Expanding the Action of Duplex RNAs into the Nucleus: Redirecting Alternative Splicing

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2011 Sep 28

PMID 21948593

Citations 49

Authors

Jing Liu

Jiaxin Hu

David R Corey

Affiliations

Soon will be listed here.

Abstract

Double-stranded RNAs are powerful agents for silencing gene expression in the cytoplasm of mammalian cells. The potential for duplex RNAs to control expression in the nucleus has received less attention. Here, we investigate the ability of small RNAs to redirect splicing. We identify RNAs targeting an aberrant splice site that restore splicing and production of functional protein. RNAs can target sequences within exons or introns and affect the inclusion of exons within SMN2 and dystrophin, genes responsible for spinal muscular atrophy and Duchenne muscular dystrophy, respectively. Duplex RNAs recruit argonaute 2 (AGO2) to pre-mRNA transcripts and altered splicing requires AGO2 expression. AGO2 promotes transcript cleavage in the cytoplasm, but recruitment of AGO2 to pre-mRNAs does not reduce transcript levels, exposing a difference between cytoplasmic and nuclear pathways. Involvement of AGO2 in splicing, a classical nuclear process, reinforces the conclusion from studies of RNA-mediated transcriptional silencing that RNAi pathways can be adapted to function in the mammalian nucleus. These data provide a new strategy for controlling splicing and expand the reach of small RNAs within the nucleus of mammalian cells.

Citing Articles

RNA structure in alternative splicing regulation: from mechanism to therapy.

Bao N, Wang Z, Fu J, Dong H, Jin Y Acta Biochim Biophys Sin (Shanghai). 2024; 57(1):3-21.

PMID: 39034824 PMC: 11802352. DOI: 10.3724/abbs.2024119.

Identification of functional genes in liver fibrosis based on bioinformatics analysis of a lncRNA-mediated ceRNA network.

Zhang F, Pei S, Xiao M BMC Med Genomics. 2024; 17(1):56.

PMID: 38378545 PMC: 10877760. DOI: 10.1186/s12920-024-01813-x.

Nuclear localization of Argonaute 2 is affected by cell density and may relieve repression by microRNAs.

Johnson K, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S Nucleic Acids Res. 2023; 52(4):1930-1952.

PMID: 38109320 PMC: 10899759. DOI: 10.1093/nar/gkad1155.

Targeting RNA with synthetic oligonucleotides: Clinical success invites new challenges.

Hofman C, Corey D Cell Chem Biol. 2023; 31(1):125-138.

PMID: 37804835 PMC: 10841528. DOI: 10.1016/j.chembiol.2023.09.005.

Nuclear Localization of Argonaute is affected by Cell Density and May Relieve Repression by microRNAs.

Johnson K, Kilikevicius A, Hofman C, Hu J, Liu Y, Aguilar S bioRxiv. 2023; .

PMID: 37461596 PMC: 10350042. DOI: 10.1101/2023.07.07.548119.

References

Kang S, Cho M, Kole R . Up-regulation of luciferase gene expression with antisense oligonucleotides: implications and applications in functional assay development. Biochemistry. 1998; 37(18):6235-9. DOI: 10.1021/bi980300h. View

Liu J, Valencia-Sanchez M, Hannon G, Parker R . MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat Cell Biol. 2005; 7(7):719-23. PMC: 1855297. DOI: 10.1038/ncb1274. View

Dominski Z, Kole R . Restoration of correct splicing in thalassemic pre-mRNA by antisense oligonucleotides. Proc Natl Acad Sci U S A. 1993; 90(18):8673-7. PMC: 47420. DOI: 10.1073/pnas.90.18.8673. View

Hu J, Liu J, Corey D . Allele-selective inhibition of huntingtin expression by switching to an miRNA-like RNAi mechanism. Chem Biol. 2010; 17(11):1183-8. PMC: 3021381. DOI: 10.1016/j.chembiol.2010.10.013. View

Guang S, Bochner A, Pavelec D, Burkhart K, Harding S, Lachowiec J . An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science. 2008; 321(5888):537-41. PMC: 2771369. DOI: 10.1126/science.1157647. View

