title: Species-specific alternative splicing leads to unique expression of sno-lncRNAs.
abstract: BACKGROUND
  Intron-derived long noncoding RNAs with snoRNA ends (sno-lncRNAs) are highly expressed from the imprinted Prader-Willi syndrome (PWS) region on human chromosome 15. However, sno-lncRNAs from other regions of the human genome or from other genomes have not yet been documented.
  
  
  RESULTS
  By exploring non-polyadenylated transcriptomes from human, rhesus and mouse, we have systematically annotated sno-lncRNAs expressed in all three species. In total, using available data from a limited set of cell lines, 19 sno-lncRNAs have been identified with tissue- and species-specific expression patterns. Although primary sequence analysis revealed that snoRNAs themselves are conserved from human to mouse, sno-lncRNAs are not. PWS region sno-lncRNAs are highly expressed in human and rhesus monkey, but are undetectable in mouse. Importantly, the absence of PWS region sno-lncRNAs in mouse suggested a possible reason why current mouse models fail to fully recapitulate pathological features of human PWS. In addition, a RPL13A region sno-lncRNA was specifically revealed in mouse embryonic stem cells, and its snoRNA ends were reported to influence lipid metabolism. Interestingly, the RPL13A region sno-lncRNA is barely detectable in human. We further demonstrated that the formation of sno-lncRNAs is often associated with alternative splicing of exons within their parent genes, and species-specific alternative splicing leads to unique expression pattern of sno-lncRNAs in different animals.
  
  
  CONCLUSIONS
  Comparative transcriptomes of non-polyadenylated RNAs among human, rhesus and mouse revealed that the expression of sno-lncRNAs is species-specific and that their processing is closely linked to alternative splicing of their parent genes. This study thus further demonstrates a complex regulatory network of coding and noncoding parts of the mammalian genome.
authors.forename: Xiao-Ou
authors.initials: XO
authors.lastname: Zhang
authors.forename: Qing-Fei
authors.initials: QF
authors.lastname: Yin
authors.forename: Hai-Bin
authors.initials: HB
authors.lastname: Wang
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
authors.forename: Tian
authors.initials: T
authors.lastname: Chen
authors.forename: Ping
authors.initials: P
authors.lastname: Zheng
authors.forename: Xuhua
authors.initials: X
authors.lastname: Lu
authors.affiliation: Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. linglingchen@sibcb.ac.cn.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
authors.forename: Li
authors.initials: L
authors.lastname: Yang
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D002884:Chromosomes, Human, Pair 15; D006801:Humans; D051379:Mice; D062085:RNA, Long Noncoding / Q000235:genetics*; D013045:Species Specificity
chemical_list: D062085:RNA, Long Noncoding
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