Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.
Identifieur interne : 001F53 ( PubMed/Curation ); précédent : 001F52; suivant : 001F54Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.
Auteurs : Francesco Catania [États-Unis] ; Michael LynchSource :
- BMC evolutionary biology [ 1471-2148 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Paramecium, Protéines ribosomiques.
- métabolisme : microARN.
- Gènes de protozoaire, Séquence conservée, Séquence nucléotidique.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Ribosomal Proteins.
- chemical , metabolism : MicroRNAs.
- genetics : Paramecium.
- Base Sequence, Conserved Sequence, Genes, Protozoan.
Abstract
In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue.
DOI: 10.1186/1471-2148-10-129
PubMed: 20441586
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Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20441586</PMID><DateCompleted><Year>2010</Year><Month>06</Month><Day>21</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2148</ISSN><JournalIssue CitedMedium="Internet"><Volume>10</Volume><PubDate><Year>2010</Year><Month>May</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC evolutionary biology</Title><ISOAbbreviation>BMC Evol. Biol.</ISOAbbreviation></Journal><ArticleTitle>Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.</ArticleTitle><Pagination><MedlinePgn>129</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2148-10-129</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our observations 1) shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2) are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Catania</LastName><ForeName>Francesco</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Biology, Indiana University, 1001E 3rd Street, Bloomington, IN 47405, USA. fcatania@indiana.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lynch</LastName><ForeName>Michael</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>05</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Evol Biol</MedlineTA><NlmUniqueID>100966975</NlmUniqueID><ISSNLinking>1471-2148</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012269">Ribosomal 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IdType="pmc">PMC2874801</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Curr Biol. 1998 Apr 23;8(9):489-96</Citation><ArticleIdList><ArticleId IdType="pubmed">9560341</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2007;8:274</Citation><ArticleIdList><ArticleId IdType="pubmed">17663765</ArticleId></ArticleIdList></Reference><Reference><Citation>Genetics. 1999 Feb;151(2):667-74</Citation><ArticleIdList><ArticleId IdType="pubmed">9927459</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2007;8:432</Citation><ArticleIdList><ArticleId IdType="pubmed">17996040</ArticleId></ArticleIdList></Reference><Reference><Citation>Genes Dev. 2008 Jun 1;22(11):1501-12</Citation><ArticleIdList><ArticleId IdType="pubmed">18519642</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W70-4</Citation><ArticleIdList><ArticleId IdType="pubmed">18424795</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W358-63</Citation><ArticleIdList><ArticleId IdType="pubmed">18487275</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2008 Sep 1;24(17):1843-9</Citation><ArticleIdList><ArticleId IdType="pubmed">18611947</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17061-6</Citation><ArticleIdList><ArticleId IdType="pubmed">18952845</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2009 Feb;26(2):421-31</Citation><ArticleIdList><ArticleId IdType="pubmed">19023087</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2009 Feb;37(3):903-15</Citation><ArticleIdList><ArticleId IdType="pubmed">19103667</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2009 May;26(5):1067-72</Citation><ArticleIdList><ArticleId IdType="pubmed">19218282</ArticleId></ArticleIdList></Reference><Reference><Citation>Gene. 2009 Aug 15;443(1-2):100-9</Citation><ArticleIdList><ArticleId IdType="pubmed">19422892</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2008;9(1):R22</Citation><ArticleIdList><ArticleId IdType="pubmed">18226245</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Cell Biol. 1995 Apr;15(4):2010-18</Citation><ArticleIdList><ArticleId IdType="pubmed">7891696</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2000 Feb 24;403(6772):901-6</Citation><ArticleIdList><ArticleId IdType="pubmed">10706289</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 2002 Aug 23;110(4):513-20</Citation><ArticleIdList><ArticleId IdType="pubmed">12202040</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Genet. 2003 Sep;19(9):473-6</Citation><ArticleIdList><ArticleId IdType="pubmed">12957538</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2004 Jan 1;32(Database issue):D115-9</Citation><ArticleIdList><ArticleId IdType="pubmed">14681372</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Biol. 2004 Mar;2(3):E79</Citation><ArticleIdList><ArticleId IdType="pubmed">15024427</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2004 Jun;14(6):1188-90</Citation><ArticleIdList><ArticleId IdType="pubmed">15173120</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 1993 Dec 3;75(5):843-54</Citation><ArticleIdList><ArticleId IdType="pubmed">8252621</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell. 1993 Dec 3;75(5):855-62</Citation><ArticleIdList><ArticleId IdType="pubmed">8252622</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1994 Nov 11;22(22):4673-80</Citation><ArticleIdList><ArticleId IdType="pubmed">7984417</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Phylogenet Evol. 1998 Dec;10(3):299-309</Citation><ArticleIdList><ArticleId IdType="pubmed">10051383</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2005 Feb 17;433(7027):769-73</Citation><ArticleIdList><ArticleId IdType="pubmed">15685193</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2005 Mar 17;434(7031):338-45</Citation><ArticleIdList><ArticleId IdType="pubmed">15735639</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2005;6(10):R86</Citation><ArticleIdList><ArticleId IdType="pubmed">16207357</ArticleId></ArticleIdList></Reference><Reference><Citation>Cell Mol Life Sci. 2006 Jan;63(2):246-54</Citation><ArticleIdList><ArticleId IdType="pubmed">16395542</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4487-92</Citation><ArticleIdList><ArticleId IdType="pubmed">16537387</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Comput Biol. 2005 Dec;1(7):e69</Citation><ArticleIdList><ArticleId IdType="pubmed">16355253</ArticleId></ArticleIdList></Reference><Reference><Citation>RNA. 2006 Oct;12(10):1786-9</Citation><ArticleIdList><ArticleId IdType="pubmed">16917125</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2006 Nov 9;444(7116):171-8</Citation><ArticleIdList><ArticleId IdType="pubmed">17086204</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2007 Jan;35(Database issue):D439-44</Citation><ArticleIdList><ArticleId IdType="pubmed">17142227</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biochem Parasitol. 2007 Jun;153(2):125-32</Citation><ArticleIdList><ArticleId IdType="pubmed">17433460</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2007;8:174</Citation><ArticleIdList><ArticleId IdType="pubmed">17524134</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2007 Jul;35(Web Server issue):W193-200</Citation><ArticleIdList><ArticleId IdType="pubmed">17478515</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2007 Aug;24(8):1596-9</Citation><ArticleIdList><ArticleId IdType="pubmed">17488738</ArticleId></ArticleIdList></Reference><Reference><Citation>Development. 1998 Oct;125(20):4077-88</Citation><ArticleIdList><ArticleId IdType="pubmed">9735368</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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