Guterstam P, Lindgren M, Johansson H, Tedebark U, Wengel J, El Andaloussi S . Splice-switching efficiency and specificity for oligonucleotides with locked nucleic acid monomers. Biochem J. 2008; 412(2):307-13. DOI: 10.1042/BJ20080013. View

Lorson C, Rindt H, Shababi M . Spinal muscular atrophy: mechanisms and therapeutic strategies. Hum Mol Genet. 2010; 19(R1):R111-8. PMC: 2875050. DOI: 10.1093/hmg/ddq147. View

Kinali M, Arechavala-Gomeza V, Feng L, Cirak S, Hunt D, Adkin C . Local restoration of dystrophin expression with the morpholino oligomer AVI-4658 in Duchenne muscular dystrophy: a single-blind, placebo-controlled, dose-escalation, proof-of-concept study. Lancet Neurol. 2009; 8(10):918-28. PMC: 2755039. DOI: 10.1016/S1474-4422(09)70211-X. View

Jeffries C, Fried H, Perkins D . Nuclear and cytoplasmic localization of neural stem cell microRNAs. RNA. 2011; 17(4):675-86. PMC: 3062178. DOI: 10.1261/rna.2006511. View

10.

Weinmann L, Hock J, Ivacevic T, Ohrt T, Mutze J, Schwille P . Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell. 2009; 136(3):496-507. DOI: 10.1016/j.cell.2008.12.023. View

11.

Robb G, Brown K, Khurana J, Rana T . Specific and potent RNAi in the nucleus of human cells. Nat Struct Mol Biol. 2005; 12(2):133-7. DOI: 10.1038/nsmb886. View

12.

Aartsma-Rus A, van Ommen G . Antisense-mediated exon skipping: a versatile tool with therapeutic and research applications. RNA. 2007; 13(10):1609-24. PMC: 1986821. DOI: 10.1261/rna.653607. View

13.

Meister G, Landthaler M, Patkaniowska A, Dorsett Y, Teng G, Tuschl T . Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol Cell. 2004; 15(2):185-97. DOI: 10.1016/j.molcel.2004.07.007. View

14.

Braasch D, Jensen S, Liu Y, Kaur K, Arar K, White M . RNA interference in mammalian cells by chemically-modified RNA. Biochemistry. 2003; 42(26):7967-75. DOI: 10.1021/bi0343774. View

15.

Sazani P, Gemignani F, Kang S, Maier M, Manoharan M, Persmark M . Systemically delivered antisense oligomers upregulate gene expression in mouse tissues. Nat Biotechnol. 2002; 20(12):1228-33. DOI: 10.1038/nbt759. View

16.

Ohrt T, Mutze J, Staroske W, Weinmann L, Hock J, Crell K . Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells. Nucleic Acids Res. 2008; 36(20):6439-49. PMC: 2582625. DOI: 10.1093/nar/gkn693. View

17.

Lu Q, Yokota T, Takeda S, Garcia L, Muntoni F, Partridge T . The status of exon skipping as a therapeutic approach to duchenne muscular dystrophy. Mol Ther. 2010; 19(1):9-15. PMC: 3017449. DOI: 10.1038/mt.2010.219. View

18.

Du Q, Thonberg H, Wang J, Wahlestedt C, Liang Z . A systematic analysis of the silencing effects of an active siRNA at all single-nucleotide mismatched target sites. Nucleic Acids Res. 2005; 33(5):1671-7. PMC: 1069010. DOI: 10.1093/nar/gki312. View

19.

Wood M, Gait M, Yin H . RNA-targeted splice-correction therapy for neuromuscular disease. Brain. 2010; 133(Pt 4):957-72. DOI: 10.1093/brain/awq002. View

20.

Bauman J, Jearawiriyapaisarn N, Kole R . Therapeutic potential of splice-switching oligonucleotides. Oligonucleotides. 2009; 19(1):1-13. PMC: 2663420. DOI: 10.1089/oli.2008.0161. View