Molecular organization of the 5S rDNA gene type II in elasmobranchs

References

• Long EO, David ID. Repeated genes in eukaryotes. Rev Biochem 1980; 49:727-64; http://dx.doi.org/10.1146/annurev.bi.49.070180.003455
   PubMed Web of Science ®Google Scholar
• Mindel DP, Honeycutt RL. Ribosomal RNA in vertebrates: evolution and phylogenetic applications. Annu Rev Ecol Syst 1990; 21:541-66; http://dx.doi.org/10.1146/annurev.es.21.110190.002545
   Google Scholar
• Lewin B. (ed.): Genes VI. Oxford University Press, New York 1997
   Google Scholar
• Barciszewska MZ, Szymanski M, Erdmann VA, Barciszewski J. Structure and function of 5S rDNA. Acta Biochim Pol 2001; 48:191-8; PMID:11440169
   PubMed Web of Science ®Google Scholar
• Nederby NH, Hallenberg C, Frederiksen S, Sorensen PD, Lomholt B. Transcription of human 5S rRNA genes is influenced by an upstream DNA sequences. Nucleic Acids Res 1993; 26:3631-6
   Google Scholar
• Campo D, Machado G, Horreo JL, García E. Molecular organization and evolution of 5S rDNA in the genus Merluccius and their phylogenetic implications. J Mol Evol 2009; 68:208-16; PMID:19247563; http://dx.doi.org/10.1007/s00239-009-9207-8
   PubMed Web of Science ®Google Scholar
• Pieler T, Oei S, Hamm J, Engelke U, Erdmann VA. Functional domains of the Xenopus laevis 5S gene promoter. EMBO J 1985; 4(13B):3751-6; PMID:3004969
   PubMed Web of Science ®Google Scholar
• Hallenberg C, Nederby J, Frederiksen S. Characterization of 5S rRNA genes from mouse. Gene (Amst.) 1994; 142:291-5; http://dx.doi.org/10.1016/0378-1119(94)90277-1
   PubMed Web of Science ®Google Scholar
• Pasolini P, Costagliola D, Rocco L, Tinti F. Molecular organization of 5S rDNA in Rajidae (Chondrichthyes): Structural features and evolution of piscine 5S rRNA genes and Nontranscribed intergenic spacer. J Mol Evol 2006; 62:564-74; PMID:16612546; http://dx.doi.org/10.1007/s00239-005-0118-z
   PubMed Web of Science ®Google Scholar
• Pinhal D, Yoshimura TS, Araki CS, Martins C. Molecular organization of 5S rDNA in sharks of the genus Rhizoprionodon: insights into the evolutionary dynamics of 5S rDNA in vertebrate genomes. Genet Res Camb 2009; 91:61-72; PMID:19220932; http://dx.doi.org/10.1017/S0016672308009993
   PubMed Web of Science ®Google Scholar
• Schramm L, Hernandez N. Recruitment of RNA polymerase III to its target promoters. Genes Dev 2002; 16:2593-620; PMID:12381659; http://dx.doi.org/10.1101/gad.1018902
   PubMed Web of Science ®Google Scholar
• Suzuki H, Sakurai S, Matsuda Y. Rat rDNA spacer sequences and chromosomal assignment of the genes to the extreme terminal region of chromosome 19. Cytogenetic Cell Genet 1996; 72:1-4; http://dx.doi.org/10.1159/000134149
   PubMedGoogle Scholar
• Pendas AM, Moran P, Freije JP, Garcia-Vazquez E. Chromosomal mapping and nucleotide sequence of two tandem repeats of Atlantic salmon 5S rDNA. Cytogenetic Cell Genet 1994; 67:31-6; http://dx.doi.org/10.1159/000133792
   PubMedGoogle Scholar
• Murakami M, Fujitani H. Characterization of repetitive DNA sequences carrying 5S rDNA of the triploid ginbuna (Japanese silver crucian carp, Carassius auratu langsdorfi). Genes Genet Syst 1998; 73:9-20; PMID:9546204; http://dx.doi.org/10.1266/ggs.73.9
   PubMed Web of Science ®Google Scholar
