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Tissue-specific changes in the RNA structurome mediate salinity response in Arabidopsis.

Tack DC, Su Z, Yu Y, Bevilacqua PC, Assmann SM.

RNA. 2020 Jan 14. pii: rna.072850.119. doi: 10.1261/rna.072850.119. [Epub ahead of print]


mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity.

Waldron JA, Tack DC, Ritchey LE, Gillen SL, Wilczynska A, Turro E, Bevilacqua PC, Assmann SM, Bushell M, Le Quesne J.

Genome Biol. 2019 Dec 30;20(1):300. doi: 10.1186/s13059-019-1901-2.


Nucleotide exchange-dependent and nucleotide exchange-independent functions of plant heterotrimeric GTP-binding proteins.

Maruta N, Trusov Y, Chakravorty D, Urano D, Assmann SM, Botella JR.

Sci Signal. 2019 Nov 5;12(606). pii: eaav9526. doi: 10.1126/scisignal.aav9526.


Metabolomics of red-light-induced stomatal opening in Arabidopsis thaliana: Coupling with abscisic acid and jasmonic acid metabolism.

Zhu M, Geng S, Chakravorty D, Guan Q, Chen S, Assmann SM.

Plant J. 2019 Nov 2. doi: 10.1111/tpj.14594. [Epub ahead of print]


Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling.

Maheshwari P, Du H, Sheen J, Assmann SM, Albert R.

PLoS Comput Biol. 2019 Oct 28;15(10):e1007429. doi: 10.1371/journal.pcbi.1007429. eCollection 2019 Oct.


Probing RNA structure in vivo.

Mitchell D 3rd, Assmann SM, Bevilacqua PC.

Curr Opin Struct Biol. 2019 Dec;59:151-158. doi: 10.1016/ Epub 2019 Sep 13. Review.


The Role of Dwarfing Traits in Historical and Modern Agriculture with a Focus on Rice.

Ferrero-Serrano Á, Cantos C, Assmann SM.

Cold Spring Harb Perspect Biol. 2019 Nov 1;11(11). pii: a034645. doi: 10.1101/cshperspect.a034645. Review.


Directions for research and training in plant omics: Big Questions and Big Data.

Argueso CT, Assmann SM, Birnbaum KD, Chen S, Dinneny JR, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall-Colón A, Mason GA, O'Lexy R, Peck SC, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM.

Plant Direct. 2019 Apr 23;3(4):e00133. doi: 10.1002/pld3.133. eCollection 2019 Apr.


In Vivo Genome-Wide RNA Structure Probing with Structure-seq.

Ritchey LE, Su Z, Assmann SM, Bevilacqua PC.

Methods Mol Biol. 2019;1933:305-341. doi: 10.1007/978-1-4939-9045-0_20.


The Arabidopsis heterotrimeric G-protein β subunit, AGB1, is required for guard cell calcium sensing and calcium-induced calcium release.

Jeon BW, Acharya BR, Assmann SM.

Plant J. 2019 Jul;99(2):231-244. doi: 10.1111/tpj.14318. Epub 2019 Apr 30.


Phenotypic and genome-wide association with the local environment of Arabidopsis.

Ferrero-Serrano Á, Assmann SM.

Nat Ecol Evol. 2019 Feb;3(2):274-285. doi: 10.1038/s41559-018-0754-5. Epub 2019 Jan 14.


G protein subunit phosphorylation as a regulatory mechanism in heterotrimeric G protein signaling in mammals, yeast, and plants.

Chakravorty D, Assmann SM.

Biochem J. 2018 Nov 9;475(21):3331-3357. doi: 10.1042/BCJ20160819. Review.


Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance.

Su Z, Tang Y, Ritchey LE, Tack DC, Zhu M, Bevilacqua PC, Assmann SM.

Proc Natl Acad Sci U S A. 2018 Nov 27;115(48):12170-12175. doi: 10.1073/pnas.1807988115. Epub 2018 Nov 9.


Evolution and Structural Characteristics of Plant Voltage-Gated K+ Channels.

Jegla T, Busey G, Assmann SM.

Plant Cell. 2018 Dec;30(12):2898-2909. doi: 10.1105/tpc.18.00523. Epub 2018 Nov 1. Review.


In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC).

Mitchell D 3rd, Renda AJ, Douds CA, Babitzke P, Assmann SM, Bevilacqua PC.

RNA. 2019 Jan;25(1):147-157. doi: 10.1261/rna.067868.118. Epub 2018 Oct 19.


Technique Development for Probing RNA Structure In Vivo and Genome-Wide.

Bevilacqua PC, Assmann SM.

Cold Spring Harb Perspect Biol. 2018 Oct 1;10(10). pii: a032250. doi: 10.1101/cshperspect.a032250. Review.


A kinase-dead version of FERONIA receptor-like kinase has dose-dependent impacts on rosette morphology and RALF1-mediated stomatal movements.

Chakravorty D, Yu Y, Assmann SM.

