Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes

dc.contributor.authorSchwartz, Schraga H.en
dc.contributor.authorSilva, Joaoen
dc.contributor.authorBurstein, Daviden
dc.contributor.authorPupko, Talen
dc.contributor.authorEyras, Eduardoen
dc.contributor.authorAst, Gilen
dc.date.accessioned2025-06-16T17:36:00Z
dc.date.available2025-06-16T17:36:00Z
dc.date.issued2008en
dc.description.abstractIntrons are among the hallmarks of eukaryotic genes. Splicing of introns is directed by three main splicing signals: the 5' splice site (5'ss), the branch site (BS), and the polypyrimdine tract/3'splice site (PPT-3'ss). To Study the evolution of these splicing signals, we have conducted a systematic comparative analysis of these signals in over 1.2 million introns from 22 eukaryotes. our analyses suggest that all these signals have dramatically evolved: The PPT is weak among most fungi, intermediate in plants and protozoans, and strongest in metazoans. Within metazoans it shows a gradual strengthening from Caenorhabditis elegans to human. The 5'ss and the BS were found to be degenerate among most organisms, but highly conserved among some fungi. A maximum parsimony-based algorithm for reconstructing ancestral position-specific scoring matrices suggested that the ancestral 5'ss and BS were degenerate, as in metazoans. To shed light on the evolutionary variation in splicing signals, we have analyzed the evolutionary changes in the factors that bind these signals. Our analysis reveals coevolution of splicing signals and their corresponding splicing factors: The strength of the PPT is correlated to changes in key residues in its corresponding splicing factor U2AF2; limited correlation was found between changes in the 5'ss and Ul snRNA that binds it; but not between the BS and U2 snRNA. Thus, although the basic ability of eukaryotes to splice introns has remained conserved throughout evolution, the splicing signals and their corresponding splicing factors have considerably evolved, uniquely shaping the splicing mechanisms of different organisms.en
dc.description.statusPeer-revieweden
dc.format.extent16en
dc.identifier.otherWOS:000251965300010en
dc.identifier.otherPubMed:18032728en
dc.identifier.otherScopus:38049029652en
dc.identifier.otherORCID:/0000-0003-0793-6218/work/162948942en
dc.identifier.urihttps://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=anu_research_portal_plus2&SrcAuth=WosAPI&KeyUT=WOS:000251965300010&DestLinkType=FullRecord&DestApp=WOS_CPLen
dc.identifier.urihttps://hdl.handle.net/1885/733763691
dc.language.isoenen
dc.sourceGenome Researchen
dc.subjectAuxiliary factor u2af(65)en
dc.subjectPolypyrimidine tracten
dc.subjectBranch-siteen
dc.subjectFission yeasten
dc.subjectIntron lossen
dc.subjectRnaen
dc.subjectSequenceen
dc.subjectU2en
dc.subjectEvolutionen
dc.subjectConservationen
dc.titleLarge-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotesen
dc.typeJournal articleen
local.bibliographicCitation.lastpage103en
local.bibliographicCitation.startpage88en
local.contributor.affiliationSchwartz, Schraga H.; Tel Aviv Universityen
local.contributor.affiliationSilva, Joao; Pompeu Fabra Universityen
local.contributor.affiliationBurstein, David; Tel Aviv Universityen
local.contributor.affiliationPupko, Tal; Tel Aviv Universityen
local.contributor.affiliationEyras, Eduardo; ICREAen
local.contributor.affiliationAst, Gil; Tel Aviv Universityen
local.identifier.citationvolume18en
local.identifier.doi10.1101/gr.6818908en
local.identifier.puredebf3011-56eb-4bcd-9dd9-4a47d489806cen
local.type.statusPublisheden

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