wiley Interdiscip Rev RNA. doi: 10.1002/wrna.1513 (Pubmed)
37. Kiefer, L., Schofield, J.A. and Simon, M.D. (2018) Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-thioguanosine. J. Am. Chem. Soc., doi: 10.1021/jacs.8b08554 (Pubmed)
36. Duffy, E.E., Canzio, D., Maniatis, T., Simon, M.D. (2018) Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleid Acids Research, 46(21), 6996-7005 (Pubmed)
35. Schofield, J.A., Duffy, E.E., Kiefer, L., Sullivan, M.C., and Simon, M.D. (2018) TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nature Methods, doi:10.1038/nmeth.4582 (Pubmed)
34. Machyna, M. and Simon, M.D. (2017) Catching RNAs on chromatin using hybridization capture methods. Brief Funct Genomics, PMID: 29126220. (Pubmed)
33. Sexton, A.N., Wang, P.Y., Rutenberg-Schoenberg, M., and Simon, M.D. (2017) Interpreting reverse transcriptase termination and mutation events for greater insight into the chemical probing of RNA. Biochemistry, 56(35), 4713-4721. PMID: 28820243. (Pubmed)
32. Li, H., Tong, Y., Zhu, S., Batista, P.J., Duffy, E.E., Zhao, J., Bailis, W., Cao, G., Kroehling, L., Chen, Y., Wang, G., Chen, Y.G., Broughton, J.P., Kluger, Y., Simon, M.D., Chang, H.Y., Yin, Z. and Flavell, R. (2017) m6A mRNA methylation controls T cell homeostasis by targeting IL-7/STAT/SOCS pathway. Nature, 548(7667), 338-342. PMID: 28792938. (Pubmed)
31. Duffy, E.E., and Simon M.D. (2016) Enriching s4U-RNA Using Methane Thiosulfonate (MTS) Chemistry. Curr Protoc Chem Bio, 8(4), 234-250. PMID: 27925666. (Pubmed)
30. Rutenberg-Schoenberg, M., Sexton, A.N., Simon, M.D. (2016) The Properties of Long Noncoding RNAs That Regulate Chromatin. Annu Rev Genom Hum Genet, 17, 69-94. PMID: 27147088 (Pubmed)
29. Simon, M.D. (2016) Insight into lncRNA biology using hybridization capture analyses. Biochim Biophys Acta, 1859(1), 121-127. PMID: 26381323. (Pubmed)
28. Sexton, A., Machyna, M., and Simon, M.D. Capture Hybridization Analysis of RNA Targets (CHART-seq) (2016) Methods Molecular Biology, 1480, 87-97. PMID: 27659977 (Pubmed)
27. Fang, R.*, Moss, W.N.*, Rutenberg-Schoenberg, M. and Simon, M.D. (2015) Probing Xist RNA structure in cells using Targeted Structure-Seq. PLoS Genetics, 11(12):e1005668. PMID: 26646615 *equal contributions (Pubmed)
26. Duffy, E.E., Rutenberg-Schoenberg, M., Stark, C.D., Kitchen, R.R., Gerstein, M.B., and Simon M.D. Tracking distinct RNA populations using effcient and reversible covalent chemistry. (2015) Mol Cell, 59(5), 858-66. PMID: 26340425.(Pubmed)
25. West, J.A., Davis, C.P., Sunwoo, H., Simon, M.D., Sadreyev, R.I., Wang, P.I., Tolstorukov, M.Y., and Kingston, R.E. The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. (2014) Mol Cell, 55(5), 791-802. PMID: 25155612.(Pubmed)
24. Alpatov, R., Lesch, B.J., Nakamoto-Kinoshita, M., Blanco, A., Chen, S., Stützer, A., Armache, K.J., Simon, M.D., Xu, C., Ali, M., Murn, J., Prisic, S., Kutateladze, T.G., Vakoc, C.R., Min, J., Kingston, R.E., Fischle, W., Warren, S.T., Page, D.C., Shi, Y. (2014) Cell 157, 869-81. PMID: 24813610. (Pubmed)
23. Simon, M. D.#,*, Pinter, S. F.*, Fang, R.*, Sarma, K., Rutenberg-Schoenberg, M., Bowman, S. K., Kesner, B. A., Maier, V.K., Kingston, R.E.#, Lee, J.T.# (2013) High resolution Xist binding maps reaveal two-step spreading durring X-chromosome inactivation. Nature 504, 465-9. (Pubmed) #corresponding authors; *equal contributions.
