title: Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.
abstract: BACKGROUND
  In the past few decades, non-coding RNAs (ncRNAs) have emerged as important regulators of gene expression in eukaryotes. Most studies of ncRNAs in plants have focused on the identification of silencing microRNAs (miRNAs) and small interfering RNAs (siRNAs). Another important family of ncRNAs that has been well characterized in plants is the small nucleolar RNAs (snoRNAs) and the related small Cajal body-specific RNAs (scaRNAs). Both target chemical modifications of ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). In plants, the snoRNA genes are organized in clusters, transcribed by RNA Pol II from a common promoter and subsequently processed into mature molecules. The promoter regions of snoRNA polycistronic genes in plants are highly enriched in two conserved cis-regulatory elements (CREs), Telo-box and Site II, which coordinate the expression of snoRNAs and ribosomal protein coding genes throughout the cell cycle.
  
  
  RESULTS
  In order to identify novel ncRNA genes, we have used the snoRNA Telo-box/Site II motifs combination as a functional promoter indicator to screen the Arabidopsis genome. The predictions generated by this process were tested by detailed exploration of available RNA-Seq and expression data sets and experimental validation. As a result, we have identified several snoRNAs, scaRNAs and 'orphan' snoRNAs. We also show evidence for 16 novel ncRNAs that lack similarity to any reported RNA family. Finally, we have identified two dicistronic genes encoding precursors that are processed to mature snoRNA and miRNA molecules. We discuss the evolutionary consequences of this result in the context of a tight link between snoRNAs and miRNAs in eukaryotes.
  
  
  CONCLUSIONS
  We present an alternative computational approach for non-coding RNA detection. Instead of depending on sequence or structure similarity in the whole genome screenings, we have explored the properties of promoter regions of well-characterized ncRNAs. Interestingly, besides expected ncRNAs predictions we were also able to recover single precursor arrangement for snoRNA-miRNA. Accompanied by analyses performed on rice sequences, we conclude that such arrangement might have interesting functional and evolutionary consequences and discuss this result in the context of a tight link between snoRNAs and miRNAs in eukaryotes.
authors.affiliation: Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland. quge@amu.edu.pl.
authors.forename: Ge
authors.initials: G
authors.lastname: Qu
authors.affiliation: Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland. kasiak08@amu.edu.pl.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Kruszka
authors.affiliation: Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland. p.plewka@amu.edu.pl.
authors.forename: Patrycja
authors.initials: P
authors.lastname: Plewka
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd. Sec. 2, Taipei, 115, Taiwan. sy521@gate.sinica.edu.tw.
authors.forename: Shu-Yi
authors.initials: SY
authors.lastname: Yang
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, No. 128 Academia Rd. Sec. 2, Taipei, 115, Taiwan. tjchiou@gate.sinica.edu.tw.
authors.forename: Tzyy-Jen
authors.initials: TJ
authors.lastname: Chiou
authors.affiliation: Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland. artjarmo@amu.edu.pl.
authors.forename: Artur
authors.initials: A
authors.lastname: Jarmolowski
authors.affiliation: Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, Poznan, 61-614, Poland. zofszwey@amu.edu.pl.
authors.forename: Zofia
authors.initials: Z
authors.lastname: Szweykowska-Kulinska
authors.affiliation: Faculté des Sciences, Université de Perpignan via Domitia, 52, Av Paul Alduy, Perpignan, 66860, France. echeverria@univ-perp.fr.
authors.forename: Manuel
authors.initials: M
authors.lastname: Echeverria
authors.affiliation: Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland. wmk@amu.edu.pl.
authors.forename: Wojciech M
authors.initials: WM
authors.lastname: Karlowski
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D023061:Gene Order; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D011401:Promoter Regions, Genetic; D034622:RNA Interference; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000235:genetics*; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid
chemical_list: D035683:MicroRNAs; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated