Lynch, M, Richardson, AO. The evolution of spliceosomal introns. Curr Opin Genet Dev 2002, 12:701–710.
Domdey, H, Apostol, B, Lin, RJ, Newman, A, Brody, E, Abelson, J. Lariat structures are in vivo intermediates in yeast pre‐mRNA splicing. Cell 1984, 39:611–621.
Rodriguez, JR, Pikielny, CW, Rosbash, M. In vivo characterization of yeast mRNA processing intermediates. Cell 1984, 39:603–610.
Zeitlin, S, Efstratiadis, A. In vivo splicing products of the rabbit β‐globin pre‐mRNA. Cell 1984, 39:589–602.
Padgett, RA, Konarska, MM, Grabowski, PJ, Hardy, SF, Sharp, PA. Lariat RNA`s as intermediates and products in the splicing of messenger RNA precursors. Science 1984, 225:898–903.
Ruskin, B, Krainer, AR, Maniatis, T, Green, MR. Excision of an intact intron as a novel lariat structure during pre‐mRNA splicing in vitro. Cell 1984, 38:317–331.
Arenas, J, Hurwitz, J. Purification of a RNA debranching activity from HeLa cells. J Biol Chem 1987, 262:4274–4279.
Krämer, A, Keller, W. Purification of a protein required for the splicing of pre‐mRNA and its separation from the lariat debranching enzyme. EMBO J 1985, 4:3571–3581.
Lasda, EL, Blumenthal, T. Trans‐splicing. WIREs RNA 2011, 2:417–434.
Pettitt, J, Harrison, N, Stansfield, I, Connolly, B, Müller, B. The evolution of spliced leader trans‐splicing in nematodes. Biochem Soc Trans 2010, 38:1125–1130.
Dorn, R, Reuter, G, Loewendorf, A. Transgene analysis proves mRNA trans‐splicing at the complex mod(mdg4) locus in Drosophila. Proc Natl Acad Sci USA 2001, 98:9724–9729.
Shao, W, Zhao, Q‐Y, Wang, X‐Y, Xu, X‐Y, Tang, Q, Li, M, Li, X, Xu, Y‐Z. Alternative splicing and trans‐splicing events revealed by analysis of the Bombyx mori transcriptome. RNA 2012, 18:1395–1407.
Kamikawa, R, Inagaki, Y, Tokoro, M, Roger, AJ, Hashimoto, T. Split introns in the genome of Giardia intestinalis are excised by spliceosome‐mediated trans‐splicing. Curr Biol 2011, 21:311–315.
Li, H, Wang, J, Mor, G, Sklar, J. A neoplastic gene fusion mimics trans‐splicing of RNAs in normal human cells. Science 2008, 321:1357–1361.
Roy, SW, Hudson, AJ, Joseph, J, Yee, J, Russell, AG. Numerous fragmented spliceosomal introns, AT‐AC splicing, and an unusual dynein gene expression pathway in Giardia lamblia. Mol Biol Evol 2012, 29:43–49.
McManus, CJ, Duff, MO, Eipper‐Mains, J, Graveley, BR. Global analysis of trans‐splicing in Drosophila. Proc Natl Acad Sci USA 2010, 107:12975–12979.
Anderson, K, Moore, MJ. Bimolecular exon ligation by the human spliceosome. Science 1997, 276:1712–1716.
Anderson, K, Moore, MJ. Bimolecular exon ligation by the human spliceosome bypasses early 3′ splice site AG recognition and requires NTP hydrolysis. RNA 2000, 6:16–25.
Lambowitz, AM, Zimmerly, S. Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb Perspect Biol 2011, 3:a003616.
Koonin, EV. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns‐early versus introns‐late debate? Biol Direct 2006, 1:22.
Yao, J, Zhong, J, Fang, Y, Geisinger, E, Novick, RP, Lambowitz, AM. Use of targetrons to disrupt essential and nonessential genes in Staphylococcus aureus reveals temperature sensitivity of Ll.LtrB group II intron splicing. RNA 2006, 12:1271–1281.
Zhuang, F, Mastroianni, M, White, TB, Lambowitz, AM. Linear group II intron RNAs can retrohome in eukaryotes and may use nonhomologous end‐joining for cDNA ligation. Proc Natl Acad Sci USA 2009, 106:18189–18194.
Chapman, KB, Boeke, JD. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell 1991, 65:483–492.
Nam, K, Hudson, RH, Chapman, KB, Ganeshan, K, Damha, MJ, Boeke, JD. Yeast lariat debranching enzyme. Substrate and sequence specificity. J Biol Chem 1994, 269:20613–20621.
Khalid, MF, Damha, MJ, Shuman, S, Schwer, B. Structure‐function analysis of yeast RNA debranching enzyme (Dbr1), a manganese‐dependent phosphodiesterase. Nucleic Acids Res 2005, 33:6349–6360.
Nam, K, Lee, G, Trambley, J, Devine, SE, Boeke, JD. Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. Mol Cell Biol 1997, 17:809–818.
Wang, H, Hill, K, Perry, SE. An Arabidopsis RNA lariat debranching enzyme is essential for embryogenesis. J Biol Chem 2004, 279:1468–1473.
Kim, JW, Kim, HC, Kim, GM, Yang, JM, Boeke, JD, Nam, K. Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants. Nucleic Acids Res 2000, 28:3666–3673.
Cheng, Z, Menees, TM. RNA branching and debranching in the yeast retrovirus‐like element Ty1. Science 2004, 303:240–243.
Karst, SM, Rütz, ML, Menees, TM. The yeast retrotransposons Ty1 and Ty3 require the RNA Lariat debranching enzyme, Dbr1p, for efficient accumulation of reverse transcripts. Biochem Biophys Res Commun 2000, 268:112–117.
Ye, Y, De Leon, J, Yokoyama, N, Naidu, Y, Camerini, D. DBR1 siRNA inhibition of HIV‐1 replication. Retrovirology 2005, 2:63.
Coombes, CE, Boeke, JD. An evaluation of detection methods for large lariat RNAs. RNA 2005, 11:323–331.
Pratico, ED, Silverman, SK. Ty1 reverse transcriptase does not read through the proposed 2″,5‐″branched retrotransposition intermediate in vitro. RNA 2007, 13:1528–1536.
Lauermann, V, Nam, K, Trambley, J, Boeke, JD. Plus‐strand strong‐stop DNA synthesis in retrotransposon Ty1. J Virol 1995, 69:7845–7850.
Armakola, M, Higgins, MJ, Figley, MD, Barmada, SJ, Scarborough, EA, Diaz, Z, Fang, X, Shorter, J, Krogan, NJ, Finkbeiner, S, et al. Inhibition of RNA lariat debranching enzyme suppresses TDP‐43 toxicity in ALS disease models. Nat Genet 2012, 44:1302–1309.
Burgess, SM, Guthrie, C. A mechanism to enhance mRNA splicing fidelity: the RNA‐dependent ATPase Prp16 governs usage of a discard pathway for aberrant lariat intermediates. Cell 1993, 73:1377–1391.
Hilleren, PJ, Parker, R. Cytoplasmic degradation of splice‐defective pre‐mRNAs and intermediates. Mol Cell 2003, 12:1453–1465.
Harigaya, Y, Parker, R. Global analysis of mRNA decay intermediates in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 2012, 109:11764–11769.
Danin‐Kreiselman, M, Lee, CY, Chanfreau, G. RNAse III‐mediated degradation of unspliced pre‐mRNAs and lariat introns. Mol Cell 2003, 11:1279–1289.
del Campo, EM, Casano, LM. Degradation of plastid unspliced transcripts and lariat group II introns. Biochimie 2008, 90:474–483.
LaCava, J, Houseley, J, Saveanu, C, Petfalski, E, Thompson, E, Jacquier, A, Tollervey, D. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 2005, 121:713–724.
San Paolo, S, Vanacova, S, Schenk, L, Scherrer, T, Blank, D, Keller, W, Gerber, AP. Distinct roles of non‐canonical poly(A) polymerases in RNA metabolism. PLoS Genet 2009, 5:e1000555.
Ruskin, B, Green, MR. An RNA processing activity that debranches RNA lariats. Science 1985, 229:135–140.
Tseng, C‐K, Cheng, S‐C. Both catalytic steps of nuclear pre‐mRNA splicing are reversible. Science 2008, 320:1782–1784.
Mayas, RM, Maita, H, Semlow, DR, Staley, JP. Spliceosome discards intermediates via the DEAH box ATPase Prp43p. Proc Natl Acad Sci USA 2010, 107:10020–10025.
Qian, L, Vu, MN, Carter, M, Wilkinson, MF. A spliced intron accumulates as a lariat in the nucleus of T cells. Nucleic Acids Res 1992, 20:5345–5350.
