Hernandez N, Keller W. Splicing of in vitro synthesized messenger RNA precursors in HeLa cell extracts. Cell. 1983;35(1):89–99.
Krainer AR, Maniatis T, Ruskin B, Green MR. Normal and mutant human beta-globin pre-mRNAs are faithfully and efficiently spliced in vitro. Cell. 1984;36(4):993–1005.
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(4665):898–903.
Lin RJ, Newman AJ, Cheng SC, Abelson J. Yeast mRNA splicing in vitro. J Biol Chem. 1985;260(27):14780–92.
Rio DC. Accurate and efficient pre-mRNA splicing in Drosophila cell-free extracts. Proc Natl Acad Sci USA. 1988;85(9):2904–8.
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(1):317–31.
Krainer AR, Maniatis T. Multiple factors including the small nuclear ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. Cell. 1985;42(3):725–36.
Black DL, Chabot B, Steitz JA. U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. Cell. 1985;42(3):737–50.
Krainer AR, Conway GC, Kozak D. Purification and characterization of pre-mRNA splicing factor SF2 from HeLa cells. Genes Dev. 1990;4(7):1158–71.
Screaton GR, Caceres JF, Mayeda A, Bell MV, Plebanski M, Jackson DG, Bell JI, Krainer AR. Identification and characterization of three members of the human SR family of pre-mRNA splicing factors. EMBO J. 1995;14(17):4336–49.
Konarska MM, Sharp PA. Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs. Cell. 1986;46(6):845–55.
Das R, Reed R. Resolution of the mammalian E complex and the ATP-dependent spliceosomal complexes on native agarose mini-gels. RNA. 1999;5(11):1504–8.
Wahl MC, Will CL, Luhrmann R. The spliceosome: design principles of a dynamic RNP machine. Cell. 2009;136(4):701–18.
Matera AG, Wang Z. A day in the life of the spliceosome. Nat Rev Mol Cell Biol. 2014;15(2):108–21.
Papasaikas P, Valcarcel J. The spliceosome: the ultimate RNA chaperone and sculptor. Trends Biochem Sci. 2016;41(1):33–45.
Galej WP, Wilkinson ME, Fica SM, Oubridge C, Newman AJ, Nagai K. Cryo-EM structure of the spliceosome immediately after branching. Nature. 2016;537(7619):197–201.
Yan C, Hang J, Wan R, Huang M, Wong CC, Shi Y. Structure of a yeast spliceosome at 3.6-angstrom resolution. Science. 2015;349(6253):1182–91.
Bertram K, Agafonov DE, Liu WT, Dybkov O, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Luhrmann R. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. Nature. 2017;542(7641):318–23.
Yan C, Wan R, Bai R, Huang G, Shi Y. Structure of a yeast step II catalytically activated spliceosome. Science. 2017;355(6321):149–55.
Fica SM, Oubridge C, Galej WP, Wilkinson ME, Bai XC, Newman AJ, Nagai K. Structure of a spliceosome remodelled for exon ligation. Nature. 2017;542(7641):377.
Plaschka C, Lin PC, Nagai K. Structure of a pre-catalytic spliceosome. Nature. 2017;546(7660):617.
Reed R, Maniatis T. A role for exon sequences and splice-site proximity in splice-site selection. Cell. 1986;46(5):681–90.
Mayeda A, Krainer AR. Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2. Cell. 1992;68(2):365–75.
Ge H, Manley JL. A protein factor, ASF, controls cell-specific alternative splicing of SV40 early pre-mRNA in vitro. Cell. 1990;62(1):25–34.
Tian M, Maniatis T. Positive control of pre-mRNA splicing in vitro. Science. 1992;256(5054):237–40.
Liu HX, Zhang M, Krainer AR. Identification of functional exonic splicing enhancer motifs recognized by individual SR proteins. Genes Dev. 1998;12(13):1998–2012.
Schaal TD, Maniatis T. Selection and characterization of pre-mRNA splicing enhancers: identification of novel SR protein-specific enhancer sequences. Mol Cell Biol. 1999;19(3):1705–19.
Hua Y, Vickers TA, Okunola HL, Bennett CF, Krainer AR. Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am J Hum Genet. 2008;82(4):834–48.
