title: Genome-wide RNA-binding analysis of the trypanosome U1 snRNP proteins U1C and U1-70K reveals cis/trans-spliceosomal network.
abstract: Trans-splicing in trypanosomes adds a 39-nucleotide mini-exon from the spliced leader (SL) RNA to the 5' end of each protein-coding sequence. On the other hand, cis-splicing of the few intron-containing genes requires the U1 small nuclear ribonucleoprotein (snRNP) particle. To search for potential new functions of the U1 snRNP in Trypanosoma brucei, we applied genome-wide individual-nucleotide resolution crosslinking-immunoprecipitation (iCLIP), focusing on the U1 snRNP-specific proteins U1C and U1-70K. Surprisingly, U1C and U1-70K interact not only with the U1, but also with U6 and SL RNAs. In addition, mapping of crosslinks to the cis-spliced PAP [poly(A) polymerase] pre-mRNA indicate an active role of these proteins in 5' splice site recognition. In sum, our results demonstrate that the iCLIP approach provides insight into stable and transient RNA-protein contacts within the spliceosomal network. We propose that the U1 snRNP may represent an evolutionary link between the cis- and trans-splicing machineries, playing a dual role in 5' splice site recognition on the trans-spliceosomal SL RNP as well as on pre-mRNA cis-introns.
authors.affiliation: Institute of Biochemistry, Justus Liebig University of Giessen, D-35392 Giessen, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Preußer
authors.affiliation: Institute of Biochemistry, Justus Liebig University of Giessen, D-35392 Giessen, Germany.
authors.forename: Oliver
authors.initials: O
authors.lastname: Rossbach
authors.affiliation: Institute of Biochemistry, Justus Liebig University of Giessen, D-35392 Giessen, Germany.
authors.forename: Lee-Hsueh
authors.initials: LH
authors.lastname: Hung
authors.affiliation: Institute of Biochemistry, Justus Liebig University of Giessen, D-35392 Giessen, Germany.
authors.forename: Dan
authors.initials: D
authors.lastname: Li
authors.affiliation: Institute of Biochemistry, Justus Liebig University of Giessen, D-35392 Giessen, Germany albrecht.bindereif@chemie.bio.uni-giessen.de.
authors.forename: Albrecht
authors.initials: A
authors.lastname: Bindereif
mesh_terms: D002467:Cell Nucleus / Q000737:chemistry; D018503:Genome, Protozoan; D015800:Protozoan Proteins / Q000032:analysis / Q000378:metabolism*; D012322:RNA Precursors / Q000378:metabolism; D022821:RNA Splice Sites; D012326:RNA Splicing; D012333:RNA, Messenger / Q000378:metabolism; D012342:RNA, Small Nuclear / Q000378:metabolism; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000032:analysis / Q000378:metabolism*; D017381:Spliceosomes / Q000378:metabolism*; D020040:Trans-Splicing; D014346:Trypanosoma brucei brucei / Q000235:genetics* / Q000378:metabolism
chemical_list: D015800:Protozoan Proteins; D012322:RNA Precursors; D022821:RNA Splice Sites; D012333:RNA, Messenger; D012342:RNA, Small Nuclear; D017412:Ribonucleoprotein, U1 Small Nuclear
references.citation: Eukaryot Cell. 2009 Jul;8(7):990-1000
references.pmid: 19429779
references.citation: Mol Cell Biol. 1991 Nov;11(11):5516-26
references.pmid: 1656232
references.citation: Nature. 2009 Mar 26;458(7237):475-80
references.pmid: 19325628
references.citation: J Biol Chem. 2000 Dec 22;275(51):40174-9
references.pmid: 11013266
references.citation: EMBO J. 2011 May 18;30(10):1965-76
references.pmid: 21468032
references.citation: Nature. 2002 Sep 5;419(6902):86-90
references.pmid: 12214237
references.citation: BMC Genomics. 2010 Feb 22;11:124
references.pmid: 20175885
references.citation: Nucleic Acids Res. 2010 Aug;38(15):4946-57
references.pmid: 20385579
references.citation: Mol Biochem Parasitol. 2001 Mar;113(1):109-15
references.pmid: 11254959
references.citation: Nature. 2010 Dec 2;468(7324):664-8
references.pmid: 20881964
references.citation: Science. 2005 Jul 15;309(5733):416-22
references.pmid: 16020726
references.citation: Science. 1990 Jan 5;247(4938):69-72
references.pmid: 2136774
references.citation: Mol Cell. 2001 Jan;7(1):227-32
references.pmid: 11172727
references.citation: PLoS Pathog. 2010 Aug 05;6(8):e1001037
references.pmid: 20700444
references.citation: Cell. 2012 Jul 6;150(1):53-64
references.pmid: 22770214
references.citation: Nucleic Acids Res. 1996 Dec 1;24(23):4614-23
references.pmid: 8972845
references.citation: Cell. 1994 Feb 11;76(3):531-41
references.pmid: 8313473
references.citation: Nature. 2001 Jan 25;409(6819):539-42
references.pmid: 11206553
references.citation: Nucleic Acids Res. 2005 Apr 29;33(8):2493-503
references.pmid: 15863726
references.citation: Genes Dev. 2009 Jul 15;23(14):1650-64
references.pmid: 19605687
references.citation: PLoS Pathog. 2010 Sep 09;6(9):e1001090
references.pmid: 20838601
references.citation: Genome Res. 2011 Jun;21(6):915-24
references.pmid: 21363968
references.citation: J Biol Chem. 2010 Sep 3;285(36):27982-99
references.pmid: 20592024
references.citation: Nature. 1988 Oct 6;335(6190):559-62
references.pmid: 2971142
references.citation: PLoS Biol. 2011 Jan 11;9(1):e1000573
references.pmid: 21264352
references.citation: RNA. 1996 Aug;2(8):735-45
references.pmid: 8752084
references.citation: Eukaryot Cell. 2009 Aug;8(8):1228-34
references.pmid: 19542313
references.citation: RNA Biol. 2011 Jan-Feb;8(1):90-100
references.pmid: 21282982
references.citation: Mol Cell. 1998 Jan;1(2):255-64
references.pmid: 9659922
references.citation: Eukaryot Cell. 2005 Nov;4(11):1942-50
references.pmid: 16278461
references.citation: RNA. 2000 Feb;6(2):163-9
references.pmid: 10688355
references.citation: Nat Struct Mol Biol. 2010 Jul;17(7):909-15
references.pmid: 20601959
references.citation: J Biol Chem. 1991 Dec 5;266(34):22792-5
references.pmid: 1835972