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The Need for Staging System in Colony Stimulating Factor 1 Receptor-Related Disorder. Mov Disord. 2026 Feb 27. Chmiela T, Spitale RC, Henchcliffe C, Wszolek ZK. PMID: 41760093.
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Fluid and Neuroimaging Biomarkers in Microgliopathy Colony-Stimulating Factor-1 Receptor-Related Disorders. Ann Clin Transl Neurol. 2026 Jan 12. Chmiela T, Reeves M, Jansen-West K, Dunmore J, Song Y, Strongosky A, Gandhi S, Pikover G, Blurton-Jones M, Spitale RC, Middlebrooks EH, Petrucelli L, Prudencio M, Wszolek ZK. PMID: 41521943.
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Human microglia differentially respond to β-amyloid, tau, and combined Alzheimer's disease pathologies in vivo. Alzheimers Dement. 2025 Nov; 21(11):e70930. Coburn MA, Eskandari-Sedighi G, Hasselmann J, England W, Shabestari SK, Mansour K, McQuade A, Mgerian MA, Chadarevian JP, Tu C, Silva J, Beck J, Keulen Z, Spitale RC, Davtyan H, Blurton-Jones M. PMID: 41268790; PMCID: PMC12635866.
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Harnessing human iPSC-microglia for CNS-wide delivery of disease-modifying proteins. Cell Stem Cell. 2025 Jun 05; 32(6):914-934.e8. Chadarevian JP, Davtyan H, Chadarevian AL, Nguyen J, Capocchi JK, Le L, Escobar A, Chadarevian T, Mansour K, Deynega E, Mgerian M, Tu C, Kiani Shabestari S, Carlen-Jones W, Eskandari-Sedighi G, Hasselmann J, Spitale RC, Blurton-Jones M. PMID: 40233761; PMCID: PMC12360426.
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Harnessing human iPSC-microglia for CNS-wide delivery of disease-modifying proteins. Cell Stem Cell. 2025 Apr 09. Chadarevian JP, Davtyan H, Chadarevian AL, Nguyen J, Capocchi JK, Le L, Escobar A, Chadarevian T, Mansour K, Deynega E, Mgerian M, Tu C, Kiani Shabestari S, Carlen-Jones W, Eskandari-Sedighi G, Hasselmann J, Spitale RC, Blurton-Jones M. PMID: 40233761.
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Quantification of subcellular RNA localization through direct detection of RNA oxidation. Nucleic Acids Res. 2025 Feb 27; 53(5). Lo HG, Goering R, Kocere A, Lo J, Pockalny MC, White LK, Ramirez H, Martinez A, Jacobson S, Spitale RC, Pearson CG, Resendiz MJE, Mosimann C, Taliaferro JM. PMID: 40037712; PMCID: PMC11879412.
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Quantification of subcellular RNA localization through direct detection of RNA oxidation. Nucleic Acids Res. 2025 Feb 27; 53(5). Lo HG, Goering R, Kocere A, Lo J, Pockalny MC, White LK, Ramirez H, Martinez A, Jacobson S, Spitale RC, Pearson CG, Resendiz MJE, Mosimann C, Taliaferro JM. PMID: 40037712; PMCID: PMC11879412.
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Novel photocrosslinking chemical probes utilized for high-resolution spatial transcriptomics. RSC Chem Biol. 2025 Mar 05; 6(3):404-411. Spitalny L, Falco N, England W, Allred T, Spitale RC. PMID: 39845105; PMCID: PMC11748054.
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Aberrant splicing in Huntington's disease accompanies disrupted TDP-43 activity and altered m6A RNA modification. Nat Neurosci. 2025 Feb; 28(2):280-292. Nguyen TB, Miramontes R, Chillon-Marinas C, Maimon R, Vazquez-Sanchez S, Lau AL, McClure NR, Wu Z, Wang KQ, England WE, Singha M, Stocksdale JT, Heath M, Jang KH, Jung S, Ling K, Jafar-Nejad P, McKnight JI, Ho LN, Dalahmah OA, Faull RLM, Steffan JS, Reidling JC, Jang C, Lee G, Cleveland DW, Lagier-Tourenne C, Spitale RC, Thompson LM. PMID: 39762660; PMCID: PMC11802453.
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Quantification of subcellular RNA localization through direct detection of RNA oxidation. bioRxiv. 2024 Nov 12. Lo HG, Goering R, Kocere A, Lo J, Pockalny MC, White LK, Ramirez H, Martinez A, Jacobson S, Spitale RC, Pearson CG, Resendiz MJE, Mosimann C, Taliaferro JM. PMID: 39605352; PMCID: PMC11601319.