• Rocco L, Russo C, Stingo V, Aprea G, Odierna G. Characterization of 5S rDNA in Gasterosteus aculeatus (teleostei, Gasterosteidae). Ital J Zool 1999; 66:285-9; http://dx.doi.org/10.1080/11250009909356266
   Google Scholar
• Martins C, Galetti PM. Organization of 5S rDNA in species of the fish Leporinus: two different genomic locations are characterized by distinct nontranscribed spacers. Genome 2001; 44:903-10; PMID:11681615; http://dx.doi.org/10.1139/g01-069
   PubMed Web of Science ®Google Scholar
• Sakonju S, Bogenhagen DF, Brown DD. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5 border of the region. Cell 1980; 19:13-25; PMID:7357599; http://dx.doi.org/10.1016/0092-8674(80)90384-0
   PubMed Web of Science ®Google Scholar
• Ohta T, Dover G. The cohesive population genetics of molecular drive. Genetics 1984; 108:501-21; PMID:6500260
   PubMed Web of Science ®Google Scholar
• Zimmer EA, Martin SL, Beverly SM, Kan YW, Wilson AC. Rapid duplication and loss of genes coding for the α chains of hemoglobin. Proc Natl Acad Sci USA 1980; 77:2158-62; PMID:6929543; http://dx.doi.org/10.1073/pnas.77.4.2158
   PubMed Web of Science ®Google Scholar
• Dover GA. Molecular drive: a cohesive mode of species evolution. Nature 1982; 299:111-6; PMID:7110332; http://dx.doi.org/10.1038/299111a0
   PubMed Web of Science ®Google Scholar
• Elder JF, Turner BJ. Concerted evolution of repetitive DNA sequences in eukaryotes. Q Rev Biol 1995; 70:297-320; PMID:7568673; http://dx.doi.org/10.1086/419073
   PubMed Web of Science ®Google Scholar
• Hillis DM, Moritz C, Porter CA, Barker RJ. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science 1991; 251:308-10; PMID:1987647; http://dx.doi.org/10.1126/science.1987647
   PubMed Web of Science ®Google Scholar
• Liao D, Pavelitz T, Kidd J, Kidd K, Weiner A. Concerted evolution of the tandemly repeated genes encoding human U2 snRNA (the RNU2 locus) involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion. EMBO J 1997; 16:588-98; PMID:9034341; http://dx.doi.org/10.1093/emboj/16.3.588
   PubMed Web of Science ®Google Scholar
• Brown DD, Wensink PC, Jordan E. Xenopus laevis and Xenopus mulleri: the evolution of tandem genes. J Mol Biol 1972; 63:57-73; PMID:5016971; http://dx.doi.org/10.1016/0022-2836(72)90521-9
   PubMed Web of Science ®Google Scholar
• Walsh JB. Persistence of tandem arrays: implication for satellite and simple sequence DNAs. Genetics 1987; 115:553-67; PMID:3569882
   PubMed Web of Science ®Google Scholar
• Stephan W. Tandem-repetitive noncoding DNA: forms and forces. Mol Biol Evol 1989; 6:198-212; PMID:2716519
   PubMed Web of Science ®Google Scholar
• Martins C, Galetti PM. Two 5S rDNA arrays in neotropical fish species: is it a general rule for fishes? Genetica 2001; 111:439-46; PMID:11841188; http://dx.doi.org/10.1023/A:1013799516717
   PubMed Web of Science ®Google Scholar
• Pinhal D, Yoshimura TS, Araki CS, Martins C. The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genome: an example from freshwater stingray. BMC Evol Biol 2011; 11:151; PMID:21627815; http://dx.doi.org/10.1186/1471-2148-11-151
   PubMed Web of Science ®Google Scholar
• Pieler T, Hamm J, Roeder RG. The 5S gene internal control region is composed of three distinct sequences elements, organized as two functional domains with variable spacing. Cell 1987; 48:91-100; PMID:3791417; http://dx.doi.org/10.1016/0092-8674(87)90359-X
   PubMed Web of Science ®Google Scholar
• Sands MS, Bogenhagen DF. TFIIIA binds to different domains of 5S RNA and the Xenopus borealis 5S RNA gene. Mol Cell Biol 1987; 7:3985-93; PMID:3431548; http://dx.doi.org/10.1128/MCB.7.11.3985
   PubMed Web of Science ®Google Scholar
• You Q, Veldhoen N, Baudin F, Romaniuk PJ. Mutations in 5S DNA and 5S RNA have different effects on the binding of Xenopus transcription factor IIIA. Biochemistry 1991; 30:2495-500; PMID:2001375; http://dx.doi.org/10.1021/bi00223a028
   PubMed Web of Science ®Google Scholar
• Christensen JH, Hansen PK, Lillelund O, Thogersen HC. Sequence-specific binding of the N-terminal three-finger fragment of Xenopus transcription factor IIIA to the interval control region of a 5S RNA gene. FEBS Lett 1991; 281:181-4; PMID:2015891; http://dx.doi.org/10.1016/0014-5793(91)80388-J
   PubMed Web of Science ®Google Scholar
• Liao XB, Clements KR, Tannant L, Wright PG, Gottesfeld JM. Specific interaction of the first three zinc finger of TFIIIA with the internal control region of the Xenopus 5S RNA gene. J Mol Biol 1992; 223:857-71; PMID:1538401; http://dx.doi.org/10.1016/0022-2836(92)90248-I
   PubMed Web of Science ®Google Scholar
• Allison DS, Hall BD. Effects of alterations in the 3' flanking sequence on in vivo and in vitro expression of the yeast SUP4-0 tRNA Tyr gene. EMBO J 1985; 4:2657-64; PMID:3902472
   PubMed Web of Science ®Google Scholar
• Gunnery S, Ma Y, Mathews MB. Termination sequence requirements vary among genes transcribed by polymerase III. J Mol Biol 1999; 286:745-57; PMID:10024448; http://dx.doi.org/10.1006/jmbi.1998.2518
   PubMed Web of Science ®Google Scholar
• Hamada M, Sakulich AL, Koduru SB, Maraia RJ. Transcription termination by RNA polymerase III fission yeast. A genetic and biochemically tractable model system. J Biol Chem 2000; 275:29076-81; PMID:10843998; http://dx.doi.org/10.1074/jbc.M003980200
   PubMed Web of Science ®Google Scholar
• Bogenhagen DF, Brown DD. Nucleotide sequences in Xenopus 5S DNA required for transcription termination. Cell 1981; 24:261-70; PMID:6263489; http://dx.doi.org/10.1016/0092-8674(81)90522-5
   PubMed Web of Science ®Google Scholar
• Mazabraud A, Scherly D, Muller F, Rungger D, Clarkson SG. Structure and transcription termination of a lysine tRNA gene from Xenopus laevis. J Mol Biol 1987; 195:835-45; PMID:2443712; http://dx.doi.org/10.1016/0022-2836(87)90488-8
   PubMed Web of Science ®Google Scholar
• Akusjarvi G, Mathews MB, Andersson P, Vennstrom B, Petterson U. Structure of genes for virus-associated RNAI and RNAII of adenovirus type-2. Proc Natl Acad Sci USA 1980; 77:2424-8; PMID:6930642; http://dx.doi.org/10.1073/pnas.77.5.2424
   PubMed Web of Science ®Google Scholar
• Liao JY, Ma LM, Guo YH, Zhang YC, Zhou H, Shao P, Chen YQ, Qu LH. Deep Sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex sub cellular distribution of miRNAs and tRNA 3' trailers. Plos One 2010; 5:e10563; PMID:20498841; http://dx.doi.org/10.1371/journal.pone.0010563
   PubMed Web of Science ®Google Scholar
• Kriwet J, Kiessling W, Klug S. Diversification trajectories and evolutionary life-history in early sharks and batoids. Proc R Soc B 2009; 276:945-51; PMID:19129130; http://dx.doi.org/10.1098/rspb.2008.1441
   PubMed Web of Science ®Google Scholar
