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
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
2011 Impact Factor: 1.551
2011 SCImago Journal Rankings: 0.112
DOIhttp://dx.doi.org/10.1016/j.compbiolchem.2010.08.001
ReferencesReferences in Scopus
DC Field
Value
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.issn1476-9271
2011 Impact Factor: 1.551
2011 SCImago Journal Rankings: 0.112
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
Author Affiliations
  1. The University of Hong Kong
  2. Prince of Wales Hospital Hong Kong
  3. Sun Yat-Sen University