Guil, S, Soler, M, Portela, A, Carrère, J, Fonalleras, E, Gómez, A, Villanueva, A, Esteller, M. Intronic RNAs mediate EZH2 regulation of epigenetic targets. Nat Struct Mol Biol 2012, 19:664–670.
Gardner, EJ, Nizami, ZF, Talbot, CC, Gall, JG. Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. Genes Dev 2012, 26:2550–2559.
Perng, GC, Jones, C, Ciacci‐Zanella, J, Stone, M, Henderson, G, Yukht, A, Slanina, SM, Hofman, FM, Ghiasi, H, Nesburn, AB, et al. Virus‐induced neuronal apoptosis blocked by the herpes simplex virus latency‐associated transcript. Science 2000, 287:1500–1503.
Nicosia, M, Zabolotny, JM, Lirette, RP, Fraser, NW. The HSV‐1 2‐kb latency‐associated transcript is found in the cytoplasm comigrating with ribosomal subunits during productive infection. Virology 1994, 204:717–728.
Clement, JQ, Qian, L, Kaplinsky, N, Wilkinson, MF. The stability and fate of a spliced intron from vertebrate cells. RNA 1999, 5:206–220.
Clement, JQ, Maiti, S, Wilkinson, MF. Localization and stability of introns spliced from the Pem homeobox gene. J Biol Chem 2001, 276:16919–16930.
Coleclough, C, Wood, D. Introns excised from immunoglobulin pre‐mRNAs exist as discrete species. Mol Cell Biol 1984, 4:2017–2022.
Yoshimoto, R, Kataoka, N, Okawa, K, Ohno, M. Isolation and characterization of post‐splicing lariat‐intron complexes. Nucleic Acids Res 2009, 37:891–902.
Fourmann, J‐B, Schmitzová, J, Christian, H, Urlaub, H, Ficner, R, Boon, K‐L, Fabrizio, P, Lührmann, R. Dissection of the factor requirements for spliceosome disassembly and the elucidation of its dissociation products using a purified splicing system. Genes Dev 2013, 27:413–428.
Martin, A, Schneider, S, Schwer, B. Prp43 is an essential RNA‐dependent ATPase required for release of lariat‐intron from the spliceosome. J Biol Chem 2002, 277:17743–17750.
Small, EC, Leggett, SR, Winans, AA, Staley, JP. The EF‐G‐like GTPase Snu114p Regulates Spliceosome Dynamics Mediated by Brr2p, a DExD/H Box ATPase. Mol Cell 2006, 23:389–399.
Kannan, R, Hartnett, S, Voelker, RB, Berglund, JA, Staley, JP, Baumann, P. Intronic sequence elements impede exon ligation and trigger a discard pathway that yields functional telomerase RNA in fission yeast. Genes Dev 2013, 27:627–638.
Pleiss, JA, Whitworth, GB, Bergkessel, M, Guthrie, C. Rapid, transcript‐specific changes in splicing in response to environmental stress. Mol Cell 2007, 27:928–937.
Albulescu, L‐O, Sabet, N, Gudipati, M, Stepankiw, N, Bergman, ZJ, Huffaker, TC, Pleiss, JA. A quantitative, high‐throughput reverse genetic screen reveals novel connections between Pre‐mRNA splicing and 5″ and 3″ end transcript determinants. PLoS Genet 2012, 8:e1002530.
Tseng, C‐K, Cheng, S‐C. The spliceosome catalyzes debranching in competition with reverse of the first chemical reaction. RNA 2013, 320:1782–1784.
Ooi, SL, Samarsky, DA, Fournier, MJ, Boeke, JD. Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat‐debranching enzyme: intron length effects and activity of a precursor snoRNA. RNA 1998, 4:1096–1110.
Tycowski, KT, Shu, MD, Steitz, JA. A mammalian gene with introns instead of exons generating stable RNA products. Nature 1996, 379:464–466.
Yin, Q‐F, Yang, L, Zhang, Y, Xiang, J‐F, Wu, Y‐W, Carmichael, GG, Chen, L‐L. Long noncoding RNAs with snoRNA ends. Mol Cell 2012, 48:219–230.
Ruby, JG, Jan, CH, Bartel, DP. Intronic microRNA precursors that bypass Drosha processing. Nature 2007, 448:83–86.
Okamura, K, Hagen, JW, Duan, H, Tyler, DM, Lai, EC. The mirtron pathway generates microRNA‐class regulatory RNAs in Drosophila. Cell 2007, 130:89–100.
