Publications
publications
Bose, E., et al. Probing RNA structure and dynamics using nanopore and next generation sequencing. JBC 2024.
RNA adopts structures that are conformationally dynamic. In this review, we compare how various deconvolution algorithms have been used to investigate the conformational dynamics of structured RNAs. A good take-away: use chemical probing experiments as a guide to gain insight about your system. Follow this up with other approaches to validate the chemical probing results.
Fallon, L., et al. RNA Chemical Probing Reagents and Protein Amino Acids: a Double-Edged Sword. BioRxiv 2023
We use RNA chemical probing experiments to identify sites of protein/RNA/ligand binding on an RNA. We asked ourselves: can the same probes that methylate or acylate RNA modify amino acids in a similar way? Yep. We find that 2’OH acylating SHAPE probes can acylate amino acid side chains. Dimethyl sulfate, which methylates atoms on RNA bases, can also methylate amino acid side chains. What we find striking is that these are often the same amino acids that interact with the RNA: chemical probes can decrease the binding affinity of a protein with its RNA target. To us, this means binding affinities cannot be determined from chemical probing experiments. We used a combination of NMR, MD simulations, MALDI mass spec, and binding shift assays to investigate this effect.
Arnold, E., et al. Cooperativity in RNA chemical probing experiments modulates RNA 2D structure. BioRxiv 2023
Chemical probing experiments are widely used to improve RNA 2D structure prediction. These chemical probes covalently modify atoms associated with flexible nucleotides. In this work, we demonstrate how over modifying an RNA can damage the structure of the RNA; this can lead to an unintended increased or decreased in the modification of bases nearby. We highlight the importance of ‘single-hit kinetics’: chemical probing experiments should aim to satisfy ‘one modification per molecule’ … and if there are more modifications, they should be far enough apart such that they do not influence the reactivity of neighboring nucleotides. We find this cooperative effect is observed for both base and ribose modifying probes, and can lead to the misprediction of RNA 2D structures and structural ensembles.
Bose, E., et al. Characterization of RBM15 protein binding with long noncoding RNAs. BioRxiv 2023
Students in my Spring 2023 Macromolecular Chemistry course at NYU mined data from the RNA atlas of structural probing (RASP) and the ENCODE database to identify lncRNA structured elements that are bound by the RNA binding protein RBM15. We found that RBM15 preferentially binds stem-loop structured RNAs, primarily through two tandom RNA recognition motifs (RRMs): RRM1 and RRM2. In the summer, high school students experimentally validated those results, preparing RNA and protein to evaluate the results from the Spring course.
Select publications prior to independent career
Jones, A.N., et al. Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure. BioRxiv 2022
We used NMR, SAXS, and RNA chemical probing to follow the structural folding pathway of the Xist A-repeat lncRNA as it is being transcribed. We discovered that the Xist A-repeat lncRNA is conformationally dynamic. A product of this work is a program that can be used by any research group to follow the cotranscriptional pathway of their RNA. Input parameters are NMR and chemical probing restraints.
Jones, A.N., et al. Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1. Science Advances 2022
The MALT1 pre-mRNA is intricately structured and modulated by protein binding partners. We used a variety of biochemical and biophysical techniques (EMSA, RNA chemical probing, fluorescence assays, ITC, and NMR) to investigate this. The structure is stabilized by the hnRNP U protein, and destabilized by the hnRNP L protein. The destabilization of the structure exposes splice sites that must be recognized by spliceosome factors to facilitate alternative splicing. The increased accessibility of these splice sites upon protein binding is required for T cells to shift from a resting to an active state.
Jones, A.N., et al. Conformational effects of a cancer-linked mutation in pri-miR-30c RNA. JMB 2022
Mutations occur in RNA sequences all of the time. How these mutations impact structure requires in-depth analysis. We investigated how a G to A mutation impacts the structure of the pri-miR-30c RNA using NMR, SAXS, CD spectroscopy, and optical tweezers. We discovered that the WT pri-miR-30c RNA forms an intermolecular kissing hairpin structure that is destabilized by the G to A mutation. The kissing hairpin sequesters an hnRNP A1 binding site. The hnRNP A1 binding site is exposed in the mutant RNA and upon binding, promotes the processing of this transcript. This processing event is linked to cancer.
Jones, A.N., et al. Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1. NAR 2022
Just like proteins, RNAs are also subjected to post (or even co-) transcriptional modifications. The lncRNA Xist experiences m6A modification at numerous sites. We used NMR, x-ray crystallography, and CD spectroscopy to investigate how an m6A modification impacts the structure of a Xist A-repeat hairpin motif. We found that the m6A modification partially opens the RNA to promote binding by the YTHDC1 protein.
Calonaci, N., Jones, A.N., et al. Machine learning a model for RNA structure prediction. NAR Genomics and Bioinformatics 2020
We don’t yet have enough data to use deep learning models to predict RNA tertiary structure, but there is enough data out there to predict RNA secondary structures using machine learning models. We established a machine learning model combining RNA sequence, chemical probing experiments, and covariational data to accurately predict RNA secondary structure. RNA tertiary structure is up next.
Jones, A.N., et al. An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano. RNA 2020
Even though long noncoding RNAs generally lack primary sequence conservation, their structures can be maintained through compensatory mutations. We used RNA chemical probing and enzymatic cleavage experiments, bioinformatics, and covariational analysis to demonstrate that despite possessing only 60% sequence identity, the structures adopted by the zebrafish, mouse, and human Cyrano lncRNAs are highly similar.
