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Article: Computational identification and characterization of primate-specific microRNAs in human genome
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TitleComputational identification and characterization of primate-specific microRNAs in human genome
 
AuthorsLin, S3
Cheung, WKC1
Chen, S3
Lu, G2
Wang, Z3
Xie, D3
Li, K3
Lin, MCM1 2
Kung, HF3 3
 
Issue Date2010
 
PublisherPergamon. The Journal's web site is located at http://www.elsevier.com/locate/cbac
 
CitationComputational Biology And Chemistry, 2010, v. 34 n. 4, p. 232-241 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.compbiolchem.2010.08.001
 
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.
 
ISSN1476-9271
2012 Impact Factor: 1.793
2012 SCImago Journal Rankings: 0.558
 
DOIhttp://dx.doi.org/10.1016/j.compbiolchem.2010.08.001
 
ReferencesReferences in Scopus
 
DC FieldValue
dc.contributor.authorLin, S
 
dc.contributor.authorCheung, WKC
 
dc.contributor.authorChen, S
 
dc.contributor.authorLu, G
 
dc.contributor.authorWang, Z
 
dc.contributor.authorXie, D
 
dc.contributor.authorLi, K
 
dc.contributor.authorLin, MCM
 
dc.contributor.authorKung, HF
 
dc.date.accessioned2012-10-08T03:19:28Z
 
dc.date.available2012-10-08T03:19:28Z
 
dc.date.issued2010
 
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.
 
dc.description.natureLink_to_subscribed_fulltext
 
dc.identifier.citationComputational Biology And Chemistry, 2010, v. 34 n. 4, p. 232-241 [How to Cite?]
DOI: http://dx.doi.org/10.1016/j.compbiolchem.2010.08.001
 
dc.identifier.citeulike7758937
 
dc.identifier.doihttp://dx.doi.org/10.1016/j.compbiolchem.2010.08.001
 
dc.identifier.epage241
 
dc.identifier.hkuros182329
 
dc.identifier.issn1476-9271
2012 Impact Factor: 1.793
2012 SCImago Journal Rankings: 0.558
 
dc.identifier.issue4
 
dc.identifier.pmid20863765
 
dc.identifier.scopuseid_2-s2.0-77958487607
 
dc.identifier.spage232
 
dc.identifier.urihttp://hdl.handle.net/10722/168482
 
dc.identifier.volume34
 
dc.languageeng
 
dc.publisherPergamon. The Journal's web site is located at http://www.elsevier.com/locate/cbac
 
dc.publisher.placeUnited Kingdom
 
dc.relation.ispartofComputational Biology and Chemistry
 
dc.relation.referencesReferences in Scopus
 
dc.subject.meshAnimals
 
dc.subject.meshCell Line
 
dc.subject.meshChromosomes, Human, Pair 19
 
dc.subject.meshChromosomes, Human, X
 
dc.subject.meshEmbryonic Stem Cells - Metabolism
 
dc.subject.meshEvolution, Molecular
 
dc.subject.meshGenome, Human
 
dc.subject.meshGenomics - Methods
 
dc.subject.meshHumans
 
dc.subject.meshMicrornas - Genetics
 
dc.subject.meshNeoplasms - Genetics
 
dc.subject.meshPrimates - Genetics
 
dc.titleComputational identification and characterization of primate-specific microRNAs in human genome
 
dc.typeArticle
 
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Author Affiliations
  1. The University of Hong Kong
  2. Prince of Wales Hospital Hong Kong
  3. Sun Yat-Sen University