Kaida D, Motoyoshi H, Tashiro E, Nojima T, Hagiwara M, Ishigami K, Watanabe H, Kitahara T, Yoshida T, Nakajima H, et al. Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat Chem Biol. 2007;3(9):576–83.
Labadorf A, Link A, Rogers MF, Thomas J, Reddy AS, Ben-Hur A. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genom. 2010;11:114.
Reddy AS. Alternative splicing of pre-messenger RNAs in plants in the genomic era. Annu Rev Plant Biol. 2007;58:267–94.
Palusa SG, Ali GS, Reddy AS. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. Plant J. 2007;49(6):1091–107.
Ali GS, Reddy AS. Regulation of alternative splicing of pre-mRNAs by stresses. Curr Top Microbiol Immunol. 2008;326:257–75.
Mazzucotelli E, Mastrangelo AM, Crosatti C, Guerra D, Stanca AM, Cattivelli L. Abiotic stress response in plants: when post-transcriptional and post-translational regulations control transcription. Plant Sci. 2008;174(4):420–31.
Lorkovic ZJ. Role of plant RNA-binding proteins in development, stress response and genome organization. Trends Plant Sci. 2009;14(4):229–36.
Lee K, Kang H. Emerging Roles of RNA-Binding Proteins in Plant Growth, Development, and Stress Responses. Mol Cells. 2016;39(3):179–85.
Staiger D, Brown JW. Alternative splicing at the intersection of biological timing, development, and stress responses. Plant Cell. 2013;25(10):3640–56.
Duque P. A role for SR proteins in plant stress responses. Plant Signal Behav. 2011;6(1):49–54.
Barta A, Marquez Y, Brown JW. Challenges in plant alternative splicing. Alternative pre-mRNA Splicing: Theory and Protocols; 2012. p. 79–91.
Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. Plant Cell. 2013;25(10):3657–83.
Lorković ZJ, Kirk DAW, Lambermon MH, Filipowicz W. Pre-mRNA splicing in higher plants. Trends Plant Sci. 2000;5(4):160–7.
Wang BB, Brendel V. The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol. 2004;5(12):R102.
Ru Y, Wang BB, Brendel V. Spliceosomal proteins in plants. Curr Top Microbiol Immunol. 2008;326:1–15.
Koncz C, Dejong F, Villacorta N, Szakonyi D, Koncz Z. The spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator. Front Plant Sci. 2012;3:9.
Brown JW, Feix G, Frendewey D. Accurate in vitro splicing of two pre-mRNA plant introns in a HeLa cell nuclear extract. EMBO J. 1986;5(11):2749–58.
Hartmuth K, Barta A. In vitro processing of a plant pre-mRNA in a HeLa cell nuclear extract. Nucleic Acids Res. 1986;14(19):7513–28.
Barta A, Sommergruber K, Thompson D, Hartmuth K, Matzke MA, Matzke MA. The expression of a nopaline synthase-human growth hormone chimeric gene in transformed tobacco and sunflower callus tissue. Plant Mol Biol. 1986;6:347–57.
Haseloff J, Siemering KR, Prasher DC, Hodge S. Removal of a cryptic intron and subcellular localization of green fluorescent protein are required to mark transgenic Arabidopsis plants brightly. Proc Natl Acad Sci USA. 1997;94(6):2122–7.
Weibauer K, Herrero J-J, Filipowicz W. Nuclear pre-mRNA processing in plants: distinct modes of 3′ splice site selection in plants and animals. Mol Cell Biol. 1988;8:2042–51.
Baynton CE, Potthoff SJ, McCullough AJ, Schuler MA. U-rich tracts enhance 3′ splice site recognition in plant nuclei. Plant J. 1996;10(4):703–11.
McCullough AJ, Schuler MA. Intronic and exonic sequences modulate 5′ splice site selection in plant nuclei. Nucleic Acids Res. 1997;25(5):1071–7.
Schuler MA. Splice site requirements and switches in plants. Curr Top Microbiol Immunol. 2008;326:39–59.
Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, Rubin E, Ophir R, Fluhr R. Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J. 2004;39(6):877–85.
Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW. Alternative splicing in plants–coming of age. Trends Plant Sci. 2012;17(10):616–23.