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Therapeutic potential of human microglia transplantation in a chimeric model of CSF1R-related leukoencephalopathy. Neuron. 2024 Aug 21; 112(16):2686-2707.e8. Chadarevian JP, Hasselmann J, Lahian A, Capocchi JK, Escobar A, Lim TE, Le L, Tu C, Nguyen J, Kiani Shabestari S, Carlen-Jones W, Gandhi S, Bu G, Hume DA, Pridans C, Wszolek ZK, Spitale RC, Davtyan H, Blurton-Jones M. PMID: 38897209; PMCID: PMC12357648.
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DNA G-Quadruplex Is a Transcriptional Control Device That Regulates Memory. J Neurosci. 2024 04 10; 44(15). Marshall PR, Davies J, Zhao Q, Liau WS, Lee Y, Basic D, Periyakaruppiah A, Zajaczkowski EL, Leighton LJ, Madugalle SU, Musgrove M, Kielar M, Brueckner AM, Gong H, Ren H, Walsh A, Kaczmarczyk L, Jackson WS, Chen A, Spitale RC, Bredy TW. PMID: 38418220; PMCID: PMC11007313.
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The anticancer compound JTE-607 reveals hidden sequence specificity of the mRNA 3' processing machinery. Nat Struct Mol Biol. 2023 12; 30(12):1947-1957. Liu L, Yu AM, Wang X, Soles LV, Teng X, Chen Y, Yoon Y, Sarkan KSK, Valdez MC, Linder J, England W, Spitale R, Yu Z, Marazzi I, Qiao F, Li W, Seelig G, Shi Y. PMID: 38087090; PMCID: PMC11663416.
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Fear extinction is regulated by the activity of long noncoding RNAs at the synapse. Nat Commun. 2023 11 22; 14(1):7616. Liau WS, Zhao Q, Bademosi A, Gormal RS, Gong H, Marshall PR, Periyakaruppiah A, Madugalle SU, Zajaczkowski EL, Leighton LJ, Ren H, Musgrove M, Davies J, Rauch S, He C, Dickinson BC, Li X, Wei W, Meunier FA, Fernández-Moya SM, Kiebler MA, Srinivasan B, Banerjee S, Clark M, Spitale RC, Bredy TW. PMID: 37993455; PMCID: PMC10665438.
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Aberrant splicing in Huntington's disease via disrupted TDP-43 activity accompanied by altered m6A RNA modification. bioRxiv. 2023 Nov 02. Nguyen TB, Miramontes R, Chillon-Marinas C, Maimon R, Vazquez-Sanchez S, Lau AL, McClure NR, England WE, Singha M, Stocksdale JT, Jang KH, Jung S, McKnight JI, Ho LN, Faull RLM, Steffan JS, Reidling JC, Jang C, Lee G, Cleveland DW, Lagier-Tourenne C, Spitale RC, Thompson LM. PMID: 37961595; PMCID: PMC10635028.
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Synapse-Enriched m6A-Modified Malat1 Interacts with the Novel m6A Reader, DPYSL2, and Is Required for Fear-Extinction Memory. J Neurosci. 2023 10 25; 43(43):7084-7100. Madugalle SU, Liau WS, Zhao Q, Li X, Gong H, Marshall PR, Periyakaruppiah A, Zajaczkowski EL, Leighton LJ, Ren H, Musgrove MRB, Davies JWA, Kim G, Rauch S, He C, Dickinson BC, Fulopova B, Fletcher LN, Williams SR, Spitale RC, Bredy TW. PMID: 37669863; PMCID: PMC10601377.
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Using 5' 32 P-labeled Primer and Reverse Transcription to Probe RNA Structure. Curr Protoc. 2023 Jul; 3(7):e830. Garfio CM, Gupta M, Spitale RC. PMID: 37471570.
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Overview of Chemical Methods to Probe RNA Structure with Radionucleotides. Curr Protoc. 2023 May; 3(5):e781. Gupta M, Garfio CM, Spitale RC. PMID: 37196139.
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Cycloaddition enabled mutational profiling of 5-vinyluridine in RNA. Chem Commun (Camb). 2023 Mar 14; 59(22):3257-3260. Gupta M, Wang J, Garfio CM, Vandewalle A, Spitale RC. PMID: 36815680; PMCID: PMC10089805.
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Engineering an inhibitor-resistant human CSF1R variant for microglia replacement. J Exp Med. 2023 03 06; 220(3). Chadarevian JP, Lombroso SI, Peet GC, Hasselmann J, Tu C, Marzan DE, Capocchi J, Purnell FS, Nemec KM, Lahian A, Escobar A, England W, Chaluvadi S, O'Brien CA, Yaqoob F, Aisenberg WH, Porras-Paniagua M, Bennett ML, Davtyan H, Spitale RC, Blurton-Jones M, Bennett FC. PMID: 36584406.
