title: U6 snRNA intron insertion occurred multiple times during fungi evolution.
abstract: U6 small nuclear RNAs are part of the splicing machinery. They exhibit several unique features setting them appart from other snRNAs. Reports of introns in structured non-coding RNAs have been very rare. U6 genes, however, were found to be interrupted by an intron in several Schizosaccharomyces species and in 2 Basidiomycota. We conducted a homology search across 147 currently available fungal genome and identified the U6 genes in all but 2 of them. A detailed comparison of their sequences and predicted secondary structures showed that intron insertion events in the U6 snRNA were much more common in the fungal lineage than previously thought. Their positional distribution across the entire mature snRNA strongly suggests a large number of independent events. All the intron sequences reported here show canonical splice site and branch site motifs indicating that they require the splicesomal pathway for their removal.
authors.affiliation: a Bioinformatics Group , Department of Computer Science,and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18 , D-04107 Leipzig , Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Canzler
authors.affiliation: a Bioinformatics Group , Department of Computer Science,and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18 , D-04107 Leipzig , Germany.|b Computational EvoDevo Group , Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18 , D-04107 Leipzig , Germany.|c LIFE - Leipzig Research Center for Civilization Diseases, Universität Leipzig , Germany.|d Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22 , D-04103 Leipzig , Germany.|e Fraunhofer Institut für Zelltherapie und Immunologie - IZI Perlickstraße 1 , D-04103 Leipzig , Germany.|f Department of Theoretical Chemistry , University of Vienna, Währingerstraße 17, A-1090 Wien , Austria.|g Center for non-coding RNA in Technology and Health , University of Copenhagen, Grønnegårdsvej 3 , DK-1870 Frederiksberg C, Denmark.|h Santa Fe Institute; 1399 Hyde Park Rd. ; Santa Fe ; NM 87501 , USA.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: a Bioinformatics Group , Department of Computer Science,and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18 , D-04107 Leipzig , Germany.|i Department of Proteomics , Helmholtz Centre for Environmental Research - UFZ , Permoserstrabe 15, 04318 Leipzig , Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Hertel
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D016681:Genome, Fungal; D007438:Introns / Q000235:genetics*; D009690:Nucleic Acid Conformation; D012326:RNA Splicing; D012342:RNA, Small Nuclear / Q000737:chemistry / Q000235:genetics*; D012568:Schizosaccharomyces / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid
chemical_list: D012342:RNA, Small Nuclear; C405486:U6 small nuclear RNA
keywords: Fungi; homology search; intron; snRNA; snRNA evolution
references.citation: Mol Cell Biol. 1993 Sep;13(9):5613-9
references.pmid: 8355704
references.citation: Nucleic Acids Res. 2015 Jan;43(Database issue):D130-7
references.pmid: 25392425
references.citation: Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36
references.pmid: 7584402
references.citation: J Biochem. 1996 Sep;120(3):677-83
references.pmid: 8902636
references.citation: Genomics. 2006 Mar;87(3):338-47
references.pmid: 16406724
references.citation: Nucleic Acids Res. 2006;34(6):1816-35
references.pmid: 16600899
references.citation: PLoS Genet. 2008;4(8):e1000148
references.pmid: 18688272
references.citation: Nucleic Acids Res. 2009 Apr;37(5):1602-15
references.pmid: 19151082
references.citation: RNA Biol. 2009 Nov-Dec;6(5):503-7
references.pmid: 19875933
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D637-9
references.pmid: 21051345
references.citation: Cell. 2012 Oct 26;151(3):671-83
references.pmid: 23101633
references.citation: BMC Genomics. 2013;14:541
references.pmid: 24060058
references.citation: Nat Rev Mol Cell Biol. 2014 Feb;15(2):108-21
references.pmid: 24452469
references.citation: Eukaryot Cell. 2004 Oct;3(5):1088-100
references.pmid: 15470237
references.citation: Nucleic Acids Res. 1984 Apr 11;12(7):3283-93
references.pmid: 6201826
references.citation: EMBO J. 1984 Jun;3(6):1357-63
references.pmid: 6204860
references.citation: J Mol Biol. 1985 Oct 20;185(4):721-31
references.pmid: 2932555
references.citation: Proc Natl Acad Sci U S A. 1986 Nov;83(22):8575-9
references.pmid: 3464970
references.citation: J Biol Chem. 1987 Jan 5;262(1):75-81
references.pmid: 3793736
references.citation: J Biol Chem. 1987 Jan 25;262(3):1187-93
references.pmid: 3027083
references.citation: EMBO J. 1987 Jun;6(6):1757-63
references.pmid: 3649292
references.citation: Nature. 1988 Jul 21;334(6179):213-8
references.pmid: 3041282
references.citation: Genes Dev. 1988 Oct;2(10):1268-76
references.pmid: 3060403
references.citation: Nature. 1989 Jan 5;337(6202):87-90
references.pmid: 2909894
references.citation: Nucleic Acids Res. 1989 Oct 11;17(19):7821-31
references.pmid: 2798130
references.citation: Proc Natl Acad Sci U S A. 1989 Nov;86(21):8280-3
references.pmid: 2813391
references.citation: EMBO J. 1990 Jan;9(1):271-7
references.pmid: 2403927
references.citation: Science. 1990 Mar 9;247(4947):1213-6
references.pmid: 1690452
references.citation: Nucleic Acids Res. 1990 Apr 25;18(8):2025-32
references.pmid: 2336389
references.citation: Genes Dev. 1990 Aug;4(8):1345-56
references.pmid: 2227412
references.citation: Genes Dev. 1991 Jun;5(6):1022-31
references.pmid: 2044950
references.citation: Science. 1993 Dec 24;262(5142):2035-9
references.pmid: 8266100