[1]
|
Banfi, S., Borsani, G., Rossi, E., Bernard, L., Guffanti, A., Rubboli, F., Marchitiello, A., Giglio, S., Coluccia, E. and Zollo, M. (1996). Identification and mapping of human cDNAs homologous to Drosophila mutant genes through EST database searching. Nature Genetics, 13, 167-174. http://dx.doi.org/10.1038/ng0696-167
|
[2]
|
Fortini, M.E., Skupski, M.P., Boguski, M.S. and Hariharan, I.K. (2000) A survey of human disease gene counterparts in the Drosophila genome. The Journal of Cell Biology, 150, F23-F30. http://dx.doi.org/10.1083/jcb.150.2.F23
|
[3]
|
Petschek, J.P., Scheckelhoff, M.R., Mermer, M.J. and Vaughn, J.C. (1997) RNA editing and alternative splicing generate mRNA transcript diversity from the Drosophila 4f-rnp locus. Gene, 204, 267-276. http://dx.doi.org/10.1016/S0378-1119(97)00465-4
|
[4]
|
Feiber, A.L., Rangarajan, J. and Vaughn, J.C. (2002) The evolution of single-copy Drosophila nuclear 4f-rnp genes, spliceosomal intron losses create polymorphic alleles. Journal of Molecular Evolution, 55, 401-413. http://dx.doi.org/10.1007/s00239-002-2336-y
|
[5]
|
Peters, N.T., Rohrbach, J.A., Zalewski, B.A., Byrkett, C.M. and Vaughn, J.C. (2003) RNA editing and regulation of Drosophila 4f-rnp expression by sas-10 antisense readthrough mRNA transcripts. RNA, 9, 698-710. http://dx.doi.org/10.1261/rna.2120703
|
[6]
|
Fetherson, R.A., Strock, S.B., White, K.N. and Vaughn, J.C. (2006) Alternative pre-mRNA splicing in Drosophila spliceosomal assembly factor RNP-4F during development. Gene, 371, 234-245. http://dx.doi.org/10.1016/j.gene.2005.12.025
|
[7]
|
Chen, J., Concel, V.J., Bhatla, S., Rajeshwaran, R., Smith, D.L.H., Varadarajan, M., Backscheider, K.L., Bockrath, R.A., Petschek, J.P. and Vaughn, J.C. (2007) Alternative splicing of an rnp-4f mRNA isoform retaining an evolutionarily-conserved 5’-UTR intronic element is developmentally regulated and shown via RNAi to be essential for normal central nervous system development in Drosophila melanogaster. Gene, 399, 91-104. http://dx.doi.org/10.1016/j.gene.2007.04.038
|
[8]
|
Chen, J., Lakshmi, G.G., Hays, D.L., McDowell, K.M., Ma, E. and Vaughn, J.C. (2009) Spatial and temporal expression of dADAR mRNA and protein isoforms during embryogenesis in Drosophila melanogaster. Differentiation, 78, 312-320. http://dx.doi.org/10.1016/j.diff.2009.08.003
|
[9]
|
Lakshmi, G.G., Ghosh, S., Jones, G.P., Parikh, R., Rawlins, B.A. and Vaughn, J.C. (2012) An RNA electrophoretic mobility shift and mutational analysis of rnp-4f 5’-UTR intron splicing regulatory proteins in Drosophila reveals a novel new role for a dADAR protein isoform. Gene, 511, 161-168. http://dx.doi.org/10.1016/j.gene.2012.09.088
|
[10]
|
Chen, J., Yang, J.T., Doctor, D.L., Rawlins, B.A., Shields, B.C. and Vaughn, J.C. (2013) 5’-UTR mediated translational control of splicing assembly factor RNP-4F expression during development of the Drosophila central nervous system. Gene, 528,154-162.
|
[11]
|
Ghosh, S., Wang, Y., Cook, J.A., Chhiba, L. and Vaughn, J.C. (2013) A molecular, phylogenetic and functional study of the dADAR mRNA truncated isoform during Drosophila embryonic development. Open Journal of Animal Sciences, (In press).