Shortridge, M.D.*, Wille, P.T.*, Jones, A.N.*, et al. An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-Tefb. NAR 2019
NMR is a powerful tool that can be used to determine structures of RNA, protein, and RNA-protein complexes. We used an NMR structure-based design approach to develop peptides that bind with picomolar binding affinity to the HIV TAR RNA. The binding of these peptides reveal the mechanism by which the P-Tefb recognizes and binds HIV TAR to promote viral replication.
*denotes shared authorship
Full list of publications – nih bibliography
17. Jones AN, Graß C, Meininger I, Geerlof A, Klostermann M, Zarnack K, Krappmann D, Sattler M. Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1. Sci Adv. 2022 Aug 5;8(31):eabp9153.
16. Jones A, Gabel F, Bohn S, Wolfe G, Sattler M. Cotranscriptional folding of the lncRNA Xist A-repeats indicates a modular structure. [BioRxiv preprint]. 2022 Jul 27;doi: 10.1101/2022.07.26.501616
15. Jones AN, Walbrun A, Falleroni F, Rief M, Sattler M. Conformational Effects of a Cancer-Linked Mutation in Pri-miR-30c RNA. J Mol Biol. 2022 Jun 24;:167705.
14. Jones AN, Mourão A, Czarna A, Matsuda A, Fino R, Pyrc K, Sattler M, Popowicz GM. Characterization of SARS-CoV-2 replication complex elongation and proofreading activity. Sci Rep. 2022 Jun 10;12(1):9593.
13. Jones AN, Tikhaia E, Mourão A, Sattler M. Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1. Nucleic Acids Res. 2022 Feb 28;50(4):2350-2362.
12. Matsuda A, Plewka J, Yuliya Y, Jones A, Panchota M, Rawski M, Mourão A, Karim A, Kresik L, Lis K, Minia I, Hartman K, Sonani R, Schlauderer F, Dubin G, Sattler M, Suder P, Popowicz G, Pyrć K, Czarna A. Despite the odds: formation of the SARS-CoV-2 methylation complex. [BioRxiv preprint]. 2022 Jan 26;doi: d10.1101/2022.01.25.477673
11. Heumüller AW, Jones AN, Mourão A, Klangwart M, Shi C, Wittig I, Fischer A, Muhly-Reinholz M, Buchmann GK, Dieterich C, Potente M, Braun T, Grote P, Jaé N, Sattler M, Dimmeler S. Locus-Conserved Circular RNA cZNF292 Controls Endothelial Cell Flow Responses. Circ Res. 2022 Jan 7;130(1):67-79.
10. Stadler D, Kächele M, Jones AN, Hess J, Urban C, Schneider J, Xia Y, Oswald A, Nebioglu F, Bester R, Lasitschka F, Ringelhan M, Ko C, Chou WM, Geerlof A, van de Klundert MA, Wettengel JM, Schirmacher P, Heikenwälder M, Schreiner S, Bartenschlager R, Pichlmair A, Sattler M, Unger K, Protzer U. Interferon-induced degradation of the persistent hepatitis B virus cccDNA form depends on ISG20. EMBO Rep. 2021 Jun 4;22(6):e49568.
9. Munshaw S, Bruche S, Redpath AN, Jones A, Patel J, Dubé KN, Lee R, Hester SS, Davies R, Neal G, Handa A, Sattler M, Fischer R, Channon KM, Smart N. Thymosin β4 protects against aortic aneurysm via endocytic regulation of growth factor signaling. J Clin Invest. 2021 May 17;131(10).
8. Calonaci N, Jones A, Cuturello F, Sattler M, Bussi G. Machine learning a model for RNA structure prediction. NAR Genom Bioinform. 2020 Dec;2(4):lqaa090.
7. Jones AN, Pisignano G, Pavelitz T, White J, Kinisu M, Forino N, Albin D, Varani G. An evolutionarily conserved RNA structure in the functional core of the lincRNA Cyrano. RNA. 2020 Sep;26(9):1234-1246.
6. Jones AN, Sattler M. Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats. J Mol Cell Biol. 2019 Oct 25;11(10):845-859.
5. von Gamm M, Schaub A, Jones AN, Wolf C, Behrens G, Lichti J, Essig K, Macht A, Pircher J, Ehrlich A, Davari K, Chauhan D, Busch B, Wurst W, Feederle R, Feuchtinger A, Tschöp MH, Friedel CC, Hauck SM, Sattler M, Geerlof A, Hornung V, Heissmeyer V, Schulz C, Heikenwalder M, Glasmacher E. Immune homeostasis and regulation of the interferon pathway require myeloid-derived Regnase-3. J Exp Med. 2019 Jul 1;216(7):1700-1723.
4. Shortridge MD, Wille PT, Jones AN, Davidson A, Bogdanovic J, Arts E, Karn J, Robinson JA, Varani G. An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb. Nucleic Acids Res. 2019 Feb 20;47(3):1523-1531.
3. Kooshapur H, Choudhury NR, Simon B, Mühlbauer M, Jussupow A, Fernandez N, Jones AN, Dallmann A, Gabel F, Camilloni C, Michlewski G, Caceres JF, Sattler M. Structural basis for terminal loop recognition and stimulation of pri-miRNA-18a processing by hnRNP A1. Nat Commun. 2018 Jun 26;9(1):2479.
2. Ni S, McGookey ME, Tinch SL, Jones AN, Jayaraman S, Tong L, Kennedy MA. The 1.7 Å resolution structure of At2g44920, a pentapeptide-repeat protein in the thylakoid lumen of Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Dec 1;67(Pt 12):1480-4.
1. Niu Y, Jones AJ, Wu H, Varani G, Cai J. γ-AApeptides bind to RNA by mimicking RNA-binding proteins. Org Biomol Chem. 2011 Oct 7;9(19):6604-9.