Charlet.-B., N. et al. Loss of the muscle-specific chloride channel in type 1 myotonic dystrophy due to misregulated alternative splicing. Mol. Cell 10, 45–53 (2002).
Mankodi, A. et al. Expanded CUG repeats trigger aberrant splicing of ClC-1 chloride channel pre-mRNA and hyperexcitability of skeletal muscle in myotonic dystrophy. Mol. Cell 10, 35–44 (2002).
Ghigna, C. et al. Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Mol. Cell 20, 881–890 (2005).
Karni, R. et al. The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat. Struct. Mol. Biol. 14, 185–93 (2007).
Kim, E., Goren, A. & Ast, G. Insights into the connection between cancer and alternative splicing. Trends Genet. 24, 7–10 (2008).
Calin, G. A. et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc. Natl. Acad. Sci. USA 99, 15524–9 (2002).
Davalos, V. et al. Dynamic epigenetic regulation of the microRNA-200 family mediates epithelial and mesenchymal transitions in human tumorigenesis. Oncogene 31, 2062–2074 (2012).
Nadal, E. et al. Epigenetic inactivation of microRNA-34b/c predicts poor disease-free survival in early stage lung adenocarcinoma. Clin. Cancer Res. 19, 6842–6852 (2013).
Wang, G. et al. Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein. J. Hum. Genet. 283–289 (2008).
Yin, Q.-F. et al. Long noncoding RNAs with snoRNA ends. Mol. Cell 48, 219–30 (2012).
Kang, M.-J. et al. HuD Regulates Coding and Noncoding RNA to Induce APP → Aβ Processing. Cell Rep. 7, 1401–1409 (2014).
Chen, Y. & Varani, G. Engineering RNA-binding proteins for biology. FEBS J. 280, 3734–54 (2013).
Ozawa, T., Natori, Y., Sato, M. & Umezawa, Y. Imaging dynamics of endogenous mitochondrial RNA in single living cells. Nat. Methods 4, 413–9 (2007).
Tilsner, J. et al. Live-cell imaging of viral RNA genomes using a Pumilio-based reporter. Plant J. 57, 758–770 (2009).
Cooke, A., Prigge, A., Opperman, L. & Wickens, M. Targeted translational regulation using the PUF protein family scaffold. TL - 108. Proc. Natl. Acad. Sci. USA 108, 15870–15875 (2011).
Wang, Y., Opperman, L., Wickens, M. & Hall, T. M. T. Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein. Proc. Natl. Acad. Sci. USA 106, 20186–20191 (2009).
Zhou, W. et al. PPR-SMR protein SOT1 has RNA endonuclease activity. Proc. Natl. Acad. Sci. USA 114, E1554–E1563 (2017).
Fujii, S., Bond, C. S. & Small, I. D. Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution. Proc. Natl. Acad. Sci. USA 108, 1723–1728 (2011).
Fujii, S., Sato, N. & Shikanai, T. Mutagenesis of individual pentatricopeptide repeat motifs affects RNA binding activity and reveals functional partitioning of Arabidopsis PROTON gradient regulation3. Plant Cell 25, 3079–88 (2013).
Miranda, R. G., Rojas, M., Montgomery, M. P., Gribbin, K. P. & Barkan, A. RNA-binding specificity landscape of the pentatricopeptide repeat protein PPR10. Rna 23, 586–599 (2017).
Lai, W. S., Perera, L., Hicks, S. N. & Blackshear, P. J. Mutational and structural analysis of the tandem zinc finger domain of tristetraprolin. J. Biol. Chem. 289, 565–80 (2014).
Perez, E. E. et al. Establishment of HIV-1 resistance in CD4+ T cells by genome editing using zinc-finger nucleases. Nat. Biotechnol. 26, 808–816 (2008).
Chou, S.-T., Leng, Q. & Mixson, A. J. Zinc Finger Nucleases: Tailor-made for Gene Therapy. Drugs Future 37, 183–196 (2012).
Loughlin, F. E. et al. The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5′ splice site-like sequences. Proc. Natl. Acad. Sci. USA 106, 5581–6 (2009).
Nguyen, C. D. et al. Characterization of a family of RanBP2-type zinc fingers that can recognize single-stranded RNA. J. Mol. Biol. 407, 273–83 (2011).
Loughlin, F. E., Lee, M., Guss, J. M. & Mackay, J. P. Crystallization of a ZRANB2-RNA complex. Acta Crystallogr. Sect. F. Struct. Biol. Cryst. Commun. 64, 1175–7 (2008).
