The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus.
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.
Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
Guramrit
G
Singh
Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
Alper
A
Kucukural
Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
Can
C
Cenik
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
John D
JD
Leszyk
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605.
Scott A
SA
Shaffer
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605.
Zhiping
Z
Weng
Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605. Electronic address: melissa.moore@umassmed.edu.
Melissa J
MJ
Moore
D005091:Exons; D006801:Humans; D046912:Multiprotein Complexes / Q000032:analysis; D020543:Proteome / Q000032:analysis*; D012322:RNA Precursors / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D012326:RNA Splicing; D012261:Ribonucleoproteins / Q000737:chemistry* / Q000378:metabolism*
D046912:Multiprotein Complexes; D020543:Proteome; D012322:RNA Precursors; D012261:Ribonucleoproteins; C026452:messenger ribonucleoprotein