Winter, J, Jung, S, Keller, S, Gregory, RI, Diederichs, S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 2009, 11:228–234.
Flynt, AS, Greimann, JC, Chung, WJ, Lima, CD, Lai, EC. MicroRNA biogenesis via splicing and exosome‐mediated trimming in Drosophila. Mol Cell 2010, 38:900–907.
Ladewig, E, Okamura, K, Flynt, AS, Westholm, JO, Lai, EC. Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Res 2012, 22:1634–1645.
Curtis, HJ, Sibley, CR, Wood, MJA. Mirtrons, an emerging class of atypical miRNA. WIREs RNA 2012, 3:617–632.
Gu, W, Lee, H‐C, Chaves, D, Youngman, EM, Pazour, GJ, Conte, D, Mello, CC. CapSeq and CIP‐TAP identify Pol II start sites and reveal capped small RNAs as C. elegans piRNA precursors. Cell 2012, 151:1488–1500.
Saito, TL, Hashimoto, S‐I, Gu, SG, Morton, JJ, Stadler, M, Blumenthal, T, Fire, A, Morishita, S. The transcription start site landscape of C. elegans. Genome Res 2013.
Morton, JJ, Blumenthal, T. Identification of transcription start sites of trans‐spliced genes: uncovering unusual operon arrangements. RNA 2011, 17:327–337.
Kent, JR, Kang, W, Miller, CG, Fraser, NW. Herpes simplex virus latency‐associated transcript gene function. J Neurovirol 2003, 9:285–290.
Wu, TT, Su, YH, Block, TM, Taylor, JM. Evidence that two latency‐associated transcripts of herpes simplex virus type 1 are nonlinear. J Virol 1996, 70:5962–5967.
Rødahl, E, Haarr, L. Analysis of the 2‐kilobase latency‐associated transcript expressed in PC12 cells productively infected with herpes simplex virus type 1: evidence for a stable, nonlinear structure. J Virol 1997, 71:1703–1707.
Kulesza, CA, Shenk, T. Murine cytomegalovirus encodes a stable intron that facilitates persistent replication in the mouse. Proc Natl Acad Sci USA 2006, 103:18302–18307.
Inman, M, Perng, GC, Henderson, G, Ghiasi, H, Nesburn, AB, Wechsler, SL, Jones, C. Region of herpes simplex virus type 1 latency‐associated transcript sufficient for wild‐type spontaneous reactivation promotes cell survival in tissue culture. J Virol 2001, 75:3636–3646.
Goldenberg, D, Mador, N, Ball, MJ, Panet, A, Steiner, I. The abundant latency‐associated transcripts of herpes simplex virus type 1 are bound to polyribosomes in cultured neuronal cells and during latent infection in mouse trigeminal ganglia. J Virol 1997, 71:2897–2904.
Knipe, DM, Lieberman, PM, Jung, JU, McBride, AA, Morris, KV, Ott, M, Margolis, D, Nieto, A, Nevels, M, Parks, RJ, et al. Snapshots: chromatin control of viral infection. Virology 2013, 435:141–156.
Cliffe, AR, Garber, DA, Knipe, DM. Transcription of the herpes simplex virus latency‐associated transcript promotes the formation of facultative heterochromatin on lytic promoters. J Virol 2009, 83:8182–8190.
Kwiatkowski, DL, Thompson, HW, Bloom, DC. The polycomb group protein Bmi1 binds to the herpes simplex virus 1 latent genome and maintains repressive histone marks during latency. J Virol 2009, 83:8173–8181.
Tsai, M‐C, Manor, O, Wan, Y, Mosammaparast, N, Wang, JK, Lan, F, Shi, Y, Segal, E, Chang, HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689–693.
Krummenacher, C, Zabolotny, JM, Fraser, NW. Selection of a nonconsensus branch point is influenced by an RNA stem‐loop structure and is important to confer stability to the herpes simplex virus 2‐kilobase latency‐associated transcript. J Virol 1997, 71:5849–5860.
Jacquier, A, Rosbash, M. RNA splicing and intron turnover are greatly diminished by a mutant yeast branch point. Proc Natl Acad Sci USA 1986, 83:5835–5839.
Reineke, LC, Lloyd, RE. Animal virus schemes for translation dominance. Curr Opin Virol 2011, 1:363–372.
Roy, SW, Gilbert, W. The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet 2006, 7:211–221.
Sharp, PA. On the origin of RNA splicing and introns. Cell 1985, 42:397–400.