• Dunn KA, Morressey JF. Molecular phylogeny of elasmobranchs. Copeia 1995; 3:526-31; http://dx.doi.org/10.2307/1446750
   Web of Science ®Google Scholar
• Kitamura T, Takemura A, Watabe S, Taniuchi T, Shimizu M. Molecular phylogeny of the sharks and rays of superorder Squalea based on mitochondrial cytochrome b gene. Fisheries Science 1996; 62:340-3
   Web of Science ®Google Scholar
• Douady CJ, Dosay M, Shivji MS, Stanhope MJ. Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol Phyl Evol 2003; 26:215-21; http://dx.doi.org/10.1016/S1055-7903(02)00333-0
   PubMed Web of Science ®Google Scholar
• Winchell CJ, Martin AP, Mallatt J. Phylogeny of elasmobranchs based on LSU and SSU ribosomal genes. Mol Phyl Evol 2004; 31:214-24; http://dx.doi.org/10.1016/j.ympev.2003.07.010
   PubMed Web of Science ®Google Scholar
• Human BA, Owen EP, Compagno LVJ, Harley EH. Testing morphologically based phylogenetic theories within the cartilaginous fishes with molecular data, with special reference to the catshark family (Chondrichthyes: Scyliorhinidae) and the interrelationships among them. Mol Phyl Evol 2006; 39:384-91; http://dx.doi.org/10.1016/j.ympev.2005.09.009
   PubMed Web of Science ®Google Scholar
• Compagno LVJ. Sharks of the World. An annotated and illustrated catalogue of sharks species know to date. Volume 2. Bullhead, mackerel and carpet sharks (Heterodontiformes, Lamniformes and Orectolobiformes). FAO Species Catalogue for Fishery Purposes 2002; 2:1-3
   Google Scholar
• Barciszewska MZ, Szymaski M, Erdmann VA, Barciszewski J. 5S ribosomal RNA. Biomacromolecules 2000; 1:291-302; http://dx.doi.org/10.1021/bm000293o
   Web of Science ®Google Scholar
• Clements KR, Wolf V, McBryant SJ, Zhang P, Liao XB, Wright PE, Romaniuk PJ, Gottesfeld JM. Molecular basis for specific recognition of both RNA and DNA by a zinc finger protein. Science 1993; 260:530-3; PMID:8475383; http://dx.doi.org/10.1126/science.8475383
   PubMed Web of Science ®Google Scholar
• Neely LS, Lee BM, Xu J, Wright PE, Gottesfeld JM. Identification of a minimal domain of 5S ribosomal RNA sufficient for high affinity interaction with the RNA-specific zinc finger of transcription factor IIIA. J Mol Biol 1999; 291:549-60; PMID:10448036; http://dx.doi.org/10.1006/jmbi.1999.2985
   PubMed Web of Science ®Google Scholar
• Theunissen O, Rudt F, Pieler T. Structural determinants in 5S RNA and TF IIIA for 7S RNP formation. Eur J Biochem 1998; 258:758-67; PMID:9874245; http://dx.doi.org/10.1046/j.1432-1327.1998.2580758.x
   PubMedGoogle Scholar
• Hanas JS, Gaskins CJ, Smith JF, Ogilvie MK. Structure, function, evolution of transcription factor IIIA. Prog Nucleic Acid Res Mol Biol 1992; 43:205-39; PMID:1410446; http://dx.doi.org/10.1016/S0079-6603(08)61048-X
   PubMed Web of Science ®Google Scholar
• Pieler T, Theunissen O. Nine fingers - three hands? Trends Biochem Sci 1993; 18:226-30; PMID:7688487; http://dx.doi.org/10.1016/0968-0004(93)90194-R
   PubMed Web of Science ®Google Scholar
• Shastry BS. Transcription factor IIIA (TFIIIA) in the second decade. Cell Science 1996; 109:535-9
   PubMed Web of Science ®Google Scholar
• McBryant SJ, Veldhoen N, Gedulin B, Leresche A, Foster MP, Wright PE, Ramaniuk PJ, Gottesfeld JM. Interaction of the RNA binding fingers of Xenopus transcription factor IIIA with specific regions of 5S ribosomal RNA. J Mol Biol 1995; 248:44-57; PMID:7731045; http://dx.doi.org/10.1006/jmbi.1995.0201