Kim E, Magen A, Ast G. Different levels of alternative splicing among eukaryotes. Nucleic Acids Res. 2007;35(1):125–31.
Sugiura M. Plant in Vitro Transcription Systems. Annu Rev Plant Physiol Plant Mol Biol. 1997;48:383–98.
Lou H. A journey. RNA. 2015;21(4):681–2.
Folta KM, Kaufman LS. Isolation of Arabidopsis nuclei and measurement of gene transcription rates using nuclear run-on assays. Nat Protoc. 2006;1(6):3094–100.
Kataoka N, Dreyfuss G. Preparation of efficient splicing extracts from whole cells, nuclei, and cytoplasmic fractions. Methods Mol Biol. 2008;488:357–65.
Xing D, Wang Y, Hamilton M, Ben-Hur A, Reddy AS. Transcriptome-wide identification of RNA targets of Arabidopsis SERINE/ARGININE-RICH45 uncovers the unexpected roles of this RNA binding protein in RNA processing. Plant Cell. 2015;27(12):3294–308.
Palusa SG, Reddy AS. Analysis of RNA-protein interactions using electrophoretic mobility shift assay (gel shift assay). Bio protocol. 2013;22(3):1–10.
Movassat M, Mueller WF, Hertel KJ. In vitro assay of pre-mRNA splicing in mammalian nuclear extract. Methods Mol Biol. 2014;1126:151–60.
Dupuy B, Sonenshein AL. Regulated transcription of Clostridium difficile toxin genes. Mol Microbiol. 1998;27(1):107–20.
Hicks MJ, Lam BJ, Hertel KJ. Analyzing mechanisms of alternative pre-mRNA splicing using in vitro splicing assays. Methods. 2005;37(4):306–13.
Watson JC, Thompson WF. Purification and restriction endonuclease analysis of plant nuclear-DNA. Method Enzymol. 1986;118:57–75.
Lin RJ, Lustig AJ, Abelson J. Splicing of yeast nuclear pre-mRNA in vitro requires a functional 40S spliceosome and several extrinsic factors. Genes Dev. 1987;1(1):7–18.
Shukla RR, Dominski Z, Zwierzynski T, Kole R. Inactivation of splicing factors in HeLa cells subjected to heat shock. J Biol Chem. 1990;265(33):20377–83.
Aebi M, Hornig H, Weissmann C. 5′ cleavage site in eukaryotic pre-mRNA splicing is determined by the overall 5′ splice region, not by the conserved 5′ GU. Cell. 1987;50(2):237–46.
Mayeda A, Krainer AR. Mammalian in vitro splicing assays. Methods Mol Biol. 1999;118:315–21.
Padgett RA, Hardy SF, Sharp PA. Splicing of adenovirus RNA in a cell-free transcription system. Proc Natl Acad Sci USA. 1983;80(17):5230–4.
Reichert V, Moore MJ. Better conditions for mammalian in vitro splicing provided by acetate and glutamate as potassium counterions. Nucleic Acids Res. 2000;28(2):416–23.
Rivero L, Scholl R, Holomuzki N, Crist D, Grotewold E, Brkljacic J. Handling Arabidopsis plants: growth, preservation of seeds, transformation, and genetic crosses. Methods Mol Biol. 2014;1062:3–25.
Padgett RA, Grabowski PJ, Konarska MM, Seiler S, Sharp PA. Splicing of messenger RNA precursors. Annu Rev Biochem. 1986;55:1119–50.
Aebi M, Hornig H, Padgett RA, Reiser J, Weissmann C. Sequence requirements for splicing of higher eukaryotic nuclear pre-mRNA. Cell. 1986;47(4):555–65.
Kole R, Weissman SM. Accurate in vitro splicing of human beta-globin RNA. Nucleic Acids Res. 1982;10(18):5429–45.
Goldenberg CJ, Hauser SD. Accurate and efficient in vitro splicing of purified precursor RNAs specified by early region 2 of the adenovirus 2 genome. Nucleic Acids Res. 1983;11(5):1337–48.
Mayeda A, Krainer AR. Preparation of HeLa cell nuclear and cytosolic S100 extracts for in vitro splicing. Methods Mol Biol. 1999;118:309–14.