Computational identification of novel microRNA homologs in the chimpanzee genome

Baev, Vesselin; Daskalova, Evelina; Minkov, Ivan

doi:10.1016/j.compbiolchem.2008.07.024

Cited by 40 publications

(21 citation statements)

References 35 publications

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“…miR-320a is mammalian-specific, and its paralogs have only been identified in previous studies (experimentally or computationally) in primates: 320b in gorilla, 320b and 320c in macaque, and all paralogs in chimpanzee and orangutan [27, 44, 45, 46]. We confirmed the presence or absence of each miR-320 paralog using blastn (see Methods, S3 Table).…”

Section: Resultssupporting

confidence: 60%

Evolution of microRNA in primates

et al. 2017

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MicroRNA play an important role in post-transcriptional regulation of most transcripts in the human genome, but their evolution across the primate lineage is largely uncharacterized. A particular miRNA can have one to thousands of messenger RNA targets, establishing the potential for a small change in sequence or overall miRNA structure to have profound phenotypic effects. However, the majority of non-human primate miRNA is predicted solely by homology to the human genome and lacks experimental validation. In the present study, we sequenced thirteen species representing a wide range of the primate phylogeny. Hundreds of miRNA were validated, and the number of species with experimentally validated miRNA was tripled. These species include a sister taxon to humans (bonobo) and basal primates (aye-aye, mouse lemur, galago). Consistent with previous studies, we found the seed region and mature miRNA to be highly conserved across primates, with overall structural conservation of the pre-miRNA hairpin. However, there were a number of interesting exceptions, including a seed shift due to structural changes in miR-501. We also identified an increase in the number of miR-320 paralogs throughout primate evolution. Many of these non-conserved miRNA appear to regulate neuronal processes, illustrating the importance of investigating miRNA to learn more about human evolution.

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Section: Resultssupporting

confidence: 60%

Evolution of microRNA in primates

et al. 2017

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“…Approximately 40% of human miRNA genes are in genomic clusters and the dense clusters are localized on chromosomes 1, 3, 4, 5, 7, 9, 11, 12 13, 14, 17, 19, 20, 21, 22 and X (http://www.diana.pcbi.upenn.edu/cgibin/miRGen/v3/ Cluster.cgi). After analysing the chimp homologues of these 58 human miRNA clusters, Baev et al found that the orthologous miRNA clusters in the chimp genome were almost identical to these in human and the only exception is the hsa-mir-132-212 cluster on chromosome 17, in which two miRNAs could not be identified at orthologous positions in the chimp genome (Baev et al, 2009;Baskerville and Bartel, 2005). miRNAs in a given cluster may not necessarily show sequence similarities or regulate the identical target genes, but they are often related to each other (Baskerville and Bartel, 2005;Rodriguez et al, 2004).…”

Section: Cluster and Familymentioning

confidence: 99%

“…To date, all known human miRNAs belong to 285 families, including some one-member families. Baev et al identified 276 homologues of 285 human families in the chimp genome, but could not find miR-941 family and the other 8 single miRNA families (Baev et al, 2009;Houbaviy et al, 2003). See also: MicroRNA Evolution in the Human Genome…”

Section: Cluster and Familymentioning

confidence: 99%

“…Taking together, of the 639 novel chimp miRNA genes, 400 (62.60%) share 100% identity with the human premiRNAs and 239 (37.40%) share between 85% and 99.9%. Most of the putative chimp pre-miRNA sequences with 85-99.9% similarity contained 1-12 mismatches compared to the human precursors sequences (Baev et al, 2009). Among human pre-miRNAs in miRBase, 39 of them appeared to have no chimpanzee orthologue and 24 of them are missing in both chimp and rhesus genomes.…”

Section: Introductionmentioning

confidence: 99%

“…Baev et al also report that most of the nucleotide changes in the miRNA precursor of chimpanzee did not destroy the stem-loop structure of the precursor RNA, so, the mature miRNA is highly identical to the human orthologue. However, they still found that some miRNAs have one or more mismatches between human and chimpanzee (Baev et al, 2009). Sequence differences may lead to the emergence of novel miRNAs with different function.…”

Section: Introductionmentioning

confidence: 99%

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Comparative Analysis of mi RNA ‐mediated Gene Regulation in Mammals

Zhang

2009

Encyclopedia of Life Sciences

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Micro ribonucleic acids (miRNAs) are a class of small noncoding RNAs, which are involved in a range of physiological and pathological processes. All animal miRNAs share common genomic structure, biosynthetic pathways and reaction mechanisms but mammals seem to have more miRNAs to match their organism complexity and longer 3′‐UTR (untranslated region) to evaluate more miRNA target sites. During the episode of miRNA innovation observed at the vertebrates to the placental mammals, multiple unique miRNAs have emerged only in primates as compared with other mammals. The dramatically expanding of mammalian miRNAs and their targets suggest that miRNAs play important roles in mammalian evolution. Key concepts MicroRNAs (miRNAs) are group of small noncoding RNAs with approximately 22 nucleotides. miRNAs play important roles in many physiological and pathological processes in almost all eukaryotes, including development, cell proliferation, apoptosis, differentiation, tumours and many others. Compared with other animals, mammalians seem to have more miRNAs. The sequence of many miRNAs is conserved, like lin‐4 and let‐7 family, indicating strong functional constraint on miRNA evolution. However, nonconserved miRNAs represent a potentially important source of functional novelties during evolution. There is a rapid evolution of the miRNA cluster in primates, including frequent tandem duplications and nucleotide substitutions. All animal miRNAs share common genomic structure, biosynthetic pathways and reaction mechanisms. Each mammalian miRNA regulates on average 200 target genes whereas many genes have multiple target sites for either one miRNA or many different miRNAs. The avoidance of miRNA targeting might be as important as conservation of miRNA target sites in the evolution of tissue‐specific gene expression patterns. Some miRNAs are similarly expressed in mammals and most metazoans, indicating an evolutionarily conserved function, but others seem to be more ubiquitously expressed and only detected in specific cell types.

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