O’Connell, M. R. et al. Modular assembly of RanBP2-type zinc finger domains to target single-stranded RNA. Angew. Chem. Int. Ed. Engl. 51, 5371–5 (2012).
Vandevenne, M. et al. Engineering specificity changes on a RanBP2 zinc finger that binds single-stranded RNA. Angew. Chem. Int. Ed. Engl. 53, 7848–52 (2014).
Dna, T. & August, I. Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage El-T. Science (80-.). 249, 505–510 (1990).
Bailey, T. L. et al. MEME Suite: Tools for motif discovery and searching. Nucleic Acids Res. 37, 202–208 (2009).
McLaughlin, K. J., Jenkins, J. L. & Kielkopf, C. L. Large favorable enthalpy changes drive specific RNA recognition by RNA recognition motif proteins. Biochemistry 50, 1429–1431 (2011).
Vandevenne, M. et al. New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217. J. Biol. Chem. 288, 10616–27 (2013).
Brown, R. S. Zinc finger proteins: Getting a grip on RNA. Curr. Opin. Struct. Biol. 15, 94–98 (2005).
Hudson, B. P., Martinez-Yamout, M. A., Dyson, H. J. & Wright, P. E. Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d. Nat. Struct. Mol. Biol. 11, 257–64 (2004).
Sternberg, C. et al. New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria. Appl. Enviromental Miccrobiology 64, 2240–2246 (1998).
Dersch, P., Khan, M. A., Mühlen, S. & Görke, B. Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets. Front. Microbiol. 8, 803 (2017).
Timmer, T. et al. A comparison of genomic structures and expression patterns of two closely related flanking genes in a critical lung cancer region at 3p21.3. Eur. J. Hum. Genet. 7, 478–86 (1999).
Sugliani, M., Brambilla, V., Clerkx, E. J. M., Koornneef, M. & Soppe, W. J. J. The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis. Plant Cell 22, 1936–46 (2010).
Dichmann, D. S. & Harland, R. M. fus/TLS orchestrates splicing of developmental regulators during gastrulation. Genes Dev. 26, 1351–63 (2012).
Zhang, Z. et al. Splicing of receptor-like kinase-encoding SNC4 and CERK1 is regulated by two conserved splicing factors that are required for plant immunity. Mol. Plant 7, 1766–75 (2014).
Hernández, J. et al. Tumor suppressor properties of the splicing regulatory factor RBM10. RNA Biol. 13, 466–72 (2016).
Galiana-Arnoux, D., Del Gatto-Konczak, F., Gesnel, M. C. & Breathnach, R. Intronic UGG repeats coordinate splicing of CD44 alternative exons v8 and v9. Biochem. Biophys. Res. Commun. 336, 667–673 (2005).
McCullough, A. J. & Berget, S. M. G triplets located throughout a class of small vertebrate introns enforce intron borders and regulate splice site selection. Mol. Cell. Biol. 17, 4562–71 (1997).
McCullough, A. J. & Berget, S. M. An intronic splicing enhancer binds U1 snRNPs to enhance splicing and select 5′ splice sites. Mol. Cell. Biol. 20, 9225–35 (2000).
Webb, C. J., Romfo, C. M., van Heeckeren, W. J. & Wise, J. A. Exonic splicing enhancers in fission yeast: functional conservation demonstrates an early evolutionary origin. Genes Dev. 19, 242–54 (2005).
Rahman, M. A. et al. SRSF1 and hnRNP H antagonistically regulate splicing of COLQ exon 16 in a congenital myasthenic syndrome. Sci. Rep. 5, 13208 (2015).
Han, K., Yeo, G., An, P., Burge, C. B. & Grabowski, P. J. A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs. PLoS Biol. 3, e158 (2005).
Licchesi, J. D. F. et al. An ankyrin-repeat ubiquitin-binding domain determines TRABID’s specificity for atypical ubiquitin chains. Nat. Struct. Mol. Biol. 19, 62–71 (2011).
Dey, A., York, D., Smalls-Mantey, A. & Summers, M. F. Composition and sequence-dependent binding of RNA to the nucleocapsid protein of moloney murine leukemia virus. Biochemistry 44, 3735–3744 (2005).
Peters, D. T. et al. Human Lin28 Forms a High-Affinity 1:1 Complex with the 106~363 Cluster miRNA miR-363. Biochemistry 55, 5021–7 (2016).
Crooks, G., Hon, G., Chandonia, J. & Brenner, S. NCBI GenBank FTP Site\nWebLogo: a sequence logo generator. Genome Res 14, 1188–1190 (2004).
