The Cellular EJC Interactome Reveals Higher-order MRNP Structure and an EJC-SR Protein Nexus

Overview

Journal Cell

Publisher Cell Press

Specialty Cell Biology

Date 2012 Oct 23

PMID 23084401

Citations 195

Authors

Guramrit Singh

Alper Kucukural

Can Cenik

John D Leszyk

Scott A Shaffer

Zhiping Weng

Melissa J Moore

Affiliations

Soon will be listed here.

Abstract

In addition to sculpting eukaryotic transcripts by removing introns, pre-mRNA splicing greatly impacts protein composition of the emerging mRNP. The exon junction complex (EJC), deposited upstream of exon-exon junctions after splicing, is a major constituent of spliced mRNPs. Here, we report comprehensive analysis of the endogenous human EJC protein and RNA interactomes. We confirm that the major "canonical" EJC occupancy site in vivo lies 24 nucleotides upstream of exon junctions and that the majority of exon junctions carry an EJC. Unexpectedly, we find that endogenous EJCs multimerize with one another and with numerous SR proteins to form megadalton sized complexes in which SR proteins are super-stoichiometric to EJC core factors. This tight physical association may explain known functional parallels between EJCs and SR proteins. Further, their protection of long mRNA stretches from nuclease digestion suggests that endogenous EJCs and SR proteins cooperate to promote mRNA packaging and compaction.

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References

Cheng H, Dufu K, Lee C, Hsu J, Dias A, Reed R . Human mRNA export machinery recruited to the 5' end of mRNA. Cell. 2006; 127(7):1389-400. DOI: 10.1016/j.cell.2006.10.044. View

Michelle L, Cloutier A, Toutant J, Shkreta L, Thibault P, Durand M . Proteins associated with the exon junction complex also control the alternative splicing of apoptotic regulators. Mol Cell Biol. 2011; 32(5):954-67. PMC: 3295189. DOI: 10.1128/MCB.06130-11. View

Saltzman A, Kim Y, Pan Q, Fagnani M, Maquat L, Blencowe B . Regulation of multiple core spliceosomal proteins by alternative splicing-coupled nonsense-mediated mRNA decay. Mol Cell Biol. 2008; 28(13):4320-30. PMC: 2447145. DOI: 10.1128/MCB.00361-08. View

Sanford J, Wang X, Mort M, VanDuyn N, Cooper D, Mooney S . Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts. Genome Res. 2009; 19(3):381-94. PMC: 2661799. DOI: 10.1101/gr.082503.108. View

Dewey C, Rogozin I, Koonin E . Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. BMC Genomics. 2006; 7:311. PMC: 1713244. DOI: 10.1186/1471-2164-7-311. View

Nott A, Le Hir H, Moore M . Splicing enhances translation in mammalian cells: an additional function of the exon junction complex. Genes Dev. 2004; 18(2):210-22. PMC: 324426. DOI: 10.1101/gad.1163204. View

Mili S, Steitz J . Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA. 2004; 10(11):1692-4. PMC: 1370654. DOI: 10.1261/rna.7151404. View

Shibuya T, Tange T, Sonenberg N, Moore M . eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay. Nat Struct Mol Biol. 2004; 11(4):346-51. DOI: 10.1038/nsmb750. View

Bono F, Gehring N . Assembly, disassembly and recycling: the dynamics of exon junction complexes. RNA Biol. 2011; 8(1):24-9. PMC: 3127076. DOI: 10.4161/rna.8.1.13618. View

10.

Zhang Z, Krainer A . Splicing remodels messenger ribonucleoprotein architecture via eIF4A3-dependent and -independent recruitment of exon junction complex components. Proc Natl Acad Sci U S A. 2007; 104(28):11574-9. PMC: 1913901. DOI: 10.1073/pnas.0704946104. View

11.

Ideue T, Sasaki Y, Hagiwara M, Hirose T . Introns play an essential role in splicing-dependent formation of the exon junction complex. Genes Dev. 2007; 21(16):1993-8. PMC: 1948854. DOI: 10.1101/gad.1557907. View

12.

Cenik C, Chua H, Zhang H, Tarnawsky S, Akef A, Derti A . Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes. PLoS Genet. 2011; 7(4):e1001366. PMC: 3077370. DOI: 10.1371/journal.pgen.1001366. View

13.

Zhang Z, Krainer A . Involvement of SR proteins in mRNA surveillance. Mol Cell. 2004; 16(4):597-607. DOI: 10.1016/j.molcel.2004.10.031. View

14.

Long J, Caceres J . The SR protein family of splicing factors: master regulators of gene expression. Biochem J. 2008; 417(1):15-27. DOI: 10.1042/BJ20081501. View

15.

Gudikote J, Imam J, Garcia R, Wilkinson M . RNA splicing promotes translation and RNA surveillance. Nat Struct Mol Biol. 2005; 12(9):801-9. DOI: 10.1038/nsmb980. View

16.

Ashton-Beaucage D, Udell C, Lavoie H, Baril C, Lefrancois M, Chagnon P . The exon junction complex controls the splicing of MAPK and other long intron-containing transcripts in Drosophila. Cell. 2010; 143(2):251-62. DOI: 10.1016/j.cell.2010.09.014. View

17.

Moore M . From birth to death: the complex lives of eukaryotic mRNAs. Science. 2005; 309(5740):1514-8. DOI: 10.1126/science.1111443. View

18.

Rebbapragada I, Lykke-Andersen J . Execution of nonsense-mediated mRNA decay: what defines a substrate?. Curr Opin Cell Biol. 2009; 21(3):394-402. DOI: 10.1016/j.ceb.2009.02.007. View

19.

McGlincy N, Smith C . Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?. Trends Biochem Sci. 2008; 33(8):385-93. DOI: 10.1016/j.tibs.2008.06.001. View

20.

Sato H, Hosoda N, Maquat L . Efficiency of the pioneer round of translation affects the cellular site of nonsense-mediated mRNA decay. Mol Cell. 2008; 29(2):255-62. DOI: 10.1016/j.molcel.2007.12.009. View