{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,2,22]],"date-time":"2024-02-22T10:06:46Z","timestamp":1708596406652},"reference-count":58,"publisher":"World Scientific Pub Co Pte Ltd","issue":"01","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2010,2]]},"abstract":"<jats:p>The structures attained by RNA molecules depend not only on their sequence but also on environmental parameters such as their temperature. So far, this effect has been largely neglected in bioinformatics studies. Here, we show that structural comparisons can be facilitated and more coherent structural models can be obtained when differences in environmental parameters are taken into account. We re-evaluate the secondary structures of the spliced leader (SL) RNAs from the seven eukaryotic phyla in which SL RNA trans-splicing has been described. Adjusting structure prediction to the natural growth temperatures and considering energetically similar secondary structures, we observe striking similarities among Euglenida, Kinetoplastida, Dinophyceae, Cnidaria, Rotifera, Nematoda, Platyhelminthes, and Tunicata that cannot be explained easily by the independent innovation of SL RNAs in each of these phyla. Supplementary Table is available at .<\/jats:p>","DOI":"10.1142\/s0219720010004525","type":"journal-article","created":{"date-parts":[[2010,2,22]],"date-time":"2010-02-22T11:18:45Z","timestamp":1266837525000},"page":"1-17","source":"Crossref","is-referenced-by-count":8,"title":["TEMPERATURE-DEPENDENT STRUCTURAL VARIABILITY OF RNAs: SPLICED LEADER RNAs AND THEIR EVOLUTIONARY HISTORY"],"prefix":"10.1142","volume":"08","author":[{"given":"MANJA","family":"MARZ","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, University of Leipzig, H\u00e4rtelstra\u00dfe 16-18, D-04107 Leipzig, Germany"}]},{"given":"NATHALIE","family":"VANZO","sequence":"additional","affiliation":[{"name":"Centre de Biologie du D\u00e9veloppement, UMR 5547 C. N. R. S. Universit\u00e9 Paul Sabatier, F-31062 Toulouse Cedex, France"}]},{"given":"PETER F.","family":"STADLER","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, H\u00e4rtelstra\u00dfe 16-18, D-04107 Leipzig, Germany"},{"name":"Max Planck Institute for Mathematics in the Sciences, Inselstra\u00dfe 22, D-04103 Leipzig, Germany"},{"name":"Fraunhofer Institut f\u00fcr Zelltherapie und Immunologie \u2013 IZI, Perlickstra\u00dfe 1, D-04103 Leipzig, Germany"},{"name":"Department of Theoretical Chemistry, University of Vienna, W\u00e4hringerstra\u00dfe 17, A-1090 Wien, Austria"},{"name":"Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA"}]}],"member":"219","published-online":{"date-parts":[[2011,11,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1999.2700"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkl472"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg595"},{"key":"rf4","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg599"},{"key":"rf5","first-page":"13","volume":"22","author":"Bonhoeffer S.","journal-title":"Eur. Biophys. J."},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(86)90616-1"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2005.02.005"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1016\/S0168-9525(01)02499-4"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000315"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(84)90267-8"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/12.11.4431"},{"key":"rf12","doi-asserted-by":"crossref","first-page":"2621","DOI":"10.1002\/j.1460-2075.1991.tb07804.x","volume":"10","author":"Tessier L. H.","journal-title":"EMBO J."},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(87)90613-1"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.87.22.8879"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.101049998"},{"key":"rf16","doi-asserted-by":"publisher","DOI":"10.1101\/gad.865401"},{"key":"rf17","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.24.17.7795-7805.2004"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi139"},{"key":"rf19","doi-asserted-by":"publisher","DOI":"10.1111\/j.1550-7408.2007.00282.x"},{"key":"rf20","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0700258104"},{"key":"rf21","first-page":"1025","volume":"26","author":"Blaxter M.","journal-title":"Int. J. Parasitol."},{"key":"rf22","doi-asserted-by":"publisher","DOI":"10.1261\/rna.948008"},{"key":"rf23","doi-asserted-by":"publisher","DOI":"10.1128\/MCB.20.18.6659-6667.2000"},{"key":"rf24","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki081"},{"key":"rf25","doi-asserted-by":"publisher","DOI":"10.1007\/s002940000116"},{"key":"rf26","first-page":"714","volume":"1","author":"Maroney P. A.","journal-title":"RNA"},{"key":"rf27","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(01)00438-3"},{"key":"rf28","doi-asserted-by":"publisher","DOI":"10.1016\/S0166-6851(01)00331-0"},{"key":"rf29","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msg225"},{"key":"rf30","doi-asserted-by":"crossref","first-page":"20026","DOI":"10.1016\/S0021-9258(17)32122-1","volume":"269","author":"Davis R. E.","journal-title":"J. Biol. Chem."},{"key":"rf31","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M006091200"},{"key":"rf32","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msi200"},{"key":"rf33","doi-asserted-by":"publisher","DOI":"10.1007\/s002940050451"},{"key":"rf34","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/14.18.7341"},{"key":"rf35","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/15.7.3141"},{"key":"rf36","doi-asserted-by":"publisher","DOI":"10.1016\/0006-291X(92)91838-H"},{"key":"rf37","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm404"},{"key":"rf39","doi-asserted-by":"publisher","DOI":"10.1126\/science.2468181"},{"key":"rf40","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G"},{"key":"rf42","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msj030"},{"key":"rf44","doi-asserted-by":"publisher","DOI":"10.1042\/BC20050083"},{"key":"rf45","first-page":"11","author":"Guiliano D. B.","journal-title":"PLoS Genet."},{"key":"rf46","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-192"},{"key":"rf47","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msp083"},{"key":"rf48","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.274.45.31947"},{"key":"rf49","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(02)00308-X"},{"key":"rf50","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-5-105"},{"key":"rf51","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkh983"},{"key":"rf52","doi-asserted-by":"publisher","DOI":"10.1038\/419270a"},{"key":"rf53","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0003106"},{"key":"rf54","doi-asserted-by":"publisher","DOI":"10.1261\/rna.1045408"},{"key":"rf55","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg213"},{"key":"rf56","doi-asserted-by":"crossref","first-page":"3869","DOI":"10.1002\/j.1460-2075.1991.tb04956.x","volume":"10","author":"Maroney P. A.","journal-title":"EMBO J."},{"key":"rf57","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80687-X"},{"key":"rf58","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M708032200"},{"key":"rf59","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-007-9052-6"},{"key":"rf60","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msn140"},{"key":"rf61","doi-asserted-by":"publisher","DOI":"10.1007\/BF00818163"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720010004525","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,23]],"date-time":"2021-10-23T17:32:15Z","timestamp":1635010335000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720010004525"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,2]]},"references-count":58,"journal-issue":{"issue":"01","published-online":{"date-parts":[[2011,11,21]]},"published-print":{"date-parts":[[2010,2]]}},"alternative-id":["10.1142\/S0219720010004525"],"URL":"https:\/\/doi.org\/10.1142\/s0219720010004525","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,2]]}}}