Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs.

BMC Genomics
Yong ZhangDahai Zhu

Abstract

Recent studies have demonstrated that non-protein-coding RNAs (npcRNAs/ncRNAs) play important roles during eukaryotic development, species evolution, and in the etiology of disease. Rhesus macaques are the most widely used primate model in both biomedical research and primate evolutionary studies. However, most reports on these animals focus on the functional roles of protein-coding sequences, whereas very little is known about macaque ncRNAs. In the present study, we performed the first systematic profiling of intermediate-size ncRNAs (50 to 500 nt) from the rhesus monkey by constructing a cDNA library. We identified 117 rhesus monkey ncRNAs, including 80 small nucleolar RNAs (snoRNAs), 29 other types of known RNAs (snRNAs, Y RNA, and others), and eight unclassified ncRNAs. Comparative genomic analysis and northern blot hybridizations demonstrated that some snoRNAs were lineage- or species-specific. Paralogous sequences were found for most rhesus monkey snoRNAs, the expression of which might be attributable to extensive duplication within the rhesus monkey genome. Further investigation of snoRNA flanking sequences showed that some rhesus monkey snoRNAs are retrogenes derived from L1-mediated integration. Finally, phylogenetic ...Continue Reading

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Datasets Mentioned

BETA
FJ915946
FJ916062

Methods Mentioned

BETA
cDNA library
PCR
in vitro transcription
X-ray

Software Mentioned

Staden
PERL scripts
UCSC liftOver
BLASTN
Mfold
RepeatMasker
MEGA
INFERNAL
CENSER
UCSC genome browser

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