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An Optimized Enzyme-Nucleobase Pair Enables In Vivo RNA Metabolic Labeling with Improved Cell-Specificity. Biochemistry. 2022 12 06; 61(23):2638-2642. Singha MK, Zimak J, Levine SR, Dai N, Hong C, Anaraki C, Gupta M, Halbrook CJ, Atwood SX, Spitale RC. PMID: 36383486; PMCID: PMC10149115.
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Probing the dynamic RNA structurome and its functions. Nat Rev Genet. 2023 03; 24(3):178-196. Spitale RC, Incarnato D. PMID: 36348050; PMCID: PMC9644009.
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mRNAs encoding neurodevelopmental regulators have equal N6-methyladenosine stoichiometry in Drosophila neuroblasts and neurons. Neural Dev. 2022 10 15; 17(1):9. Sami JD, Spitale RC, Cleary MD. PMID: 36243726; PMCID: PMC9571443.
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Probing Nascent RNA with Metabolic Incorporation of Modified Nucleosides. Acc Chem Res. 2022 09 20; 55(18):2647-2659. Gupta M, Levine SR, Spitale RC. PMID: 36073807.
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A Fluorescent Reverse-Transcription Assay to Detect Chemical Adducts on RNA. Biochemistry. 2022 08 16; 61(16):1665-1668. Falco N, Garfio CM, Spitalny L, Spitale RC. PMID: 35876726; PMCID: PMC10010264.
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Reply to: On gene silencing by the X10-23 DNAzyme. Nat Chem. 2022 08; 14(8):859-861. Spitale RC, Chaput JC. PMID: 35851838.
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Repurposing a DNA-Repair Enzyme for Targeted Protein Degradation. Chembiochem. 2022 10 06; 23(19):e202200053. Fredlender C, Levine S, Zimak J, Spitale RC. PMID: 35750646; PMCID: PMC10010263.
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An atlas of posttranslational modifications on RNA binding proteins. Nucleic Acids Res. 2022 05 06; 50(8):4329-4339. England WE, Wang J, Chen S, Baldi P, Flynn RA, Spitale RC. PMID: 35438783; PMCID: PMC9071496.
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Halo-seq: An RNA Proximity Labeling Method for the Isolation and Analysis of Subcellular RNA Populations. Curr Protoc. 2022 May; 2(5):e424. Lo HG, Engel KL, Goering R, Li Y, Spitale RC, Taliaferro JM. PMID: 35532287; PMCID: PMC9097300.
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Exploiting Endogenous Enzymes for Cancer-Cell Selective Metabolic Labeling of RNA in Vivo. J Am Chem Soc. 2022 04 27; 144(16):7085-7088. Beasley S, Vandewalle A, Singha M, Nguyen K, England W, Tarapore E, Dai N, Corrêa IR, Atwood SX, Spitale RC. PMID: 35416650; PMCID: PMC10032647.
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ADRAM is an experience-dependent long noncoding RNA that drives fear extinction through a direct interaction with the chaperone protein 14-3-3. Cell Rep. 2022 03 22; 38(12):110546. Wei W, Zhao Q, Wang Z, Liau WS, Basic D, Ren H, Marshall PR, Zajaczkowski EL, Leighton LJ, Madugalle SU, Musgrove M, Periyakaruppiah A, Shi J, Zhang J, Mattick JS, Mercer TR, Spitale RC, Li X, Bredy TW. PMID: 35320727; PMCID: PMC9015815.
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Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq. Nucleic Acids Res. 2022 02 28; 50(4):e24. Engel KL, Lo HG, Goering R, Li Y, Spitale RC, Taliaferro JM. PMID: 34875090; PMCID: PMC8887463.
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The P522R protective variant of PLCG2 promotes the expression of antigen presentation genes by human microglia in an Alzheimer's disease mouse model. Alzheimers Dement. 2022 10; 18(10):1765-1778. Claes C, England WE, Danhash EP, Kiani Shabestari S, Jairaman A, Chadarevian JP, Hasselmann J, Tsai AP, Coburn MA, Sanchez J, Lim TE, Hidalgo JLS, Tu C, Cahalan MD, Lamb BT, Landreth GE, Spitale RC, Blurton-Jones M, Davtyan H. PMID: 35142046; PMCID: PMC9360195.
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Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing. Nucleic Acids Res. 2021 11 18; 49(20):11868-11882. Chan D, Feng C, England WE, Wyman D, Flynn RA, Wang X, Shi Y, Mortazavi A, Spitale RC. PMID: 34634799; PMCID: PMC8599799.
