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Article: Long inverted repeats in eukaryotic genomes: Recombinogenic motifs determine genomic plasticity

TitleLong inverted repeats in eukaryotic genomes: Recombinogenic motifs determine genomic plasticity
Authors
KeywordsEukaryotic genomes
Long inverted repeat
Recombinogenic LIRs
Issue Date2006
PublisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/febslet
Citation
Febs Letters, 2006, v. 580 n. 5, p. 1277-1284 How to Cite?
AbstractInverted repeats are unstable motifs in a genome, having a causal relation to fragment rearrangements and recombination events. We have investigated long inverted repeats (LIR) of >30 bp in length in eukaryotic genomes to assess their contribution to genome stability. An algorithm was first designed for searching for LIRs with <2 kb internal spacers and >85% identity (degree of homology between repeat copies of a LIR). There are much fewer LIRs in yeast, fruitfly, pufferfish and chicken than in Caenorhabditis elegans, zebrafish, frog and human. However, the high LIR frequencies do not necessarily imply high genome instability because of variant internal spacers and stem lengths and identities. From the collection of identified LIRs, we selected recombinogenic LIRs that had a short internal spacer and a high copy identity and were prone to induce high instability. We found that a relatively high proportion (5-9.8%) of the LIRs in C. elegans, zebrafish and frog were recombinogenic LIRs. In contrast, the proportions in human and mouse LIRs were quite low (0.4-1.1%) basically accounting for long internal spacers. We suggest that C. elegans, zebrafish and frog genomes are unstable in terms of the LIR frequency and the proportion of recombinogenic LIRs. For the other genomes, LIRs most likely have a minor impact. © 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Persistent Identifierhttp://hdl.handle.net/10722/84881
ISSN
2015 Impact Factor: 3.519
2015 SCImago Journal Rankings: 2.026
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_HK
dc.contributor.authorLeung, FCCen_HK
dc.date.accessioned2010-09-06T08:58:12Z-
dc.date.available2010-09-06T08:58:12Z-
dc.date.issued2006en_HK
dc.identifier.citationFebs Letters, 2006, v. 580 n. 5, p. 1277-1284en_HK
dc.identifier.issn0014-5793en_HK
dc.identifier.urihttp://hdl.handle.net/10722/84881-
dc.description.abstractInverted repeats are unstable motifs in a genome, having a causal relation to fragment rearrangements and recombination events. We have investigated long inverted repeats (LIR) of >30 bp in length in eukaryotic genomes to assess their contribution to genome stability. An algorithm was first designed for searching for LIRs with <2 kb internal spacers and >85% identity (degree of homology between repeat copies of a LIR). There are much fewer LIRs in yeast, fruitfly, pufferfish and chicken than in Caenorhabditis elegans, zebrafish, frog and human. However, the high LIR frequencies do not necessarily imply high genome instability because of variant internal spacers and stem lengths and identities. From the collection of identified LIRs, we selected recombinogenic LIRs that had a short internal spacer and a high copy identity and were prone to induce high instability. We found that a relatively high proportion (5-9.8%) of the LIRs in C. elegans, zebrafish and frog were recombinogenic LIRs. In contrast, the proportions in human and mouse LIRs were quite low (0.4-1.1%) basically accounting for long internal spacers. We suggest that C. elegans, zebrafish and frog genomes are unstable in terms of the LIR frequency and the proportion of recombinogenic LIRs. For the other genomes, LIRs most likely have a minor impact. © 2006 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.en_HK
dc.languageengen_HK
dc.publisherElsevier BV. The Journal's web site is located at http://www.elsevier.com/locate/febsleten_HK
dc.relation.ispartofFEBS Lettersen_HK
dc.rightsF E B S Letters. Copyright © Elsevier BV.en_HK
dc.subjectEukaryotic genomesen_HK
dc.subjectLong inverted repeaten_HK
dc.subjectRecombinogenic LIRsen_HK
dc.titleLong inverted repeats in eukaryotic genomes: Recombinogenic motifs determine genomic plasticityen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=0014-5793&volume=580&spage=1277&epage=1284&date=2006&atitle=Long+inverted+repeats+in+eukaryotic+genomes:+Recombinogenic+motifs+determine+genomic+plasticityen_HK
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1016/j.febslet.2006.01.045en_HK
dc.identifier.pmid16466723-
dc.identifier.scopuseid_2-s2.0-32344440873en_HK
dc.identifier.hkuros122975en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-32344440873&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume580en_HK
dc.identifier.issue5en_HK
dc.identifier.spage1277en_HK
dc.identifier.epage1284en_HK
dc.identifier.isiWOS:000235597700014-
dc.publisher.placeNetherlandsen_HK
dc.identifier.scopusauthoridWang, Y=12240680100en_HK
dc.identifier.scopusauthoridLeung, FCC=7103078633en_HK

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