Matt Simon, PhD

• Andrew Xiao
• Anna Marie Pyle
• Craig B. Wilen
• Craig M Crews
• David van Dijk
• Haifan Lin
• Joan Steitz
• Karla M Neugebauer
• Qin Yan
• Richard Flavell
• Richard Kibbey
• Stephanie Halene

Biochemistry; Biophysics; Chromatin; RNA, Untranslated

• STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcriptsZimmer 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.
• Acetyl-methyllysine marks chromatin at active transcription start sitesLu-Culligan W, Connor L, Xie Y, Ekundayo B, Rose B, Machyna M, Pintado-Urbanc A, Zimmer J, Vock I, Bhanu N, King M, Garcia B, Bleichert F, Simon M. Acetyl-methyllysine marks chromatin at active transcription start sites. Nature 2023, 622: 173-179. PMID: 37731000, PMCID: PMC10845139, DOI: 10.1038/s41586-023-06565-9.
• Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatinMachyna 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.
• TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recodingSchofield 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.
• High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivationSimon 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.
• ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability controlGao Y, Zimmer J, Vasic R, Liu C, Gbyli R, Zheng S, Patel A, Liu W, Qi Z, Li Y, Nelakanti R, Song Y, Biancon G, Xiao A, Slavoff S, Kibbey R, Flavell R, Simon M, Tebaldi T, Li H, Halene S. ALKBH5 modulates hematopoietic stem and progenitor cell energy metabolism through m6A modification-mediated RNA stability control. Cell Reports 2023, 42: 113163. PMID: 37742191, PMCID: PMC10636609, DOI: 10.1016/j.celrep.2023.113163.
• Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1Abini-Agbomson S, Gretarsson K, Shih R, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon M, Armache J, Nudler E, Narlikar G, Liu S, Lu C, Armache K. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Molecular Cell 2023, 83: 2872-2883.e7. PMID: 37595555, DOI: 10.1016/j.molcel.2023.07.020.
• Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seqPatel S, Sexton A, Strine M, Wilen C, Simon M, Pyle A. Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq. Nature Communications 2023, 14: 3426. PMID: 37296103, PMCID: PMC10255950, DOI: 10.1038/s41467-023-38623-1.
• bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modelingVock I, Simon M. bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling. RNA 2023, 29: 958-976. PMID: 37028916, PMCID: PMC10275263, DOI: 10.1261/rna.079451.122.
• Internally controlled RNA sequencing comparisons using nucleoside recoding chemistryCourvan MCS, Niederer RO, Vock IW, Kiefer L, Gilbert WV, Simon MD. Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry. Nucleic Acids Research 2022, 50: e110-e110. PMID: 36018791, PMCID: PMC9638901, DOI: 10.1093/nar/gkac693.
• Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTACSwartzel JC, Bond MJ, Pintado-Urbanc AP, Daftary M, Krone MW, Douglas T, Carder EJ, Zimmer JT, Maeda T, Simon MD, Crews CM. Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC. ACS Chemical Biology 2022, 17: 1789-1798. PMID: 35749470, PMCID: PMC10367122, DOI: 10.1021/acschembio.2c00145.
• Functional elements of the cis-regulatory lincRNA-p21Winkler 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.
• Precision analysis of mutant U2AF1 activity reveals deployment of stress granules in myeloid malignanciesBiancon 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.
• Noncoding RNAs: biology and applications—a Keystone Symposia reportCable J, Heard E, Hirose T, Prasanth KV, Chen L, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen C, 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, PMCID: PMC9808899, DOI: 10.1111/nyas.14713.
• ALKBH5 Modulates Hematopoietic Stem and Progenitor Cell Energy Metabolism through m 6a Modification-Mediated RNA StabilityGao Y, Zimmer J, Vasic R, Liu C, Gbyli R, Zheng S, Patel A, Wei L, Nelakanti R, Song Y, Biancon G, Xiao A, Slavoff S, Simon M, Flavell R, Tebaldi T, Li H, Halene S. ALKBH5 Modulates Hematopoietic Stem and Progenitor Cell Energy Metabolism through m 6a Modification-Mediated RNA Stability. Blood 2021, 138: 298. DOI: 10.1182/blood-2021-146049.
• U2AF1 Mutations Enhance Stress Granule Response in Myeloid MalignanciesBiancon G, Joshi P, Zimmer J, Hunck T, Gao Y, Lessard M, Courchaine E, Barentine A, Machyna M, Botti V, Qin A, Gbyli R, Patel A, Song Y, Kiefer L, Viero G, Neuenkirchen N, Lin H, Bewersdorf J, Simon M, Neugebauer K, Tebaldi T, Halene S. U2AF1 Mutations Enhance Stress Granule Response in Myeloid Malignancies. Blood 2021, 138: 321. DOI: 10.1182/blood-2021-149618.
