annotation of primate mirnas by high throughput sequencing of small rna libraries注释的灵长类microrna的高通量测序的小rna库.pdfVIP

Dannemann et al. BMC Genomics 2012, 13:116 /1471-2164/13/116 RESEARCH ARTICLE Open Access Annotation of primate miRNAs by high throughput sequencing of small RNA libraries 1* 1 1,2 1,3† 1*† Michael Dannemann , Birgit Nickel , Esther Lizano , Hernán A Burbano and Janet Kelso Abstract Background: In addition to genome sequencing, accurate functional annotation of genomes is required in order to carry out comparative and evolutionary analyses between species. Among primates, the human genome is the most extensively annotated. Human miRNA gene annotation is based on multiple lines of evidence including evidence for expression as well as prediction of the characteristic hairpin structure. In contrast, most miRNA genes in non-human primates are annotated based on homology without any expression evidence. We have sequenced small-RNA libraries from chimpanzee, gorilla, orangutan and rhesus macaque from multiple individuals and tissues. Using patterns of miRNA expression in conjunction with a model of miRNA biogenesis we used these high- throughput sequencing data to identify novel miRNAs in non-human primates. Results: We predicted 47 new miRNAs in chimpanzee, 240 in gorilla, 55 in orangutan and 47 in rhesus macaque. The algorithm we used was able to predict 64% of the previously known miRNAs in chimpanzee, 94% in gorilla, 61% in orangutan and 71% in rhesus macaque. We therefore added evidence for expression in between one and five tissues to miRNAs that were previously annotated based only on homology to human miRNAs. We increased from 60 to 175 the number miRNAs that are located in orthologous regions in humans and the four non-human primate species studied here. Conclusions: In this study we prov