Matt Simon, PhD

• Brett Lindenbach
• Craig B. Wilen
• David van Dijk
• Fernando de Miguel
• Giulia Biancon
• Haifan Lin
• Jesse Rinehart
• Jin Wei
• Joan Steitz
• Joerg Bewersdorf
• Karla M Neugebauer
• Katerina Politi
• Mark Gerstein
• Nadya Dimitrova
• Nils Neuenkirchen
• Qin Yan
• Sarah Slavoff
• Stephanie Halene
• Toma Tebaldi

Biochemistry; Biophysics; Chromatin; RNA, Untranslated

• Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin.Machyna M, Kiefer L, Simon MD. Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. Nature Structural & Molecular Biology 2020, 27: 297-304. PMID: 32157249, DOI: 10.1038/s41594-020-0390-z.
• Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates.Smith TS, Zoltek MA, Simon MD. Reengineering a tRNA Methyltransferase To Covalently Capture New RNA Substrates. Journal Of The American Chemical Society 2019, 141: 17460-17465. PMID: 31626536, DOI: 10.1021/jacs.9b08529.
• Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine.Kiefer L, Schofield JA, Simon MD. Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine. Journal Of The American Chemical Society 2018, 140: 14567-14570. PMID: 30353734, PMCID: PMC6779120, DOI: 10.1021/jacs.8b08554.
• TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding.Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD. TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. Nature Methods 2018, 15: 221-225. PMID: 29355846, PMCID: PMC5831505, DOI: 10.1038/nmeth.4582.
• Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry.Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD. Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. Molecular Cell 2015, 59: 858-66. PMID: 26340425, PMCID: PMC4560836, DOI: 10.1016/j.molcel.2015.07.023.
• Probing Xist RNA Structure in Cells Using Targeted Structure-Seq.Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD. Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. PLoS Genetics 2015, 11: e1005668. PMID: 26646615, PMCID: PMC4672913, DOI: 10.1371/journal.pgen.1005668.
• High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation.Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, Bowman SK, Kesner BA, Maier VK, Kingston RE, Lee JT. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 2013, 504: 465-469. PMID: 24162848, PMCID: PMC3904790, DOI: 10.1038/nature12719.
• Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA.Sexton AN, Wang PY, Rutenberg-Schoenberg M, Simon MD. Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA. Biochemistry 2017, 56: 4713-4721. PMID: 28820243, PMCID: PMC5648349, DOI: 10.1021/acs.biochem.7b00323.
• The genomic binding sites of a noncoding RNA.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. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 20497-502. PMID: 22143764, PMCID: PMC3251105, DOI: 10.1073/pnas.1113536108.
• The site-specific installation of methyl-lysine analogs into recombinant histones.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, 128: 1003-12. PMID: 17350582, PMCID: PMC2932701, DOI: 10.1016/j.cell.2006.12.041.
• Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection.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. Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell 2021, 184: 76-91.e13. PMID: 33147444, PMCID: PMC7574718, DOI: 10.1016/j.cell.2020.10.028.
• Dissecting the Engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning.Sato K, Simon MD, Levin AM, Shokat KM, Weiss GA. Dissecting the Engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning. Chemistry & Biology 2004, 11: 1017-23. PMID: 15271360, DOI: 10.1016/j.chembiol.2004.05.008.
• Catching RNAs on chromatin using hybridization capture methods.Machyna M, Simon MD. Catching RNAs on chromatin using hybridization capture methods. Briefings In Functional Genomics 2018, 17: 96-103. PMID: 29126220, PMCID: PMC5888980, DOI: 10.1093/bfgp/elx038.
• Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor.Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA. Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. Cell Chemical Biology 2021, 28: 463-474.e7. PMID: 33357462, PMCID: PMC8052284, DOI: 10.1016/j.chembiol.2020.12.003.
• Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression.Rosa-Mercado NA, Zimmer JT, Apostolidi M, Rinehart J, Simon MD, Steitz JA. Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repression. Molecular Cell 2021, 81: 502-513.e4. PMID: 33400923, PMCID: PMC7867636, DOI: 10.1016/j.molcel.2020.12.002.
• STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts.Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD. STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. Molecular Cell 2021, 81: 4398-4412.e7. PMID: 34520723, PMCID: PMC9020433, DOI: 10.1016/j.molcel.2021.08.019.
• Noncoding RNAs: biology and applications-a Keystone Symposia report.Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Annals Of The New York Academy Of Sciences 2021, 1506: 118-141. PMID: 34791665, DOI: 10.1111/nyas.14713.
• Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies.Biancon G, Joshi P, Zimmer JT, Hunck T, Gao Y, Lessard MD, Courchaine E, Barentine AES, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon MD, Neugebauer KM, Tebaldi T, Halene S. Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignancies. Molecular Cell 2022, 82: 1107-1122.e7. PMID: 35303483, PMCID: PMC8988922, DOI: 10.1016/j.molcel.2022.02.025.
• Functional elements of the cis-regulatory lincRNA-p21.Winkler L, Jimenez M, Zimmer JT, Williams A, Simon MD, Dimitrova N. Functional elements of the cis-regulatory lincRNA-p21. Cell Reports 2022, 39: 110687. PMID: 35443176, PMCID: PMC9118141, DOI: 10.1016/j.celrep.2022.110687.