• Hyperosmotic stress alters the RNA polymerase II interactome and induces readthrough transcription despite widespread transcriptional repressionRosa-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.
• Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitorLuo 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 2020, 28: 463-474.e7. PMID: 33357462, PMCID: PMC8052284, DOI: 10.1016/j.chembiol.2020.12.003.
• High-Resolution Binding Atlas of U2AF1 Mutants Uncovers New Complexity in Splicing Alterations and Kinetics in Myeloid MalignanciesBiancon G, Joshi P, Hunck T, Zimmer J, Gao Y, Machyna M, Botti V, Qin A, Viero G, Neuenkirchen N, Taylor A, Gbyli R, Patel A, Ardasheva A, Fu X, Lin H, Simon M, Neugebauer K, Tebaldi T, Halene S. High-Resolution Binding Atlas of U2AF1 Mutants Uncovers New Complexity in Splicing Alterations and Kinetics in Myeloid Malignancies. Blood 2020, 136: 3-4. DOI: 10.1182/blood-2020-142854.
• Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 InfectionWei 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 2020, 184: 76-91.e13. PMID: 33147444, PMCID: PMC7574718, DOI: 10.1016/j.cell.2020.10.028.
• Reengineering a tRNA Methyltransferase To Covalently Capture New RNA SubstratesSmith 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.
• Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter ChoiceCanzio D, Nwakeze CL, Horta A, Rajkumar SM, Coffey EL, Duffy EE, Duffié R, Monahan K, O'Keeffe S, Simon MD, Lomvardas S, Maniatis T. Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice. Cell 2019, 177: 639-653.e15. PMID: 30955885, PMCID: PMC6823843, DOI: 10.1016/j.cell.2019.03.008.
• Carbodiimide reagents for the chemical probing of RNA structure in cellsWang PY, Sexton AN, Culligan WJ, Simon MD. Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA 2018, 25: 135-146. PMID: 30389828, PMCID: PMC6298570, DOI: 10.1261/rna.067561.118.
• Gaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridineDuffy EE, Schofield JA, Simon MD. Gaining insight into transcriptome‐wide RNA population dynamics through the chemistry of 4‐thiouridine. Wiley Interdisciplinary Reviews - RNA 2018, 10: e1513. PMID: 30370679, PMCID: PMC6768404, DOI: 10.1002/wrna.1513.
• Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6‑ThioguanosineKiefer 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.
• Solid phase chemistry to covalently and reversibly capture thiolated RNADuffy EE, Canzio D, Maniatis T, Simon MD. Solid phase chemistry to covalently and reversibly capture thiolated RNA. Nucleic Acids Research 2018, 46: gky556-. PMID: 29986098, PMCID: PMC6101502, DOI: 10.1093/nar/gky556.
• Catching RNAs on chromatin using hybridization capture methodsMachyna M, Simon MD. Catching RNAs on chromatin using hybridization capture methods. Briefings In Functional Genomics 2017, 17: 96-103. PMID: 29126220, PMCID: PMC5888980, DOI: 10.1093/bfgp/elx038.
• Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNASexton 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.
• Probing Xist RNA Structure in Cells Using Targeted Structure-SeqFang 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.
• Tracking Distinct RNA Populations Using Efficient and Reversible Covalent ChemistryDuffy 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: 858-866. PMID: 26340425, PMCID: PMC4560836, DOI: 10.1016/j.molcel.2015.07.023.
• The Properties of Long Noncoding RNAs that Regulate ChromatinRutenberg-Schoenberg M, Sexton A, Simon M. The Properties of Long Noncoding RNAs that Regulate Chromatin. Annual Review Of Genomics And Human Genetics 2014, 17: 1-26. DOI: 10.1146/annurev-genom-090314-024939.
• The genomic binding sites of a noncoding RNASimon 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: 20497-20502. PMID: 22143764, PMCID: PMC3251105, DOI: 10.1073/pnas.1113536108.
• The Site-Specific Installation of Methyl-Lysine Analogs into Recombinant HistonesSimon 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: 1003-1012. PMID: 17350582, PMCID: PMC2932701, DOI: 10.1016/j.cell.2006.12.041.
• Dissecting the Engrailed Homeodomain-DNA Interaction by Phage-Displayed Shotgun ScanningSato K, Simon MD, Levin AM, Shokat KM, Weiss GA. Dissecting the Engrailed Homeodomain-DNA Interaction by Phage-Displayed Shotgun Scanning. Cell Chemical Biology 2004, 11: 1017-1023. PMID: 15271360, DOI: 10.1016/j.chembiol.2004.05.008.