22. Bowman, S. K., Simon, M. D., Deaton, A. M., Tolstorukov, M., Borowsky, M. L., Kingston, R. E. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. (2013) BMC Genomics 14, 466. PMID:23837789. (Pubmed)
21. Simon, M. D. (2013) Capture Hybridization Analysis of RNA Targets (CHART), Curr Protoc Mol Biol Chapter 21, Unit 21 21.25. PMID:23288463. (Pubmed)
20. Simon, M. D., and Shokat, K. M. (2012) A method to site-specifically incorporate methyl-lysine analogues into recombinant proteins, Methods Enzymol 512, 57-69. PMID:22910202. (Pubmed)
19. Fang, R., Chen, F., Dong, Z., Hu, D., Barbera, A. J., Clark, E. A., Fang, J., Yang, Y., Mei, P., Rutenberg, M., Li, Z., Zhang, Y., Xu, Y., Yang, H., Wang, P., Simon, M. D., Zhou, Q., Li, J., Marynick, M. P., Li, X., Lu, H., Kaiser, U. B., Kingston, R. E., Xu, Y., and Shi, Y. G. (2012) LSD2/KDM1B and Its Cofactor NPAC/GLYR1 Endow a Structural and Molecular Model for Regulation of H3K4 Demethylation, Mol Cell 49, 558-70. PMID:23260659. (Pubmed)
18. Simon, M. D., Wang, C. I., Kharchenko, P. V., West, J. A., Chapman, B. A., Alekseyenko, A. A., Borowsky, M. L., Kuroda, M. I., and Kingston, R. E. (2011) The genomic binding sites of a noncoding RNA, Proc Natl Acad Sci U S A 108, 20497-20502. PMID:22143764. (Pubmed)
17. Canzio, D., Chang, E. Y., Shankar, S., Kuchenbecker, K. M., Simon, M. D., Madhani, H. D., Narlikar, G. J., and Al-Sady, B. (2011) Chromodomain-mediated oligomerization of HP1 suggests a nucleosome-bridging mechanism for heterochromatin assembly, Mol Cell 41, 67-81. PMID:21211724. (Pubmed)
16. Simon, M. D. (2010) Installation of site-specific methylation into histones using methyl lysine analogs, Curr Protoc Mol Biol Chapter 21, Unit 21 18 21-10. PMID:20373501. (Pubmed)
15. Millet, Y. A., Danna, C. H., Clay, N. K., Songnuan, W., Simon, M. D., Werck-Reichhart, D., and Ausubel, F. M. (2010) Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns, Plant Cell 22, 973-990. PMID:20348432. (Pubmed)
14. Shen, X., Kim, W., Fujiwara, Y., Simon, M. D., Liu, Y., Mysliwiec, M. R., Yuan, G. C., Lee, Y., and Orkin, S. H. (2009) Jumonji modulates polycomb activity and self-renewal versus differentiation of stem cells, Cell 139, 1303-1314. PMID:20064376. (Pubmed)
13. Li, B., Jackson, J., Simon, M. D., Fleharty, B., Gogol, M., Seidel, C., Workman, J. L., and Shilatifard, A. (2009) Histone H3 lysine 36 dimethylation (H3K36me2) is sufficient to recruit the Rpd3s histone deacetylase complex and to repress spurious transcription, J Biol Chem 284, 7970-7976. PMID:19155214. (Pubmed)
12. Hung, T., Binda, O., Champagne, K. S., Kuo, A. J., Johnson, K., Chang, H. Y., Simon, M. D., Kutateladze, T. G., and Gozani, O. (2009) ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation, Mol Cell 33, 248-256. PMID:19187765. (Pubmed)
11. Francis, N. J., Follmer, N. E., Simon, M. D., Aghia, G., and Butler, J. D. (2009) Polycomb proteins remain bound to chromatin and DNA during DNA replication in vitro, Cell 137, 110-122. PMID:19303136. (Pubmed)
10. Lu, X., Simon, M. D., Chodaparambil, J. V., Hansen, J. C., Shokat, K. M., and Luger, K. (2008) The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure, Nat Struct Mol Biol 15, 1122-1124. PMID:18794842. (Pubmed)
9. Simon, M. D., Chu, F., Racki, L. R., de la Cruz, C. C., Burlingame, A. L., Panning, B., Narlikar, G. J., and Shokat, K. M. (2007) The site-specific installation of methyl-lysine analogs into recombinant histones, Cell 128, 1003-1012. PMID:17350582. (Pubmed)
8. de la Cruz, C. C., Kirmizis, A., Simon, M. D., Isono, K., Koseki, H., and Panning, B. (2007) The polycomb group protein SUZ12 regulates histone H3 lysine 9 methylation and HP1 alpha distribution, Chromosome Res 15, 299-314. PMID:17406994. (Pubmed)
7. Simon, M.D. and Shokat, K.M. Revealing biological specify by engineering protein-ligand interactions. Chemical Biology: From Small Molecules to System Biology and Drug Discovery, Wiley, 2006.
6. Simon, M. D.*, Feldman, M. E.*, Rauh, D., Maris, A. E., Wemmer, D. E., and Shokat, K. M. (2006) Structure and properties of a re-engineered homeodomain protein-DNA interface, ACS Chem Biol 1, 755-760. PMID:17240973. (Pubmed)*equal contributions.
5. Simon, M. D., and Shokat, K. M. (2004) Adaptability at a protein-DNA interface: re-engineering the engrailed homeodomain to recognize an unnatural nucleotide, J Am Chem Soc 126, 8078-8079. PMID:15225024. (Pubmed)
4. Simon, M. D., Sato, K., Weiss, G. A., and Shokat, K. M. (2004) A phage display selection of engrailed homeodomain mutants and the importance of residue Q50, Nucleic Acids Res 32, 3623-3631. PMID:15247345. (Pubmed)
3. Sato, K., Simon, M. D., Levin, A. M., Shokat, K. M., and Weiss, G. A. (2004) Dissecting the Engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning, Chem Biol11, 1017-1023. PMID:15271360. (Pubmed)
2. Zahn, T., Eilers, M., Guo, Z., Ksebati, M., Simon, M., Scholten, J., Smith, S., and Gibbs, R. (2000) 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. J Am Chem Soc122, 153-7164.
1. Berlin, K., Jain, K.R., Simon, M.D., and Richert, C. A porphyrin embedded in DNA. (1998) J Org Chem , 63, 1527-1535.