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Article: A study on genomic distribution and sequence features of human long inverted repeats reveals species-specific intronic inverted repeats

TitleA study on genomic distribution and sequence features of human long inverted repeats reveals species-specific intronic inverted repeats
Authors
KeywordsHuman
Intron
Long inverted repeat
Primates
Stem-loop
Issue Date2009
PublisherWiley-Blackwell Publishing Ltd.. The Journal's web site is located at http://www.febsjournal.org/
Citation
Febs Journal, 2009, v. 276 n. 7, p. 1986-1998 How to Cite?
AbstractThe inverted repeats present in a genome play dual roles. They can induce genomic instability and, on the other hand, regulate gene expression. In the present study, we report the distribution and sequence features of recombinogenic long inverted repeats (LIRs) that are capable of forming stable stem-loops or palindromes within the human genome. A total of 2551 LIRs were identified, and 37% of them were located in long introns (largely > 10 kb) of genes. Their distribution appears to be random in introns and is not restrictive, even for regions near intron-exon boundaries. Almost half of them comprise TG/CA-rich repeats, inversely arranged Alu repeats and MADE1 mariners. The remaining LIRs are mostly unique in their sequence features. Comparative studies of human, chimpanzee, rhesus monkey and mouse orthologous genes reveal that human genes have more recombinogenic LIRs than other orthologs, and over 80% are human-specific. The human genes associated with the human-specific LIRs are involved in the pathways of cell communication, development and the nervous system, as based on significantly over-represented Gene Ontology terms. The functional pathways related to the development and functions of the nervous system are not enriched in chimpanzee and mouse orthologs. The findings of the present study provide insight into the role of intronic LIRs in gene regulation and primate speciation. © 2009 FEBS.
Persistent Identifierhttp://hdl.handle.net/10722/60134
ISSN
2015 Impact Factor: 4.237
2015 SCImago Journal Rankings: 2.141
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorWang, Yen_HK
dc.contributor.authorLeung, FCCen_HK
dc.date.accessioned2010-05-31T04:04:19Z-
dc.date.available2010-05-31T04:04:19Z-
dc.date.issued2009en_HK
dc.identifier.citationFebs Journal, 2009, v. 276 n. 7, p. 1986-1998en_HK
dc.identifier.issn1742-464Xen_HK
dc.identifier.urihttp://hdl.handle.net/10722/60134-
dc.description.abstractThe inverted repeats present in a genome play dual roles. They can induce genomic instability and, on the other hand, regulate gene expression. In the present study, we report the distribution and sequence features of recombinogenic long inverted repeats (LIRs) that are capable of forming stable stem-loops or palindromes within the human genome. A total of 2551 LIRs were identified, and 37% of them were located in long introns (largely > 10 kb) of genes. Their distribution appears to be random in introns and is not restrictive, even for regions near intron-exon boundaries. Almost half of them comprise TG/CA-rich repeats, inversely arranged Alu repeats and MADE1 mariners. The remaining LIRs are mostly unique in their sequence features. Comparative studies of human, chimpanzee, rhesus monkey and mouse orthologous genes reveal that human genes have more recombinogenic LIRs than other orthologs, and over 80% are human-specific. The human genes associated with the human-specific LIRs are involved in the pathways of cell communication, development and the nervous system, as based on significantly over-represented Gene Ontology terms. The functional pathways related to the development and functions of the nervous system are not enriched in chimpanzee and mouse orthologs. The findings of the present study provide insight into the role of intronic LIRs in gene regulation and primate speciation. © 2009 FEBS.en_HK
dc.languageengen_HK
dc.publisherWiley-Blackwell Publishing Ltd.. The Journal's web site is located at http://www.febsjournal.org/en_HK
dc.relation.ispartofFEBS Journalen_HK
dc.subjectHumanen_HK
dc.subjectIntronen_HK
dc.subjectLong inverted repeaten_HK
dc.subjectPrimatesen_HK
dc.subjectStem-loopen_HK
dc.titleA study on genomic distribution and sequence features of human long inverted repeats reveals species-specific intronic inverted repeatsen_HK
dc.typeArticleen_HK
dc.identifier.emailLeung, FCC: fcleung@hkucc.hku.hken_HK
dc.identifier.authorityLeung, FCC=rp00731en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1111/j.1742-4658.2009.06930.xen_HK
dc.identifier.pmid19243432-
dc.identifier.scopuseid_2-s2.0-62149126551en_HK
dc.identifier.hkuros166126en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-62149126551&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume276en_HK
dc.identifier.issue7en_HK
dc.identifier.spage1986en_HK
dc.identifier.epage1998en_HK
dc.identifier.isiWOS:000264021900017-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridWang, Y=12240680100en_HK
dc.identifier.scopusauthoridLeung, FCC=7103078633en_HK
dc.identifier.citeulike4171762-

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