   PubMed Web of Science ®Google Scholar
• Sun FJ, Caetano-Anollés G. The evolutionary history of the structure of 5S ribosomal RNA. J Mol Evol 2009; 69:430-543; PMID:19639237; http://dx.doi.org/10.1007/s00239-009-9264-z
   PubMed Web of Science ®Google Scholar
• Hosikawa Y, Iida Y, Iwabuchi M. Nucleotide sequence of the transcriptional initiation region of Dictyostelium discoideum rRNA gene and comparison of the initiation regions of three lower eukaryotes genes. Nucl Acids Res 1983; 11:1725-34; PMID:6300775; http://dx.doi.org/10.1093/nar/11.6.1725
   PubMed Web of Science ®Google Scholar
• Suzuki H, Moriwaki K, Sakurai S. Sequences and evolutionary analysis of mouse 5S rDNA. Mol Biol Evol 1994; 11:704-10; PMID:8078409
   PubMed Web of Science ®Google Scholar
• Hallenberg C, Frederiksen S. Effects of mutations in the upstream promoter on the transcription of human 5S rRNA genes. Biochim Biophys Acta 2001; 1520:169-73; PMID:11513959; http://dx.doi.org/10.1016/S0167-4781(01)00264-0
   PubMed Web of Science ®Google Scholar
• Inafaku J, Nabeyama M, Kikuma Y, Saitoh J, Kubota S, Kohono S. Chromosomal location and nucleotide sequence of 5S ribosomal DNA of two cyprinid species (Osteichthyes, Pisces). Chromosome Res 2000; 8:193-9; PMID:10841046; http://dx.doi.org/10.1023/A:1009292610618
   PubMed Web of Science ®Google Scholar
• Brown DA, Guthrie C. Transcription of a yeast U6 snRNA gene requires a polymerase III promoter element in a novel position. Genes Dev 1990; 4:1345-56; PMID:2227412; http://dx.doi.org/10.1101/gad.4.8.1345
   PubMed Web of Science ®Google Scholar
• Eschenlauer JB, Kaiser MW, Gerlach VL, Brown DA. Architecture of a yeast U6 RNA gene promoter. Mol Cell Biol 1993; 13:3015-26; PMID:8474459
   PubMed Web of Science ®Google Scholar
• Yukawa Y, Sugita M, Choisne N, Small I, Sugiura M. The TATA motif, the CAA motif and the poly(T) transcription termination motif are important for transcription re-initiation on plant tRNA. Plant J 2000; 22:439-47; PMID:10849359; http://dx.doi.org/10.1046/j.1365-313X.2000.00752.x
   PubMed Web of Science ®Google Scholar
• Dieci G, Percudani R, Giuliodori S, Bottarelli L, Ottonello S. TFIIIC-independent in vitro transcription of yeast tRNA genes. J Mol Biol 2000; 299:601-13; PMID:10835271; http://dx.doi.org/10.1006/jmbi.2000.3783
   PubMed Web of Science ®Google Scholar
• Ouyang C, Martinez MJ, Young LS, Sprague KU. TATA-binding protein-TATA interaction is a key determinant of differential transcription of skillworn constitutive and silk gland-specific tRNA Ala genes. Mol Cell Biol 2000; 20:1329-43; PMID:10648619; http://dx.doi.org/10.1128/MCB.20.4.1329-1343.2000
   PubMed Web of Science ®Google Scholar
• Catasti P, Chen X, Mariappan SV, Bradbury EM, Gupta G. DNA repeats in the human genome. Genetica 1999; 106:15-36; PMID:10710707; http://dx.doi.org/10.1023/A:1003716509180
   PubMed Web of Science ®Google Scholar
• Valsecchi E, Pasolini P, Bertozzi M, Garoia F, Ungaro N, Vacchi M, Sabelli B, Tinti F. Rapid Miocene-Pliocene dispersal and evolution of Mediterranean rajid fauna as inferred by mitochondrial gene variation. J Evol Biol 2005; 18:436-46; PMID:15715849; http://dx.doi.org/10.1111/j.1420-9101.2004.00829.x
   PubMed Web of Science ®Google Scholar