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Mutually Orthogonal Bioconjugation of Vinyl Nucleosides for RNA Metabolic Labeling. Org Lett. 2021 09 17; 23(18):7183-7187. Gupta M, Singha M, Rasale DB, Zhou Z, Bhandari S, Beasley S, Sakr J, Parker SM, Spitale RC. PMID: 34496205.
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Taylor-made production of pyrimidine nucleoside-5'-monophosphate analogues by highly stabilized mutant uracil phosphoribosyltransferase from Toxoplasma gondii. Bioresour Technol. 2021 Nov; 339:125649. Acosta J, Nguyen K, Spitale RC, Fernández-Lucas J. PMID: 34329899.
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Plaque-associated human microglia accumulate lipid droplets in a chimeric model of Alzheimer's disease. Mol Neurodegener. 2021 07 23; 16(1):50. Claes C, Danhash EP, Hasselmann J, Chadarevian JP, Shabestari SK, England WE, Lim TE, Hidalgo JLS, Spitale RC, Davtyan H, Blurton-Jones M. PMID: 34301296; PMCID: PMC8305935.
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Huntington's disease mice and human brain tissue exhibit increased G3BP1 granules and TDP43 mislocalization. J Clin Invest. 2021 06 15; 131(12). Sanchez II, Nguyen TB, England WE, Lim RG, Vu AQ, Miramontes R, Byrne LM, Markmiller S, Lau AL, Orellana I, Curtis MA, Faull RLM, Yeo GW, Fowler CD, Reidling JC, Wild EJ, Spitale RC, Thompson LM. PMID: 33945510; PMCID: PMC8203471.
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A biologically stable DNAzyme that efficiently silences gene expression in cells. Nat Chem. 2021 04; 13(4):319-326. Wang Y, Nguyen K, Spitale RC, Chaput JC. PMID: 33767363; PMCID: PMC12582164.
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Allele-Specific RNA Knockdown with a Biologically Stable and Catalytically Efficient XNAzyme. J Am Chem Soc. 2021 03 31; 143(12):4519-4523. Nguyen K, Wang Y, England WE, Chaput JC, Spitale RC. PMID: 33750115.
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Chemical methods for measuring RNA expression with metabolic labeling. Wiley Interdiscip Rev RNA. 2021 09; 12(5):e1650. Singha M, Spitalny L, Nguyen K, Vandewalle A, Spitale RC. PMID: 33738981.
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RNA structure probing to characterize RNA-protein interactions on low abundance pre-mRNA in living cells. RNA. 2021 Feb 16; 27(3):343-358. Bubenik JL, Hale M, McConnell O, Wang ET, Swanson MS, Spitale RC, Berglund JA. PMID: 33310817; PMCID: PMC7901844.
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Chemical Approaches To Analyzing RNA Structure Transcriptome-Wide. Chembiochem. 2021 04 06; 22(7):1114-1121. England WE, Garfio CM, Spitale RC. PMID: 32737940; PMCID: PMC8769560.
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Identification of novel regulators of dendrite arborization using cell type-specific RNA metabolic labeling. PLoS One. 2020; 15(12):e0240386. Aboukilila MY, Sami JD, Wang J, England W, Spitale RC, Cleary MD. PMID: 33264304; PMCID: PMC7710095.
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A Bump-Hole Strategy for Increased Stringency of Cell-Specific Metabolic Labeling of RNA. ACS Chem Biol. 2020 12 18; 15(12):3099-3105. Nguyen K, Kubota M, Arco JD, Feng C, Singha M, Beasley S, Sakr J, Gandhi SP, Blurton-Jones M, Fernández Lucas J, Spitale RC. PMID: 33222436; PMCID: PMC7814973.
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Structural disruption of exonic stem-loops immediately upstream of the intron regulates mammalian splicing. Nucleic Acids Res. 2020 06 19; 48(11):6294-6309. Saha K, England W, Fernandez MM, Biswas T, Spitale RC, Ghosh G. PMID: 32402057; PMCID: PMC7293017.
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Assaying RNA solvent accessibility in living cells with LASER. Methods Enzymol. 2020; 641:401-411. Feng C, Spitale RC. PMID: 32713532.
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Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression. Oncogenesis. 2020 Feb 18; 9(2):25. Zocchi L, Mehta A, Wu SC, Wu J, Gu Y, Wang J, Suh S, Spitale RC, Benavente CA. PMID: 32071286; PMCID: PMC7028996.
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An optimized chemical-genetic method for cell-specific metabolic labeling of RNA. Nat Methods. 2020 03; 17(3):311-318. Nainar S, Cuthbert BJ, Lim NM, England WE, Ke K, Sophal K, Quechol R, Mobley DL, Goulding CW, Spitale RC. PMID: 32015544; PMCID: PMC8518020.
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Identification of Adenosine-to-Inosine RNA Editing with Acrylonitrile Reagents. Org Lett. 2019 10 04; 21(19):7948-7951. Li Y, Göhl M, Ke K, Vanderwal CD, Spitale RC. PMID: 31516001; PMCID: PMC7308179.
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Functional Conservation of LncRNA JPX Despite Sequence and Structural Divergence. J Mol Biol. 2020 01 17; 432(2):283-300. Karner H, Webb CH, Carmona S, Liu Y, Lin B, Erhard M, Chan D, Baldi P, Spitale RC, Sun S. PMID: 31518612.
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Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo. Neuron. 2019 09 25; 103(6):1016-1033.e10. Hasselmann J, Coburn MA, England W, Figueroa Velez DX, Kiani Shabestari S, Tu CH, McQuade A, Kolahdouzan M, Echeverria K, Claes C, Nakayama T, Azevedo R, Coufal NG, Han CZ, Cummings BJ, Davtyan H, Glass CK, Healy LM, Gandhi SP, Spitale RC, Blurton-Jones M. PMID: 31375314; PMCID: PMC7138101.
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Expanding the Scope of RNA Metabolic Labeling with Vinyl Nucleosides and Inverse Electron-Demand Diels-Alder Chemistry. ACS Chem Biol. 2019 08 16; 14(8):1698-1707. Kubota M, Nainar S, Parker SM, England W, Furche F, Spitale RC. PMID: 31310712; PMCID: PMC8061575.
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The DNA modification N6-methyl-2'-deoxyadenosine (m6dA) drives activity-induced gene expression and is required for fear extinction. Nat Neurosci. 2019 04; 22(4):534-544. Li X, Zhao Q, Wei W, Lin Q, Magnan C, Emami MR, Wearick-Silva LE, Viola TW, Marshall PR, Yin J, Madugalle SU, Wang Z, Nainar S, Vågbø CB, Leighton LJ, Zajaczkowski EL, Ke K, Grassi-Oliveira R, Bjørås M, Baldi PF, Spitale RC, Bredy TW. PMID: 30778148; PMCID: PMC6462436.
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Assaying RNA structure with LASER-Seq. Nucleic Acids Res. 2019 01 10; 47(1):43-55. Zinshteyn B, Chan D, England W, Feng C, Green R, Spitale RC. PMID: 30476193; PMCID: PMC6326810.
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Biochemical Methods To Image and Analyze RNA Localization: From One to Many. Biochemistry. 2019 02 05; 58(5):379-386. Li Y, Ke K, Spitale RC. PMID: 30444114.
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Protected pyrimidine nucleosides for cell-specific metabolic labeling of RNA. Tetrahedron Lett. 2018 Oct 31; 59(44):3912-3915. Beasley S, Nguyen K, Fazio M, Spitale RC. PMID: 31031425; PMCID: PMC6483386.
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Bioorthogonal Metabolic Labeling of Nascent RNA in Neurons Improves the Sensitivity of Transcriptome-Wide Profiling. ACS Chem Neurosci. 2018 07 18; 9(7):1858-1865. Zajaczkowski EL, Zhao QY, Zhang ZH, Li X, Wei W, Marshall PR, Leighton LJ, Nainar S, Feng C, Spitale RC, Bredy TW. PMID: 29874042; PMCID: PMC6272126.
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Spatially Restricting Bioorthogonal Nucleoside Biosynthesis Enables Selective Metabolic Labeling of the Mitochondrial Transcriptome. ACS Chem Biol. 2018 06 15; 13(6):1474-1479. Nguyen K, Aggarwal MB, Feng C, Balderrama G, Fazio M, Mortazavi A, Spitale RC. PMID: 29756767; PMCID: PMC6234202.
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Improved Analysis of RNA Localization by Spatially Restricted Oxidation of RNA-Protein Complexes. Biochemistry. 2018 03 13; 57(10):1577-1581. Li Y, Aggarwal MB, Ke K, Nguyen K, Spitale RC. PMID: 29474061; PMCID: PMC6234203.
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Light-activated chemical probing of nucleobase solvent accessibility inside cells. Nat Chem Biol. 2018 02 14; 14(3):325. Feng C, Chan D, Joseph J, Muuronen M, Coldren WH, Dai N, Corrêa IR, Furche F, Hadad CM, Spitale RC. PMID: 29443971.
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Facile synthesis and evaluation of a dual-functioning furoyl probe for in-cell SHAPE. Bioorg Med Chem Lett. 2018 02 15; 28(4):601-605. Chan D, Beasley S, Zhen Y, Spitale RC. PMID: 29398542; PMCID: PMC6258071.
