title: Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing.
abstract: BACKGROUND
  In recent years, a variety of small RNAs derived from other RNAs with well-known functions such as tRNAs and snoRNAs, have been identified. The functional relevance of these RNAs is largely unknown. To gain insight into the complexity of snoRNA processing and the functional relevance of snoRNA-derived small RNAs, we sequence long and short RNAs, small RNAs that co-precipitate with the Argonaute 2 protein and RNA fragments obtained in photoreactive nucleotide-enhanced crosslinking and immunoprecipitation (PAR-CLIP) of core snoRNA-associated proteins.
  
  
  RESULTS
  Analysis of these data sets reveals that many loci in the human genome reproducibly give rise to C/D box-like snoRNAs, whose expression and evolutionary conservation are typically less pronounced relative to the snoRNAs that are currently cataloged. We further find that virtually all C/D box snoRNAs are specifically processed inside the regions of terminal complementarity, retaining in the mature form only 4-5 nucleotides upstream of the C box and 2-5 nucleotides downstream of the D box. Sequencing of the total and Argonaute 2-associated populations of small RNAs reveals that despite their cellular abundance, C/D box-derived small RNAs are not efficiently incorporated into the Ago2 protein.
  
  
  CONCLUSIONS
  We conclude that the human genome encodes a large number of snoRNAs that are processed along the canonical pathway and expressed at relatively low levels. Generation of snoRNA-derived processing products with alternative, particularly miRNA-like, functions appears to be uncommon.
authors.forename: Shivendra
authors.initials: S
authors.lastname: Kishore
authors.forename: Andreas R
authors.initials: AR
authors.lastname: Gruber
authors.forename: Dominik J
authors.initials: DJ
authors.lastname: Jedlinski
authors.forename: Afzal P
authors.initials: AP
authors.lastname: Syed
authors.forename: Hadi
authors.initials: H
authors.lastname: Jorjani
authors.forename: Mihaela
authors.initials: M
authors.lastname: Zavolan
mesh_terms: D060565:Argonaute Proteins / Q000378:metabolism*; D003432:Cross-Linking Reagents / Q000378:metabolism; D015894:Genome, Human; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D047468:Immunoprecipitation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020537:RNA, Small Nucleolar / Q000032:analysis* / Q000378:metabolism; D020718:Ribonucleoproteins, Small Nucleolar / Q000032:analysis*; D017423:Sequence Analysis, RNA
chemical_list: C466422:AGO2 protein, human; D060565:Argonaute Proteins; D003432:Cross-Linking Reagents; D020537:RNA, Small Nucleolar; D020718:Ribonucleoproteins, Small Nucleolar