|
[12]
|
Brow, D.A. and Guthrie, C. (1988) Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature, 334, 213-218. http://dx.doi.org/10.1038/334213a0
|
[13]
|
Bell, M., Schreiner, S., Damianov, A., Reddy, R. and Bindereif, A. (2002) p110, a novel human U6 snRNP protein and U4/U6 snRNP recycling factor. The EMBO Journal, 21, 2724-2735. http://dx.doi.org/10.1093/emboj/21.11.2724
|
[14]
|
Rader, S.D. and Guthrie, C. (2002) A conserved Lsminteraction motif in Prp24 required for efficient U4/U6 di-snRNP formation. RNA, 8, 1378-1392. http://dx.doi.org/10.1017/S1355838202020010
|
[15]
|
Karaduman, R., Fabrizio, P., Hartmuth, K., Urlaub, H. and Luhrmann, R. (2006) RNA structure and RNA-protein interactions in purified yeast U6 snRNPs. Journal of Molecular Biology, 356, 1248-1262. http://dx.doi.org/10.1016/j.jmb.2005.12.013
|
[16]
|
Bae, E., Reiter, N.J., Bingman, C.A., Kwan, S.S., Lee, D., Phillips, G.N., Butcher, S.E. and Brow, D.A. (2007) Structure and interactions of the first three RNA recognition motifs of splicing factor Prp24. Journal of Molecular Biology, 367, 1447-1458. http://dx.doi.org/10.1016/j.jmb.2007.01.078
|
[17]
|
Moore, M.J., Query, C.C. and Sharp, P.A. (1993) Splicing of precursors to mRNA by the spliceosome. In: Gesteland, R.F. and Atkins, J.F., Ed., The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 303-357.
|
[18]
|
Will, C.L. and Luhrmann, R. (2006) Spliceosome structure and function. In: Gesteland, R.F., Cech, T.R. and Atkins, J.F., Ed., The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 369-400.
|
[19]
|
Jurica, M.S. and Moore, M.J. (2003) Pre-mRNA splicing, awash in a sea of proteins. Molecular Cell, 12, 5-14. http://dx.doi.org/10.1016/S1097-2765(03)00270-3
|
[20]
|
Noller, H.F., Kop, J.A., Wheaton, V., Brosius, J., Gutell, R.R., Kopylov, A.M., Dohme, F., Herr, W., Stahl, D.A., Gupta, R. and Woese, C.R. (1981) Secondary structure model for 23S ribosomal RNA. Nucleic Acids Research, 9, 6167-6189. http://dx.doi.org/10.1093/nar/9.22.6167
|
[21]
|
Vaughn, J.C., Sperbeck, S.J., Ramsey, W.J. and Lawrence, C.B. (1984) A universal model for the secondary structure of 5.8S ribosomal RNA molecules, their contact sites with 28S ribosomal RNAs, and their prokaryotic equivalent. Nucleic Acids Research, 12, 7479-7502. http://dx.doi.org/10.1093/nar/12.19.7479
|
[22]
|
Orum, H., Nielsen, H. and Engberg, J. (1991) Spliceosomal small nuclear RNAs of Tetrahymena thermophila and some possible snRNA-snRNA base-pairing interactions. Journal of Molecular Biology, 222, 219-232. http://dx.doi.org/10.1016/0022-2836(91)90208-N
|
[23]
|
Hofmann, C.J.B., Marshallsay, C., Waibel, F. and Filipowicz, W. (1992) Characterization of the genes encoding U4 small nuclear RNAs in Arabidopsis thaliana. Molecular Biology Reports, 17, 21-28. http://dx.doi.org/10.1007/BF01006396
|
[24]
|
Jakab, G., Mougin, A., Kis, M., Pollak, T., Antal, M., Branlant, C. and Solymosy, F. (1997) Chlamydomonas U2, U4 and U6 snRNAs. An evolutionary conserved putative third interaction between U4 and U6 snRNAs which has a counterpart in the U4atac-U6atac snRNA duplex. Biochimie, 79, 387-395. http://dx.doi.org/10.1016/S0300-9084(97)86148-2
|
[25]
|
Hinas, A., Larsson, P., Avesson, L., Kirsebom, L.A., Virtanen, A. and Soderbom, F. (2006) Identification of the major spliceosomal RNAs in Dictyostelium discoideum reveals developmentally regulated U2 variants and polyadenylated snRNAs. Eukaryot. Cell, 5, 924-934. http://dx.doi.org/10.1128/EC.00065-06
|
[26]
|
Davis, C.A., Brown, M.P.S. and Singh, U. (2007) Functional characterization of spliceosomal introns and identification of U2, U4, and U5 snRNAs in the deep-branching eukaryote Entamoeba histolytica. Eukaryotic Cell, 6, 940-948. http://dx.doi.org/10.1128/EC.00059-07
|
[27]
|
Gu, J., Chen, Y. and Reddy, R. (1998) Small RNA database. Nucl. Acids Res. 26, 160-162. http://dx.doi.org/10.1093/nar/26.1.160
|
[28]
|
Stark, A., Lin, M.F., Kheradpour, P., et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature, 450, 219-232. http://dx.doi.org/10.1038/nature06340
|
[29]
|
Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31, 3406-3415. http://dx.doi.org/10.1093/nar/gkg595
|
[30]
|
Rinke, J., Appel, B., Digweed, M. and Luhrmann, R. (1985) Localization of a base paired interaction between small nuclear RNAs U4 and U6 in intact U4/U6 ribonucleoprotein particles by psoralem cross-linking. Journal of Molecular Biology, 185, 721-731. http://dx.doi.org/10.1016/0022-2836(85)90057-9
|
[31]
|
Steenkamp, E.T., Wright, J. and Baldauf, S.L. (2006). The protistan origins of animals and fungi. Molecular Biology and Evolution, 23, 93-106. http://dx.doi.org/10.1093/molbev/msj011
|
[32]
|
Myslinski, E. and Branlant, C. (1991) A phylogenetic study of U4 snRNA reveals the existence of an evolutionarily conserved secondary structure corresponding to “free” U4 snRNA. Biochimie, 73, 17-28. http://dx.doi.org/10.1016/0300-9084(91)90069-D
|
[33]
|
Mitrovich, Q.M. and Guthrie, C. (2007) Evolution of small nuclear RNAs in S. cerevisiae, C. albicans, and other hemiascomycetous yeasts. RNA, 13, 2066-2080. http://dx.doi.org/10.1261/rna.766607
|
[34]
|
Krol, A., Branlant, C., Lazar, E., Gallinaro, H. and Jacob, M. (1988) Primary and secondary structures of chicken, rat and man nuclear U4 RNAs. Homologies with U1 and U5 RNAs. Nucleic Acids Research, 9, 2699-2716. http://dx.doi.org/10.1093/nar/9.12.2699
|
[35]
|
Epstein, P., Reddy, R., Henning, D. and Busch, H. (1980). The nucleotide sequence of nuclear U6 (4.7S) RNA. Journal of Molecular Biology, 255, 8901-8906.
|
[36]
|
Fortner, D.M., Troy, R.G. and Brow, D.A. (1994) A stem/loop in U6 RNA defines a conformational switch required for pre-mRNA splicing. Genes & Development, 8, 221-233. http://dx.doi.org/10.1101/gad.8.2.221
|
[37]
|
Mougin, A., Gottschalk, A., Fabrizio, P., Luhrmann, R. and Branlant, C. (2002) Direct probing of RNA structure and RNA-protein interactions in purified HeLa cell’s and yeast spliceosomal U4/U6.U5 tri-snRNP particles. Journal of Molecular Biology, 317, 631-649. http://dx.doi.org/10.1006/jmbi.2002.5451
|
[38]
|
Stark, H. and Luhrmann, R. (2006) Cryo-electron microscopy of spliceosomal components. Annual Review of Biophysics and Biomolecular Structure, 35, 435-457. http://dx.doi.org/10.1146/annurev.biophys.35.040405.101953
|
[39]
|
McArthur, A.G., Morrison, H.G., Nixon, J.E.J., et al. (2000) The Giardia genome project database. FEMS Microbiology Letters, 189, 271-273. http://dx.doi.org/10.1111/j.1574-6968.2000.tb09242.x
|
[40]
|
Carlton, J.M., Hirt, R.P., Silva, J.C., et al. (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science, 315, 207-212. http://dx.doi.org/10.1126/science.1132894
|
[41]
|
Bonen, L. and Vogel, J. (2001) The ins and outs of group II introns. Trends in Genetics, 17, 322-331. http://dx.doi.org/10.1016/S0168-9525(01)02324-1
|
[42]
|
Fedorova, O. and Zingler, N. (2007) Group II introns, structure, folding and splicing mechanism. The Journal of Biological Chemistry, 388, 665-678. http://dx.doi.org/10.1515/BC.2007.090
|
[43]
|
Vanacova, S., Yan, W., Carlton, J.M. and Johnson, P.J. (2005) Spliceosomal introns in the deep-branching eukaryote Trichomonas vaginalis. Proceedings of the National Academy of Sciences, 102, 4430-4435. http://dx.doi.org/10.1073/pnas.0407500102
|