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Light-activated chemical probing of nucleobase solvent accessibility inside cells. Nat Chem Biol. 2018 03; 14(3):276-283. Feng C, Chan D, Joseph J, Muuronen M, Coldren WH, Dai N, Corrêa IR, Furche F, Hadad CM, Spitale RC. PMID: 29334380; PMCID: PMC6203945.
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Defining Functional Structured RNA inside Living Cells. Biochemistry. 2017 11 07; 56(44):5847-5848. Chan D, Spitale RC. PMID: 29064690.
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Experience-dependent neural plasticity, learning, and memory in the era of epitranscriptomics. Genes Brain Behav. 2018 03; 17(3):e12426. Leighton LJ, Ke K, Zajaczkowski EL, Edmunds J, Spitale RC, Bredy TW. PMID: 28926184; PMCID: PMC5858957.
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Assaying RNA Localization in Situ with Spatially Restricted Nucleobase Oxidation. ACS Chem Biol. 2017 11 17; 12(11):2709-2714. Li Y, Aggarwal MB, Nguyen K, Ke K, Spitale RC. PMID: 28952711.
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Initial in vitro functional characterization of serum exosomal microRNAs from patients with metastatic basal cell carcinoma. Br J Dermatol. 2017 11; 177(5):e187-e190. Chang J, Tran DC, Zhu GA, Li R, Whitson R, Kim YH, Gupta A, Afshari A, Antes T, Spitale RC, Chang ALS. PMID: 28369780.
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EC-tagging allows cell type-specific RNA analysis. Nucleic Acids Res. 2017 Sep 06; 45(15):e138. Hida N, Aboukilila MY, Burow DA, Paul R, Greenberg MM, Fazio M, Beasley S, Spitale RC, Cleary MD. PMID: 28641402; PMCID: PMC5587779.
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Multiplex Aptamer Discovery through Apta-Seq and Its Application to ATP Aptamers Derived from Human-Genomic SELEX. ACS Chem Biol. 2017 08 18; 12(8):2149-2156. Abdelsayed MM, Ho BT, Vu MMK, Polanco J, Spitale RC, Lupták A. PMID: 28661647; PMCID: PMC5775184.
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MotifMap-RNA: a genome-wide map of RBP binding sites. Bioinformatics. 2017 Jul 01; 33(13):2029-2031. Liu Y, Sun S, Bredy T, Wood M, Spitale RC, Baldi P. PMID: 28334276.
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Photo-controlled cell-specific metabolic labeling of RNA. Org Biomol Chem. 2017 Jun 21; 15(24):5117-5120. Feng C, Li Y, Spitale RC. PMID: 28569333; PMCID: PMC6193551.
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Temporal Labeling of Nascent RNA Using Photoclick Chemistry in Live Cells. J Am Chem Soc. 2017 06 21; 139(24):8090-8093. Nainar S, Kubota M, McNitt C, Tran C, Popik VV, Spitale RC. PMID: 28562039.
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Comparative Analysis Reveals Furoyl in Vivo Selective Hydroxyl Acylation Analyzed by Primer Extension Reagents Form Stable Ribosyl Ester Adducts. Biochemistry. 2017 Apr 04; 56(13):1811-1814. Chan D, Feng C, Zhen Y, Flynn RA, Spitale RC. PMID: 28319368; PMCID: PMC10884885.
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Measuring RNA structure transcriptome-wide with icSHAPE. Methods. 2017 05 01; 120:85-90. Chan D, Feng C, Spitale RC. PMID: 28336307; PMCID: PMC6193560.
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Cell-Selective Bioorthogonal Metabolic Labeling of RNA. J Am Chem Soc. 2017 02 15; 139(6):2148-2151. Nguyen K, Fazio M, Kubota M, Nainar S, Feng C, Li X, Atwood SX, Bredy TW, Spitale RC. PMID: 28139910.
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Assaying RNA Structure Inside Living Cells with SHAPE. Methods Mol Biol. 2017; 1648:247-256. Feng C, Chan D, Spitale RC. PMID: 28766302.
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Novel Gene Expression Profile of Women with Intrinsic Skin Youthfulness by Whole Transcriptome Sequencing. PLoS One. 2016; 11(11):e0165913. Xu J, Spitale RC, Guan L, Flynn RA, Torre EA, Li R, Raber I, Qu K, Kern D, Knaggs HE, Chang HY, Chang AL. PMID: 27829007; PMCID: PMC5102383.
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Metabolic Incorporation of Azide Functionality into Cellular RNA. Chembiochem. 2016 Nov 17; 17(22):2149-2152. Nainar S, Beasley S, Fazio M, Kubota M, Dai N, Corrêa IR, Spitale RC. PMID: 27595557; PMCID: PMC5115926.
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Evolving insights into RNA modifications and their functional diversity in the brain. Nat Neurosci. 2016 09 27; 19(10):1292-8. Nainar S, Marshall PR, Tyler CR, Spitale RC, Bredy TW. PMID: 27669990; PMCID: PMC5068363.
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Chemical Tools for Dissecting the Role of lncRNAs in Epigenetic Regulation. ACS Chem Biol. 2016 08 19; 11(8):2091-100. Nainar S, Feng C, Spitale RC. PMID: 27267401; PMCID: PMC5068361.
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Defining the identity of mouse embryonic dermal fibroblasts. Genesis. 2016 08; 54(8):415-30. Budnick I, Hamburg-Shields E, Chen D, Torre E, Jarrell A, Akhtar-Zaidi B, Cordovan O, Spitale RC, Scacheri P, Atit RP. PMID: 27265328; PMCID: PMC4990491.
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Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. Cell Metab. 2016 05 10; 23(5):909-20. Arda HE, Li L, Tsai J, Torre EA, Rosli Y, Peiris H, Spitale RC, Dai C, Gu X, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, Bottino R, Powers AC, Chang HY, Kim SK. PMID: 27133132; PMCID: PMC4864151.
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Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nat Protoc. 2016 Feb; 11(2):273-90. Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. PMID: 26766114; PMCID: PMC4896316.
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The CDKN2A/p16(INK) (4a) 5'UTR sequence and translational regulation: impact of novel variants predisposing to melanoma. Pigment Cell Melanoma Res. 2016 Mar; 29(2):210-21. Andreotti V, Bisio A, Bressac-de Paillerets B, Harland M, Cabaret O, Newton-Bishop J, Pastorino L, Bruno W, Bertorelli R, De Sanctis V, Provenzani A, Menin C, Fronza G, Queirolo P, Spitale RC, Bianchi-Scarrà G, Inga A, Ghiorzo P. PMID: 26581427.
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The 5'-untranslated region of p16INK4a melanoma tumor suppressor acts as a cellular IRES, controlling mRNA translation under hypoxia through YBX1 binding. Oncotarget. 2015 Nov 24; 6(37):39980-94. Bisio A, Latorre E, Andreotti V, Bressac-de Paillerets B, Harland M, Scarra GB, Ghiorzo P, Spitale RC, Provenzani A, Inga A. PMID: 26498684; PMCID: PMC4741874.
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Progress and challenges for chemical probing of RNA structure inside living cells. Nat Chem Biol. 2015 Dec; 11(12):933-41. Kubota M, Tran C, Spitale RC. PMID: 26575240; PMCID: PMC5068366.
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The emerging functions of regulatory RNA species in skin biology. Exp Dermatol. 2015 Nov; 24(11):827-8. Beasley SM, Plikus MV, Spitale RC, Pedersen IM. PMID: 26309056; PMCID: PMC4715513.
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Erratum: Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 2015 Nov 12; 527(7577):264. Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. PMID: 26416736; PMCID: PMC6545576.
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RNA structure: merging chemistry and genomics for a holistic perspective. Bioessays. 2015 Oct; 37(10):1129-38. Kubota M, Chan D, Spitale RC. PMID: 26288173.
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Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proc Natl Acad Sci U S A. 2015 Jul 07; 112(27):E3485-94. Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE. PMID: 26106162; PMCID: PMC4500280.
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Structural imprints in vivo decode RNA regulatory mechanisms. Nature. 2015 Mar 26; 519(7544):486-90. Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY. PMID: 25799993; PMCID: PMC4376618.
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Assessment of the genetic basis of rosacea by genome-wide association study. J Invest Dermatol. 2015 Jun; 135(6):1548-1555. Chang ALS, Raber I, Xu J, Li R, Spitale R, Chen J, Kiefer AK, Tian C, Eriksson NK, Hinds DA, Tung JY. PMID: 25695682; PMCID: PMC4434179.
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Technologies to probe functions and mechanisms of long noncoding RNAs. Nat Struct Mol Biol. 2015 Jan; 22(1):29-35. Chu C, Spitale RC, Chang HY. PMID: 25565030.
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RNA helicase DDX21 coordinates transcription and ribosomal RNA processing. Nature. 2015 Feb 12; 518(7538):249-53. Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J. PMID: 25470060; PMCID: PMC4827702.
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Dissecting noncoding and pathogen RNA-protein interactomes. RNA. 2015 Jan; 21(1):135-43. Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY. PMID: 25411354; PMCID: PMC4274633.