Tani, T, Ohshima, Y. mRNA‐type introns in U6 small nuclear RNA genes: implications for the catalysis in pre‐mRNA splicing. Genes Dev 1991, 5:1022–1031.
Coghlan, A, Wolfe, KH. Origins of recently gained introns in Caenorhabditis. Proc Natl Acad Sci USA 2004, 101:11362–11367.
Schwer, B. A conformational rearrangement in the spliceosome sets the stage for Prp22‐dependent mRNA release. Mol Cell 2008, 30:743–754.
Schwer, B, Meszaros, T. RNA helicase dynamics in pre‐mRNA splicing. EMBO J 2000, 19:6582–6591.
Wahl, MC, Will, CL, Lührmann, R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009, 136:701–718.
Huelga, SC, Vu, AQ, Arnold, JD, Liang, TY, Liu, PP, Yan, BY, Donohue, JP, Shiue, L, Hoon, S, Brenner, S, et al. Integrative genome‐wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep 2012, 1:167–178.
Wang, Y, Ma, M, Xiao, X, Wang, Z. Intronic splicing enhancers, cognate splicing factors and context‐dependent regulation rules. Nat Struct Mol Biol 2012, 19:1044–1052.
Brent, MR. Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet 2008, 9:62–73.
Zhang, Z, Hesselberth, JR, Fields, S. Genome‐wide identification of spliced introns using a tiling microarray. Genome Res 2007, 17:503–509.
Juneau, K, Palm, C, Miranda, M, Davis, RW. High‐density yeast‐tiling array reveals previously undiscovered introns and extensive regulation of meiotic splicing. Proc Natl Acad Sci USA 2007, 104:1522–1527.
Clement, JQ, Wilkinson, MF. Rapid induction of nuclear transcripts and inhibition of intron decay in response to the polymerase II inhibitor DRB. J Mol Biol 2000, 299:1179–1191.
Chi, SW, Zang, JB, Mele, A, Darnell, RB. Argonaute HITS‐CLIP decodes microRNA‐mRNA interaction maps. Nature 2009, 460:479–486.
Tsai, R‐T, Fu, R‐H, Yeh, F‐L, Tseng, C‐K, Lin, Y‐C, Huang, Y‐H, Cheng, S‐C. Spliceosome disassembly catalyzed by Prp43 and its associated components Ntr1 and Ntr2. Genes Dev 2005, 19:2991–3003.
Freeberg, MA, Han, T, Moresco, JJ, Kong, A, Yang, Y‐C, Lu, ZJ, Yates, JR, Kim, JK. Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae. Genome Biol 2013, 14:R13.
Windhager, L, Bonfert, T, Burger, K, Ruzsics, Z, Krebs, S, Kaufmann, S, Malterer, G, L`Hernault, A, Schilhabel, M, Schreiber, S, et al. Ultrashort and progressive 4sU‐tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Res 2012, 22:2031–2042.
Taggart, AJ, DeSimone, AM, Shih, JS, Filloux, ME, Fairbrother, WG. Large‐scale mapping of branchpoints in human pre‐mRNA transcripts in vivo. Nat Struct Mol Biol 2012, 19:719–721.
Suzuki, H, Zuo, Y, Wang, J, Zhang, MQ, Malhotra, A, Mayeda, A. Characterization of RNase R‐digested cellular RNA source that consists of lariat and circular RNAs from pre‐mRNA splicing. Nucleic Acids Res 2006, 34:e63.
Wang, Y, Silverman, SK. Efficient one‐step synthesis of biologically related lariat RNAs by a deoxyribozyme. Angew Chem Int Ed 2005, 44:5863–5866.
Mui, TP, Silverman, SK. Convergent and general one‐step DNA‐catalyzed synthesis of multiply branched DNA. Org Lett 2008, 10:4417–4420.
Lee, CS, Mui, TP, Silverman, SK. Improved deoxyribozymes for synthesis of covalently branched DNA and RNA. Nucleic Acids Res 2010, 39:269–279.
Carriero, S, Damha, MJ. Solid‐phase synthesis of branched oligonucleotides. In: Beaucage S, ed. Current protocols in nucleic acid chemistry. Hoboken, NJ: John Wiley %26 Sons; 2002, Unit 4.14: 1–32.
Mourani, R, Damha, MJ. Synthesis, characterization, and biological properties of small branched RNA fragments containing chiral (Rp and Sp) 2″,5‐″phosphorothioate linkages. Nucleosides Nucleotides Nucleic Acids 2006, 25:203–229.