MA Modification of U6 SnRNA Modulates Usage of Two Major Classes of Pre-mRNA 5' Splice Site

Overview

Journal Elife

Specialty Biology

Date 2022 Nov 21

PMID 36409063

Authors

Matthew T Parker

Beth K Soanes

Jelena Kusakina

Antoine Larrieu

Katarzyna Knop

Nisha Joy

Friedrich Breidenbach

Anna V Sherwood

Geoffrey J Barton

Sebastian M Fica

Brendan H Davies

Gordon G Simpson

Affiliations

Soon will be listed here.

Abstract

Alternative splicing of messenger RNAs is associated with the evolution of developmentally complex eukaryotes. Splicing is mediated by the spliceosome, and docking of the pre-mRNA 5' splice site into the spliceosome active site depends upon pairing with the conserved ACAGA sequence of U6 snRNA. In some species, including humans, the central adenosine of the ACGA box is modified by methylation, but the role of this mA modification is poorly understood. Here, we show that mA modified U6 snRNA determines the accuracy and efficiency of splicing. We reveal that the conserved methyltransferase, FIONA1, is required for U6 snRNA mA modification. mutants show disrupted patterns of splicing that can be explained by the sequence composition of 5' splice sites and cooperative roles for U5 and U6 snRNA in splice site selection. U6 snRNA mA influences 3' splice site usage. We generalise these findings to reveal two major classes of 5' splice site in diverse eukaryotes, which display anti-correlated interaction potential with U5 snRNA loop 1 and the U6 snRNA ACGA box. We conclude that U6 snRNA mA modification contributes to the selection of degenerate 5' splice sites crucial to alternative splicing.

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References

Clough S, Bent A . Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1999; 16(6):735-43. DOI: 10.1046/j.1365-313x.1998.00343.x. View

Lutz U, Pose D, Pfeifer M, Gundlach H, Hagmann J, Wang C . Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M. PLoS Genet. 2015; 11(10):e1005588. PMC: 4619661. DOI: 10.1371/journal.pgen.1005588. View

Neuveglise C, Marck C, Gaillardin C . The intronome of budding yeasts. C R Biol. 2011; 334(8-9):662-70. DOI: 10.1016/j.crvi.2011.05.015. View

Patro R, Duggal G, Love M, Irizarry R, Kingsford C . Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017; 14(4):417-419. PMC: 5600148. DOI: 10.1038/nmeth.4197. View

Scortecci K, Michaels S, Amasino R . Identification of a MADS-box gene, FLOWERING LOCUS M, that represses flowering. Plant J. 2001; 26(2):229-36. DOI: 10.1046/j.1365-313x.2001.01024.x. View

Plaschka C, Newman A, Nagai K . Structural Basis of Nuclear pre-mRNA Splicing: Lessons from Yeast. Cold Spring Harb Perspect Biol. 2019; 11(5). PMC: 6496352. DOI: 10.1101/cshperspect.a032391. View

. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000; 408(6814):796-815. DOI: 10.1038/35048692. View

Lee J, Ryu H, Chung K, Pose D, Kim S, Schmid M . Regulation of temperature-responsive flowering by MADS-box transcription factor repressors. Science. 2013; 342(6158):628-32. DOI: 10.1126/science.1241097. View

Fica S . Cryo-EM snapshots of the human spliceosome reveal structural adaptions for splicing regulation. Curr Opin Struct Biol. 2020; 65:139-148. DOI: 10.1016/j.sbi.2020.06.018. View

10.

Wilkinson M, Charenton C, Nagai K . RNA Splicing by the Spliceosome. Annu Rev Biochem. 2019; 89:359-388. DOI: 10.1146/annurev-biochem-091719-064225. View

11.

Bensmihen S, To A, Lambert G, Kroj T, Giraudat J, Parcy F . Analysis of an activated ABI5 allele using a new selection method for transgenic Arabidopsis seeds. FEBS Lett. 2004; 561(1-3):127-31. DOI: 10.1016/S0014-5793(04)00148-6. View

12.

Andres F, Coupland G . The genetic basis of flowering responses to seasonal cues. Nat Rev Genet. 2012; 13(9):627-39. DOI: 10.1038/nrg3291. View

13.

Carmel I, Tal S, Vig I, Ast G . Comparative analysis detects dependencies among the 5' splice-site positions. RNA. 2004; 10(5):828-40. PMC: 1370573. DOI: 10.1261/rna.5196404. View

14.

Chen L, Bush S, Tovar-Corona J, Castillo-Morales A, Urrutia A . Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. Mol Biol Evol. 2014; 31(6):1402-13. PMC: 4032128. DOI: 10.1093/molbev/msu083. View

15.

Aoyama T, Yamashita S, Tomita K . Mechanistic insights into m6A modification of U6 snRNA by human METTL16. Nucleic Acids Res. 2020; 48(9):5157-5168. PMC: 7229813. DOI: 10.1093/nar/gkaa227. View

16.

Charenton C, Wilkinson M, Nagai K . Mechanism of 5' splice site transfer for human spliceosome activation. Science. 2019; 364(6438):362-367. PMC: 6525098. DOI: 10.1126/science.aax3289. View

17.

Balasubramanian S, Sureshkumar S, Lempe J, Weigel D . Potent induction of Arabidopsis thaliana flowering by elevated growth temperature. PLoS Genet. 2006; 2(7):e106. PMC: 1487179. DOI: 10.1371/journal.pgen.0020106. View

18.

Mizoguchi T, Wheatley K, Hanzawa Y, Wright L, Mizoguchi M, Song H . LHY and CCA1 are partially redundant genes required to maintain circadian rhythms in Arabidopsis. Dev Cell. 2002; 2(5):629-41. DOI: 10.1016/s1534-5807(02)00170-3. View

19.

Lesser C, Guthrie C . Mutations in U6 snRNA that alter splice site specificity: implications for the active site. Science. 1993; 262(5142):1982-8. DOI: 10.1126/science.8266093. View

20.

Gamaarachchi H, Lam C, Jayatilaka G, Samarakoon H, Simpson J, Smith M . GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis. BMC Bioinformatics. 2020; 21(1):343. PMC: 7430849. DOI: 10.1186/s12859-020-03697-x. View