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RNA structural analysis by evolving SHAPE chemistry. Wiley Interdiscip Rev RNA. 2014 Nov-Dec; 5(6):867-81. Spitale RC, Flynn RA, Torre EA, Kool ET, Chang HY. PMID: 25132067; PMCID: PMC5592018.
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Molecular targets of aspirin and cancer prevention. Br J Cancer. 2014 Jul 08; 111(1):61-7. Alfonso L, Ai G, Spitale RC, Bhat GJ. PMID: 24874482; PMCID: PMC4090734.
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Landscape and variation of RNA secondary structure across the human transcriptome. Nature. 2014 Jan 30; 505(7485):706-9. Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. PMID: 24476892; PMCID: PMC3973747.
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Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol Cell. 2013 Jul 25; 51(2):156-73. Ilik IA, Quinn JJ, Georgiev P, Tavares-Cadete F, Maticzka D, Toscano S, Wan Y, Spitale RC, Luscombe N, Backofen R, Chang HY, Akhtar A. PMID: 23870142; PMCID: PMC3804161.
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Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013 Jan 10; 493(7431):231-5. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA. PMID: 23201690; PMCID: PMC3674581.
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RNA SHAPE analysis in living cells. Nat Chem Biol. 2013 Jan; 9(1):18-20. Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY. PMID: 23178934; PMCID: PMC3706714.
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Differential effects of dietary supplements on metabolomic profile of smokers versus non-smokers. Genome Med. 2012 Feb 23; 4(2):14. Spitale RC, Cheng MY, Chun KA, Gorell ES, Munoz CA, Kern DG, Wood SM, Knaggs HE, Wulff J, Beebe KD, Chang AL. PMID: 22360970; PMCID: PMC3392760.
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Understanding the transcriptome through RNA structure. Nat Rev Genet. 2011 Aug 18; 12(9):641-55. Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY. PMID: 21850044; PMCID: PMC3858389.
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RNA templating the epigenome: long noncoding RNAs as molecular scaffolds. Epigenetics. 2011 May; 6(5):539-43. Spitale RC, Tsai MC, Chang HY. PMID: 21393997; PMCID: PMC3230545.
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Long intergenic noncoding RNAs: new links in cancer progression. Cancer Res. 2011 Jan 01; 71(1):3-7. Tsai MC, Spitale RC, Chang HY. PMID: 21199792; PMCID: PMC3057914.
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Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation. J Am Chem Soc. 2009 Sep 16; 131(36):12908-9. Guo M, Spitale RC, Volpini R, Krucinska J, Cristalli G, Carey PR, Wedekind JE. PMID: 19702306; PMCID: PMC2776658.
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Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core. Biochemistry. 2009 Aug 25; 48(33):7777-9. Spitale RC, Volpini R, Mungillo MV, Krucinska J, Cristalli G, Wedekind JE. PMID: 19634899; PMCID: PMC2754253.
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Exploring ribozyme conformational changes with X-ray crystallography. Methods. 2009 Oct; 49(2):87-100. Spitale RC, Wedekind JE. PMID: 19559088; PMCID: PMC2782588.
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Identification of an imino group indispensable for cleavage by a small ribozyme. J Am Chem Soc. 2009 May 06; 131(17):6093-5. Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE. PMID: 19354216; PMCID: PMC2692201.
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The structural basis for recognition of the PreQ0 metabolite by an unusually small riboswitch aptamer domain. J Biol Chem. 2009 Apr 24; 284(17):11012-6. Spitale RC, Torelli AT, Krucinska J, Bandarian V, Wedekind JE. PMID: 19261617; PMCID: PMC2670106.
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Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme. Biochem Biophys Res Commun. 2008 Jun 20; 371(1):154-8. Torelli AT, Spitale RC, Krucinska J, Wedekind JE. PMID: 18423397; PMCID: PMC2464297.
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Efficient syntheses of 5'-deoxy-5'-fluoroguanosine and -inosine. J Org Chem. 2007 Oct 26; 72(22):8551-4. Spitale RC, Heller MG, Pelly AJ, Wedekind JE. PMID: 17902696; PMCID: PMC2546599.
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A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme. Acta Crystallogr D Biol Crystallogr. 2007 Jul; 63(Pt 7):812-25. MacElrevey C, Spitale RC, Krucinska J, Wedekind JE. PMID: 17582172; PMCID: PMC2483500.
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[Study of visual-perceptive ability in patients with parkinsonism]. Acta Neurol (Napoli). 1981 Feb; 3(1):197-203. Villardita C, Smirni P, Le Pira F, Spitale R, Zappala G. PMID: 7246292.
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[Visual perceptive ability in Parkinson patients]. Acta Neurol Quad (Napoli). 1981; 42:197-203. Villardita C, Smirni P, Le Pira F, Spitale R, Zappala G. PMID: 7270050.
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