• Rocco L, Costagliola D, Fiorillo M, Tinti F, Stingo V. Molecular and chromosomal analysis of ribosomal cistrons in two cartilaginous fish, Taeniura lymma and Raja montagui (Chondricthyes, Batoidea). Genetica 2005; 123:245-53; PMID:15954495; http://dx.doi.org/10.1007/s10709-004-2451-3
   PubMed Web of Science ®Google Scholar
• Longmire JL, Maltbie M, Baker RJ. Use of “lysis buffer” in DNA isolation and its implications for museum collection. Occasional Papers, The Museum of Texas Tech University 1997; 163:1-3
   Google Scholar
• Hleap JS, Cárdenas H, García-Vallejo F. Preservación no criogénica de tejido y extracción de ADN: Una aplicación para peces cartilaginosos. PanamJAS 2009; 4:283-93
   Google Scholar
• Lis JT. Fractionation of DNA fragments by polyethylene glycol induced precipitation. Methods Enzymol 1980; 65:347-53; PMID:6246357; http://dx.doi.org/10.1016/S0076-6879(80)65044-7
   PubMedGoogle Scholar
• Morgulis A, Coulouris G, Raytselis Y, Madden TL, Agarwala R, Schaffer AA. Database indexing for production MegaBLAST searches. Bioinformatics 2008; 24:1757-64; PMID:18567917; http://dx.doi.org/10.1093/bioinformatics/btn322
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acid Res 2004; 32:1792-7; PMID:15034147; http://dx.doi.org/10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular evolutionary genetics analysis using Maximum Likelihood, Evolutionary distances, and Maximum parsimony methods. Mol Biol Evol 2011; 282731-2739
   Google Scholar
• Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator. Genome Res 2004; 14:1188-90; PMID:15173120; http://dx.doi.org/10.1101/gr.849004
   PubMed Web of Science ®Google Scholar
• Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 2008; 9:474; PMID:19014431; http://dx.doi.org/10.1186/1471-2105-9-474
   PubMed Web of Science ®Google Scholar
• Hofacker IL, Fekete M, Stadler PF. Secondary Structure Prediction for Aligned RNA Sequences. J Mol Biol 2002; 319:1059-66; PMID:12079347; http://dx.doi.org/10.1016/S0022-2836(02)00308-X
   PubMed Web of Science ®Google Scholar
• Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplataform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010; 27:221-4; PMID:19854763; http://dx.doi.org/10.1093/molbev/msp259
   PubMed Web of Science ®Google Scholar
• Clarck PJ, Evans FC. Distance to nearest neighbor as a measure of spatial relationships in populations. Ecology 1954; 35:445-53; http://dx.doi.org/10.2307/1931034
   Web of Science ®Google Scholar
• Loosmore N, Ford ED. Statistical inference using the G or K point pattern spatial statistics. Ecology 2006; 87:1925-31; PMID:16937629; http://dx.doi.org/10.1890/0012-9658(2006)87%5b1925:SIUTGO%5d2.0.CO;2
   PubMed Web of Science ®Google Scholar
• Baddeley A, Turner R. Spatstat: an R package for analyzing spatial point patterns. J Stat Soft 2005; 12:1-42; http://dx.doi.org/10.18637/jss.v012.i06
   Web of Science ®Google Scholar
• Huthoff H, Girard F, Wijmenga SS, Berkhout B.: Evidence for a base triple in the free HIV-1 TAR RNA. RNA 2004; 10:412-23; PMID:14970387; http://dx.doi.org/10.1261/rna.5161304
   PubMed Web of Science ®Google Scholar
• Ben-Shem A, Jenner L, Yusupova G, Yusupov M. Crystal Structure of the Eukaryotic Ribosome. Science 2010; 330:1203-9; PMID:21109664; http://dx.doi.org/10.1126/science.1194294
   PubMed Web of Science ®Google Scholar