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Article: Computational identification and characterization of primate-specific microRNAs in human genome

TitleComputational identification and characterization of primate-specific microRNAs in human genome
Authors
Issue Date2010
PublisherPergamon. The Journal's web site is located at http://www.elsevier.com/locate/cbac
Citation
Computational Biology And Chemistry, 2010, v. 34 n. 4, p. 232-241 How to Cite?
AbstractA number of microRNAs (miRNAs) that are evolutionarily conserved not beyond primate lineage have been identified. These primate-specific miRNAs (ps-miRNAs) may attribute to the difference between high-level primates and non-primate mammals or lower vertebrates. Despite of their importance, the genome-wide miRNA conservation patterns and the properties of these ps-miRNAs are largely elusive. In this study, we developed a robust classification system to assess the conservation pattern of all human mature miRNAs across 44 vertebrate genomes. By this comparative genomic analysis, a novel set of 269 ps-miRNAs were identified. We found that many ps-miRNAs were enriched in chromosome 19 and X, forming two main clusters hereafter referred as C19MC and CXMC, respectively. When comparing the seed of ps-miRNAs themselves or with non-ps-miRNAs, more than one half ps-miRNAs sharing common seeds were belonged to C19MC, 9 of which retained a unique seed that had been reported to be enriched in human embryonic stem cells (hESCs) specific miRNAs. Moreover, the most abundant ps-miRNA common seed was possessed by miR-548 family. Most ps-miRNAs had very low expression in adult tissues, which may be attributed to temporal and spatial specific transcript regulation. The ps-miRNAs with relatively high expression were mainly belonged to C19MC and CXMC, and preferentially expressed in hESCs and reproductive system. Sequence anatomy revealed that C19MC ps-miRNAs were highly conserved but not beyond primates and of great sequence similarity. Gene Ontology and KEGG pathway enrichment analyses of predicted target genes indicated that C19MC ps-miRNAs were strongly associated with developmental processes and various cancers. In conclusion, ps-miRNAs may play critical roles in differentiation and growth regulation during early development, especially in maintaining the pluripotency of hESCs. Results from this study may help explaining the differences between primates and lower vertebrates at genetic level. © 2010 Elsevier Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/168482
ISSN
2014 Impact Factor: 1.117
2014 SCImago Journal Rankings: 0.464
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorLin, Sen_US
dc.contributor.authorCheung, WKCen_US
dc.contributor.authorChen, Sen_US
dc.contributor.authorLu, Gen_US
dc.contributor.authorWang, Zen_US
dc.contributor.authorXie, Den_US
dc.contributor.authorLi, Ken_US
dc.contributor.authorLin, MCMen_US
dc.contributor.authorKung, HFen_US
dc.date.accessioned2012-10-08T03:19:28Z-
dc.date.available2012-10-08T03:19:28Z-
dc.date.issued2010en_US
dc.identifier.citationComputational Biology And Chemistry, 2010, v. 34 n. 4, p. 232-241en_US
dc.identifier.issn1476-9271en_US
dc.identifier.urihttp://hdl.handle.net/10722/168482-
dc.description.abstractA number of microRNAs (miRNAs) that are evolutionarily conserved not beyond primate lineage have been identified. These primate-specific miRNAs (ps-miRNAs) may attribute to the difference between high-level primates and non-primate mammals or lower vertebrates. Despite of their importance, the genome-wide miRNA conservation patterns and the properties of these ps-miRNAs are largely elusive. In this study, we developed a robust classification system to assess the conservation pattern of all human mature miRNAs across 44 vertebrate genomes. By this comparative genomic analysis, a novel set of 269 ps-miRNAs were identified. We found that many ps-miRNAs were enriched in chromosome 19 and X, forming two main clusters hereafter referred as C19MC and CXMC, respectively. When comparing the seed of ps-miRNAs themselves or with non-ps-miRNAs, more than one half ps-miRNAs sharing common seeds were belonged to C19MC, 9 of which retained a unique seed that had been reported to be enriched in human embryonic stem cells (hESCs) specific miRNAs. Moreover, the most abundant ps-miRNA common seed was possessed by miR-548 family. Most ps-miRNAs had very low expression in adult tissues, which may be attributed to temporal and spatial specific transcript regulation. The ps-miRNAs with relatively high expression were mainly belonged to C19MC and CXMC, and preferentially expressed in hESCs and reproductive system. Sequence anatomy revealed that C19MC ps-miRNAs were highly conserved but not beyond primates and of great sequence similarity. Gene Ontology and KEGG pathway enrichment analyses of predicted target genes indicated that C19MC ps-miRNAs were strongly associated with developmental processes and various cancers. In conclusion, ps-miRNAs may play critical roles in differentiation and growth regulation during early development, especially in maintaining the pluripotency of hESCs. Results from this study may help explaining the differences between primates and lower vertebrates at genetic level. © 2010 Elsevier Ltd.en_US
dc.languageengen_US
dc.publisherPergamon. The Journal's web site is located at http://www.elsevier.com/locate/cbacen_US
dc.relation.ispartofComputational Biology and Chemistryen_US
dc.subject.meshAnimalsen_US
dc.subject.meshCell Lineen_US
dc.subject.meshChromosomes, Human, Pair 19en_US
dc.subject.meshChromosomes, Human, Xen_US
dc.subject.meshEmbryonic Stem Cells - Metabolismen_US
dc.subject.meshEvolution, Molecularen_US
dc.subject.meshGenome, Humanen_US
dc.subject.meshGenomics - Methodsen_US
dc.subject.meshHumansen_US
dc.subject.meshMicrornas - Geneticsen_US
dc.subject.meshNeoplasms - Geneticsen_US
dc.subject.meshPrimates - Geneticsen_US
dc.titleComputational identification and characterization of primate-specific microRNAs in human genomeen_US
dc.typeArticleen_US
dc.identifier.emailLin, MCM:mcllin@hkucc.hku.hken_US
dc.identifier.authorityLin, MCM=rp00746en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1016/j.compbiolchem.2010.08.001en_US
dc.identifier.pmid20863765en_US
dc.identifier.scopuseid_2-s2.0-77958487607en_US
dc.identifier.hkuros182329-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-77958487607&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume34en_US
dc.identifier.issue4en_US
dc.identifier.spage232en_US
dc.identifier.epage241en_US
dc.identifier.isiWOS:000284300800003-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridLin, S=37034534000en_US
dc.identifier.scopusauthoridCheung, WKC=35080070600en_US
dc.identifier.scopusauthoridChen, S=37033456200en_US
dc.identifier.scopusauthoridLu, G=36619108300en_US
dc.identifier.scopusauthoridWang, Z=37035371600en_US
dc.identifier.scopusauthoridXie, D=35070710200en_US
dc.identifier.scopusauthoridLi, K=13604752100en_US
dc.identifier.scopusauthoridLin, MCM=7404816359en_US
dc.identifier.scopusauthoridKung, HF=7402514190en_US
dc.identifier.citeulike7758937-

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