Galej, W. P., Toor, N., Newman, A. J. & Nagai, K. Molecular mechanism and evolution of nuclear pre-mrna and group ii intron splicing: insights from cryo-electron microscopy structures. Chem. Rev. 118, 4156–4176 (2018).
Article CAS PubMed Google Scholar
Grabowski, P. J., Padgett, R. A. & Sharp, P. A. Messenger RNA splicing in vitro: an excised intervening sequence and a potential intermediate. Cell 37, 415–427 (1984).
Article CAS PubMed Google Scholar
Toor, N., Keating, K. S., Taylor, S. D. & Pyle, A. M. Crystal structure of a self-spliced group II intron. Science 320, 77–82 (2008).
Article CAS PubMed PubMed Central Google Scholar
Galej, W. P. et al. Cryo-EM structure of the spliceosome immediately after branching. Nature 537, 197–201 (2016).
Article CAS PubMed PubMed Central Google Scholar
Hang, J., Wan, R., Yan, C. & Shi, Y. Structural basis of pre-mRNA splicing. Science 349, 1191–1198 (2015).
Article CAS PubMed Google Scholar
Padgett, R. A., Konarska, M. M., Grabowski, P. J., Hardy, S. F. & Sharp, P. A. Lariat RNA’s as intermediates and products in the splicing of messenger RNA precursors. Science 225, 898–903 (1984).
Article CAS PubMed Google Scholar
Konarska, M. M., Grabowski, P. J., Padgett, R. A. & Sharp, P. A. Characterization of the branch site in lariat RNAs produced by splicing of mRNA precursors. Nature 313, 552–557 (1985).
Article CAS PubMed Google Scholar
Peebles, C. L. et al. A self-splicing RNA excises an intron lariat. Cell 44, 213–223 (1986).
Article CAS PubMed Google Scholar
Robart, A. R., Chan, R. T., Peters, J. K., Rajashankar, K. R. & Toor, N. Crystal structure of a eukaryotic group II intron lariat. Nature 514, 193–197 (2014).
Article CAS PubMed PubMed Central Google Scholar
Gao, K., Masuda, A., Matsuura, T. & Ohno, K. Human branch point consensus sequence is yUnAy. Nucleic Acids Res. 36, 2257–2267 (2008).
Article CAS PubMed PubMed Central Google Scholar
Wan, R., Bai, R., Yan, C., Lei, J. & Shi, Y. Structures of the catalytically activated yeast spliceosome reveal the mechanism of branching. Cell 177, 339–351 (2019).
Article CAS PubMed Google Scholar
Wilkinson, M. E., Fica, S. M., Galej, W. P. & Nagai, K. Structural basis for conformational equilibrium of the catalytic spliceosome. Mol. Cell 81, 1439–1452 (2021).
Article CAS PubMed PubMed Central Google Scholar
Jacquier, A. & Michel, F. Multiple exon-binding sites in class II self-splicing introns. Cell 50, 17–29 (1987).
Article CAS PubMed Google Scholar
Haack, D. B. et al. Cryo-EM structures of a group II intron reverse splicing into DNA. Cell 178, 612–623 (2019).
Article CAS PubMed PubMed Central Google Scholar
Fedorova, O. & Pyle, A. M. Linking the group II intron catalytic domains: tertiary contacts and structural features of domain 3. EMBO J. 24, 3906–3916 (2005).
Article CAS PubMed PubMed Central Google Scholar
Bertram, K. et al. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Nature 542, 318–323 (2017).
Article CAS PubMed Google Scholar
Fica, S. M., Mefford, M. A., Piccirilli, J. A. & Staley, J. P. Evidence for a group II intron-like catalytic triplex in the spliceosome. Nat. Struct. Mol. Biol. 21, 464–471 (2014).
Article CAS PubMed PubMed Central Google Scholar
Fica, S. M. et al. RNA catalyses nuclear pre-mRNA splicing. Nature 503, 229–234 (2013).
Article CAS PubMed PubMed Central Google Scholar
Padgett, R. A., Podar, M., Boulanger, S. C. & Perlman, P. S. The stereochemical course of group II intron self-splicing. Science 266, 1685–1688 (1994).
Article CAS PubMed Google Scholar
Fica, S. M. et al. Structure of a spliceosome remodelled for exon ligation. Nature 542, 377–380 (2017).
Article CAS PubMed PubMed Central Google Scholar
Galej, W. P., Oubridge, C., Newman, A. J. & Nagai, K. Crystal structure of Prp8 reveals active site cavity of the spliceosome. Nature 493, 638–643 (2013).
Article CAS PubMed PubMed Central Google Scholar
Coimbatore Narayanan, B. et al. The Nucleic Acid Database: new features and capabilities. Nucleic Acids Res. 42, 114–122 (2014).
Akiyama, B. M., Graham, M. E., O Donoghue, Z., Beckham, J. D. & Kieft, J. S. Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication. Nucleic Acids Res. 49, 7122–7138 (2021).
Article CAS PubMed PubMed Central Google Scholar
Mercer, T. R. et al. Genome-wide discovery of human splicing branchpoints. Genome Res. 25, 290–303 (2015).
Article CAS PubMed PubMed Central Google Scholar
Chu, V. T., Adamidi, C., Liu, Q., Perlman, P. S. & Pyle, A. M. Control of branch-site choice by a group II intron. EMBO J. 20, 6866–6876 (2001).
Article CAS PubMed PubMed Central Google Scholar
Liu, Q. et al. Branch-site selection in a group II intron mediated by active recognition of the adenine amino group and steric exclusion of non-adenine functionalities. J. Mol. Biol. 267, 163–171 (1997).
Article CAS PubMed Google Scholar
Mitchell, D. et al. Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA 24, 114–124 (2018).
Article CAS PubMed PubMed Central Google Scholar
Taggart, A. J. et al. Large-scale analysis of branchpoint usage across species and cell lines. Genome Res 27, 639–649 (2017).
Article CAS PubMed PubMed Central Google Scholar
Carlomagno, T. et al. Structural principles of RNA catalysis in a 2′–5′ lariat-forming ribozyme. J. Am. Chem. Soc. 135, 4403–4411 (2013).
Article CAS PubMed Google Scholar
Sharp, P. A. ‘Five easy pieces’. Science 254, 663 (1991).
Article CAS PubMed Google Scholar
Database for bacterial group II introns. (2003) University of Calgary http://webapps2.ucalgary.ca/∼groupii/
Dai, L., Toor, N., Olson, R., Keeping, A. & Zimmerly, S. Database for mobile group II introns. Nucleic Acids Res. 31, 424–426 (2003).
Article CAS PubMed PubMed Central Google Scholar
Tippmann, H. F. Analysis for free: comparing programs for sequence analysis. Brief. Bioinform. 5, 82–87 (2004).
Article CAS PubMed Google Scholar
Tan, Y. Z. et al. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods 14, 793–796 (2017).
Article CAS PubMed PubMed Central Google Scholar
Aiyer, S., Strutzenberg, T. S., Bowman, M. E., Noel, J. P. & Lyumkis, D. Single-particle cryo-EM data collection with stage tilt using Leginon. J. Vis. Exp. 185, e64136 (2022).
Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005).
Article CAS PubMed Google Scholar
Cheng, A. et al. Leginon: new features and applications. Protein Sci. 30, 136–150 (2021).
Article CAS PubMed Google Scholar
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
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