U6atac SnRNA Stem-loop Interacts with U12 P65 RNA Binding Protein and is Functionally Interchangeable with the U12 Apical Stem-loop III

Overview

Journal Sci Rep

Specialty Science

Date 2016 Aug 12

PMID 27510544

Citations 6

Authors

Jagjit Singh

Kavleen Sikand

Heike Conrad

Cindy L Will

Anton A Komar

Girish C Shukla

Affiliations

Soon will be listed here.

Abstract

Formation of catalytic core of the U12-dependent spliceosome involves U6atac and U12 interaction with the 5' splice site and branch site regions of a U12-dependent intron, respectively. Beyond the formation of intermolecular helix I region between U6atac and U12 snRNAs, several other regions within these RNA molecules are predicted to form stem-loop structures. Our previous work demonstrated that the 3' stem-loop region of U6atac snRNA contains a U12-dependent spliceosome-specific targeting activity. Here, we show a detailed structure-function analysis and requirement of a substructure of U6atac 3' stem-loop in U12-dependent in vivo splicing. We show that the C-terminal RNA recognition motif of p65, a U12 snRNA binding protein, also binds to the distal 3' stem-loop of U6atac. By using a binary splice site mutation suppressor assay we demonstrate that p65 protein-binding apical stem-loop of U12 snRNA can be replaced by this U6atac distal 3' stem-loop. Furthermore, we tested the compatibility of the U6atac 3' end from phylogenetically distant species in a human U6atac background, to establish the evolutionary relatedness of these structures and in vivo function. In summary, we demonstrate that RNA-RNA and RNA-protein interactions in the minor spliceosome are highly plastic as compared to the major spliceosome.

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References

Lopez M, Alm Rosenblad M, Samuelsson T . Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res. 2008; 36(9):3001-10. PMC: 2396436. DOI: 10.1093/nar/gkn142. View

Michel F, Costa M, Westhof E . The ribozyme core of group II introns: a structure in want of partners. Trends Biochem Sci. 2009; 34(4):189-99. DOI: 10.1016/j.tibs.2008.12.007. View

Will C, Luhrmann R . Spliceosome structure and function. Cold Spring Harb Perspect Biol. 2011; 3(7). PMC: 3119917. DOI: 10.1101/cshperspect.a003707. View

Shukla G, Padgett R . Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants. RNA. 1999; 5(4):525-38. PMC: 1369779. DOI: 10.1017/s1355838299982213. View

Will C, Schneider C, Hossbach M, Urlaub H, Rauhut R, Elbashir S . The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. RNA. 2004; 10(6):929-41. PMC: 1370585. DOI: 10.1261/rna.7320604. View

Kolossova I, Padgett R . U11 snRNA interacts in vivo with the 5' splice site of U12-dependent (AU-AC) pre-mRNA introns. RNA. 1997; 3(3):227-33. PMC: 1369475. View

Padgett R, Shukla G . A revised model for U4atac/U6atac snRNA base pairing. RNA. 2002; 8(2):125-8. PMC: 1370236. DOI: 10.1017/s1355838202017156. View

Tarn W, Steitz J . Highly diverged U4 and U6 small nuclear RNAs required for splicing rare AT-AC introns. Science. 1996; 273(5283):1824-32. DOI: 10.1126/science.273.5283.1824. View

Shukla G, Cole A, Dietrich R, Padgett R . Domains of human U4atac snRNA required for U12-dependent splicing in vivo. Nucleic Acids Res. 2002; 30(21):4650-7. PMC: 135832. DOI: 10.1093/nar/gkf609. View

10.

Hall S, Padgett R . Requirement of U12 snRNA for in vivo splicing of a minor class of eukaryotic nuclear pre-mRNA introns. Science. 1996; 271(5256):1716-8. DOI: 10.1126/science.271.5256.1716. View

11.

Dietrich R, Padgett R, Shukla G . The conserved 3' end domain of U6atac snRNA can direct U6 snRNA to the minor spliceosome. RNA. 2009; 15(6):1198-207. PMC: 2685526. DOI: 10.1261/rna.1505709. View

12.

Incorvaia R, Padgett R . Base pairing with U6atac snRNA is required for 5' splice site activation of U12-dependent introns in vivo. RNA. 1998; 4(6):709-18. PMC: 1369652. DOI: 10.1017/s1355838298980207. View

13.

Sikand K, Shukla G . Functionally important structural elements of U12 snRNA. Nucleic Acids Res. 2011; 39(19):8531-43. PMC: 3201867. DOI: 10.1093/nar/gkr530. View

14.

Candales M, Duong A, Hood K, Li T, Neufeld R, Sun R . Database for bacterial group II introns. Nucleic Acids Res. 2011; 40(Database issue):D187-90. PMC: 3245105. DOI: 10.1093/nar/gkr1043. View

15.

Will C, Luhrmann R . Protein functions in pre-mRNA splicing. Curr Opin Cell Biol. 1997; 9(3):320-8. DOI: 10.1016/s0955-0674(97)80003-8. View

16.

Lambowitz A, Zimmerly S . Mobile group II introns. Annu Rev Genet. 2004; 38:1-35. DOI: 10.1146/annurev.genet.38.072902.091600. View

17.

Tarn W, Steitz J . A novel spliceosome containing U11, U12, and U5 snRNPs excises a minor class (AT-AC) intron in vitro. Cell. 1996; 84(5):801-11. DOI: 10.1016/s0092-8674(00)81057-0. View

18.

Tarn W, Steitz J . Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge. Trends Biochem Sci. 1997; 22(4):132-7. DOI: 10.1016/s0968-0004(97)01018-9. View

19.

Shukla G, Padgett R . U4 small nuclear RNA can function in both the major and minor spliceosomes. Proc Natl Acad Sci U S A. 2003; 101(1):93-8. PMC: 314144. DOI: 10.1073/pnas.0304919101. View

20.

Lebo K, Zappulla D . Stiffened yeast telomerase RNA supports RNP function in vitro and in vivo. RNA. 2012; 18(9):1666-78. PMC: 3425781. DOI: 10.1261/rna.033555.112. View