FEBS Lett. 2018 Oct;592(20):3429-3437. doi: 10.1002/1873-3468.13249. Epub 2018 Sep 24.


Inter-relationships between the heterotrimeric Gβ subunit AGB1, the receptor-like kinase FERONIA, and RALF1 in salinity response.

Yu Y, Assmann SM.

Plant Cell Environ. 2018 Oct;41(10):2475-2489. doi: 10.1111/pce.13370. Epub 2018 Jul 24.


RNA structure: A LASER-focused view into cells.

Bevilacqua PC, Assmann SM.

Nat Chem Biol. 2018 Feb 14;14(3):200-201. doi: 10.1038/nchembio.2570. No abstract available.


StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis.

Tack DC, Tang Y, Ritchey LE, Assmann SM, Bevilacqua PC.

Methods. 2018 Jul 1;143:12-15. doi: 10.1016/j.ymeth.2018.01.018. Epub 2018 Feb 2.


The G Protein β-Subunit, AGB1, Interacts with FERONIA in RALF1-Regulated Stomatal Movement.

Yu Y, Chakravorty D, Assmann SM.

Plant Physiol. 2018 Mar;176(3):2426-2440. doi: 10.1104/pp.17.01277. Epub 2018 Jan 4.


Illuminating the role of the Gα heterotrimeric G protein subunit, RGA1, in regulating photoprotection and photoavoidance in rice.

Ferrero-Serrano Á, Su Z, Assmann SM.

Plant Cell Environ. 2018 Feb;41(2):451-468. doi: 10.1111/pce.13113. Epub 2018 Jan 9.


The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. No abstract available.


Modeling RNA secondary structure folding ensembles using SHAPE mapping data.

Spasic A, Assmann SM, Bevilacqua PC, Mathews DH.

Nucleic Acids Res. 2018 Jan 9;46(1):314-323. doi: 10.1093/nar/gkx1057.


Glyoxals as in vivo RNA structural probes of guanine base-pairing.

Mitchell D 3rd, Ritchey LE, Park H, Babitzke P, Assmann SM, Bevilacqua PC.

RNA. 2018 Jan;24(1):114-124. doi: 10.1261/rna.064014.117. Epub 2017 Oct 13.


A new discrete dynamic model of ABA-induced stomatal closure predicts key feedback loops.

Albert R, Acharya BR, Jeon BW, Zañudo JGT, Zhu M, Osman K, Assmann SM.

PLoS Biol. 2017 Sep 22;15(9):e2003451. doi: 10.1371/journal.pbio.2003451. eCollection 2017 Sep.


Redox regulation of a guard cell SNF1-related protein kinase in Brassica napus, an oilseed crop.

Zhu M, Zhang T, Ji W, Silva-Sanchez C, Song WY, Assmann SM, Harmon AC, Chen S.

Biochem J. 2017 Jul 17;474(15):2585-2599. doi: 10.1042/BCJ20170070.


Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo.

Ritchey LE, Su Z, Tang Y, Tack DC, Assmann SM, Bevilacqua PC.

Nucleic Acids Res. 2017 Aug 21;45(14):e135. doi: 10.1093/nar/gkx533.


Bridging the gap between in vitro and in vivo RNA folding.

Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC.

Q Rev Biophys. 2016 Jan;49:e10. Epub 2016 Jun 24.


Genome-Wide Analysis of RNA Secondary Structure.

Bevilacqua PC, Ritchey LE, Su Z, Assmann SM.

Annu Rev Genet. 2016 Nov 23;50:235-266. Epub 2016 Sep 14. Review.


Guard cell sensory systems: recent insights on stomatal responses to light, abscisic acid, and CO2.

Assmann SM, Jegla T.

Curr Opin Plant Biol. 2016 Oct;33:157-167. doi: 10.1016/j.pbi.2016.07.003. Epub 2016 Aug 9. Review.


The α-subunit of the rice heterotrimeric G protein, RGA1, regulates drought tolerance during the vegetative phase in the dwarf rice mutant d1.

Ferrero-Serrano Á, Assmann SM.

J Exp Bot. 2016 May;67(11):3433-43. doi: 10.1093/jxb/erw183. Epub 2016 May 18.


Molecular and systems approaches towards drought-tolerant canola crops.

Zhu M, Monroe JG, Suhail Y, Villiers F, Mullen J, Pater D, Hauser F, Jeon BW, Bader JS, Kwak JM, Schroeder JI, McKay JK, Assmann SM.

New Phytol. 2016 Jun;210(4):1169-89. doi: 10.1111/nph.13866. Epub 2016 Feb 16. Review.


Protein Structure Is Related to RNA Structural Reactivity In Vivo.

Tang Y, Assmann SM, Bevilacqua PC.

J Mol Biol. 2016 Feb 27;428(5 Pt A):758-766. doi: 10.1016/j.jmb.2015.11.012. Epub 2015 Nov 17.


Preparation of Epidermal Peels and Guard Cell Protoplasts for Cellular, Electrophysiological, and -Omics Assays of Guard Cell Function.

Zhu M, Jeon BW, Geng S, Yu Y, Balmant K, Chen S, Assmann SM.

Methods Mol Biol. 2016;1363:89-121. doi: 10.1007/978-1-4939-3115-6_9.


50 years of Arabidopsis research: highlights and future directions.

Provart NJ, Alonso J, Assmann SM, Bergmann D, Brady SM, Brkljacic J, Browse J, Chapple C, Colot V, Cutler S, Dangl J, Ehrhardt D, Friesner JD, Frommer WB, Grotewold E, Meyerowitz E, Nemhauser J, Nordborg M, Pikaard C, Shanklin J, Somerville C, Stitt M, Torii KU, Waese J, Wagner D, McCourt P.

New Phytol. 2016 Feb;209(3):921-44. doi: 10.1111/nph.13687. Epub 2015 Oct 14. Review.


The effect of NaCl on stomatal opening in Arabidopsis wild type and agb1 heterotrimeric G-protein mutant plants.

Yu Y, Assmann SM.

Plant Signal Behav. 2016;11(2):e1085275. doi: 10.1080/15592324.2015.1085275.


Extra-Large G Proteins Expand the Repertoire of Subunits in Arabidopsis Heterotrimeric G Protein Signaling.

Chakravorty D, Gookin TE, Milner MJ, Yu Y, Assmann SM.

Plant Physiol. 2015 Sep;169(1):512-29. doi: 10.1104/pp.15.00251. Epub 2015 Jul 8.


Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq.

Ding Y, Kwok CK, Tang Y, Bevilacqua PC, Assmann SM.

Nat Protoc. 2015 Jul;10(7):1050-66. doi: 10.1038/nprot.2015.064. Epub 2015 Jun 18.


The guard cell metabolome: functions in stomatal movement and global food security.

Misra BB, Acharya BR, Granot D, Assmann SM, Chen S.

Front Plant Sci. 2015 May 19;6:334. doi: 10.3389/fpls.2015.00334. eCollection 2015. Review.


Expression of potato RNA-binding proteins StUBA2a/b and StUBA2c induces hypersensitive-like cell death and early leaf senescence in Arabidopsis.

Na JK, Kim JK, Kim DY, Assmann SM.

J Exp Bot. 2015 Jul;66(13):4023-33. doi: 10.1093/jxb/erv207. Epub 2015 May 5.


StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo.

Tang Y, Bouvier E, Kwok CK, Ding Y, Nekrutenko A, Bevilacqua PC, Assmann SM.

Bioinformatics. 2015 Aug 15;31(16):2668-75. doi: 10.1093/bioinformatics/btv213. Epub 2015 Apr 16.


The heterotrimeric G-protein β subunit, AGB1, plays multiple roles in the Arabidopsis salinity response.

Yu Y, Assmann SM.

Plant Cell Environ. 2015 Oct;38(10):2143-56. doi: 10.1111/pce.12542. Epub 2015 May 12.


The RNA structurome: transcriptome-wide structure probing with next-generation sequencing.

Kwok CK, Tang Y, Assmann SM, Bevilacqua PC.

Trends Biochem Sci. 2015 Apr;40(4):221-32. doi: 10.1016/j.tibs.2015.02.005. Epub 2015 Mar 18. Review.


A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation.

Kwok CK, Ding Y, Shahid S, Assmann SM, Bevilacqua PC.

Biochem J. 2015 Apr 1;467(1):91-102. doi: 10.1042/BJ20141063.


Evidence for an unusual transmembrane configuration of AGG3, a class C Gγ subunit of Arabidopsis.

Wolfenstetter S, Chakravorty D, Kula R, Urano D, Trusov Y, Sheahan MB, McCurdy DW, Assmann SM, Jones AM, Botella JR.

Plant J. 2015 Feb;81(3):388-98. doi: 10.1111/tpj.12732. Epub 2014 Dec 22.


Multi-level modeling of light-induced stomatal opening offers new insights into its regulation by drought.

Sun Z, Jin X, Albert R, Assmann SM.

PLoS Comput Biol. 2014 Nov 13;10(11):e1003930. doi: 10.1371/journal.pcbi.1003930. eCollection 2014 Nov. Erratum in: PLoS Comput Biol. 2016 Nov 30;12 (11):e1005181.


Significant reduction of BiFC non-specific assembly facilitates in planta assessment of heterotrimeric G-protein interactors.

Gookin TE, Assmann SM.

Plant J. 2014 Nov;80(3):553-67. doi: 10.1111/tpj.12639. Epub 2014 Sep 27.


Metabolite transporter regulation of ABA function and guard cell response.

Yu Y, Assmann SM.

Mol Plant. 2014 Oct;7(10):1505-7. doi: 10.1093/mp/ssu093. Epub 2014 Aug 30. No abstract available.

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