Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity

Volker Boehm; Thiago Britto-Borges; Anna-Lena Steckelberg; Kusum K Singh; Jennifer V Gerbracht; Elif Gueney; Lorea Blazquez; Janine Altmüller; Christoph Dieterich; Niels H Gehring

doi:10.1016/j.molcel.2018.08.030

Exon Junction Complexes Suppress Spurious Splice Sites to Safeguard Transcriptome Integrity

Mol Cell. 2018 Nov 1;72(3):482-495.e7. doi: 10.1016/j.molcel.2018.08.030.

Affiliations

¹ Institute for Genetics, University of Cologne, 50674 Cologne, Germany.
² Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany.
³ Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA.
⁴ Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039-Guwahati, Assam, India.
⁵ Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
⁶ Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany; Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50937 Cologne, Germany.
⁷ Section of Bioinformatics and Systems Cardiology, Department of Internal Medicine III and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, 69120 Heidelberg, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120 Heidelberg, Germany. Electronic address: christoph.dieterich@uni-heidelberg.de.
⁸ Institute for Genetics, University of Cologne, 50674 Cologne, Germany. Electronic address: ngehring@uni-koeln.de.

PMID: 30388410
DOI: 10.1016/j.molcel.2018.08.030

Abstract

Productive splicing of human precursor messenger RNAs (pre-mRNAs) requires the correct selection of authentic splice sites (SS) from the large pool of potential SS. Although SS consensus sequence and splicing regulatory proteins are known to influence SS usage, the mechanisms ensuring the effective suppression of cryptic SS are insufficiently explored. Here, we find that many aberrant exonic SS are efficiently silenced by the exon junction complex (EJC), a multi-protein complex that is deposited on spliced mRNA near the exon-exon junction. Upon depletion of EJC proteins, cryptic SS are de-repressed, leading to the mis-splicing of a broad set of mRNAs. Mechanistically, the EJC-mediated recruitment of the splicing regulator RNPS1 inhibits cryptic 5'SS usage, while the deposition of the EJC core directly masks reconstituted 3'SS, thereby precluding transcript disintegration. Thus, the EJC protects the transcriptome of mammalian cells from inadvertent loss of exonic sequences and safeguards the expression of intact, full-length mRNAs.

Keywords: EJC; alternative splicing; cryptic splice sites; exon junction complex; gene expression; mRNA processing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alternative Splicing / physiology*
Consensus Sequence / genetics
DEAD-box RNA Helicases / metabolism
Eukaryotic Initiation Factor-4A / metabolism
Exons / physiology*
HeLa Cells
Humans
Introns
RNA Precursors / physiology
RNA Splice Sites / physiology*
RNA Splicing / physiology
RNA, Messenger / genetics
RNA-Binding Proteins / metabolism
Ribonucleoproteins / metabolism
Transcriptome / genetics

Substances

RBM8A protein, human
RNA Precursors
RNA Splice Sites
RNA, Messenger
RNA-Binding Proteins
RNPS1 protein, human
Ribonucleoproteins
Eukaryotic Initiation Factor-4A
EIF4A3 protein, human
DEAD-box RNA Helicases