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DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

Abstract

Alternative messenger RNA splicing is the main reason that vast mammalian proteomic complexity can be achieved with a limited number of genes. Splicing is physically and functionally coupled to transcription, and is greatly affected by the rate of transcript elongation1,2,3. As the nascent pre-mRNA emerges from transcribing RNA polymerase II (RNAPII), it is assembled into a messenger ribonucleoprotein (mRNP) particle; this is the functional form of the nascent pre-mRNA and determines the fate of the mature transcript4. However, factors that connect the transcribing polymerase with the mRNP particle and help to integrate transcript elongation with mRNA splicing remain unclear. Here we characterize the human interactome of chromatin-associated mRNP particles. This led us to identify deleted in breast cancer 1 (DBC1) and ZNF326 (which we call ZNF-protein interacting with nuclear mRNPs and DBC1 (ZIRD)) as subunits of a novel protein complexnamed DBIRDthat binds directly to RNAPII. DBIRD regulates alternative splicing of a large set of exons embedded in (A + T)-rich DNA, and is present at the affected exons. RNA-interference-mediated DBIRD depletion results in region-specific decreases in transcript elongation, particularly across areas encompassing affected exons. Together, these data indicate that the DBIRD complex acts at the interface between mRNP particles and RNAPII, integrating transcript elongation with the regulation of alternative splicing.

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Figure 1: Purification of nascent nuclear mRNP particles.
Figure 2: DBC1 and ZIRD form a stable complex that binds RNAPII.
Figure 3: DBIRD affects alternative splicing and is present at the affected exons.
Figure 4: DBC1 and ZIRD link exon skipping to RNAPII transcription.

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Primary accessions

Gene Expression Omnibus

Data deposits

Gene-expression andsplicing data sets have been deposited in the GEO database under accession code GSE35480.

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Acknowledgements

This work was supported by grants from Cancer Research UK and the European Research council (ERC) (to J.Q.S.), by an European Molecular Biology Organization (EMBO) long-term fellowship and by the Fonds Leon Fredericq foundation (to P.C.). We thank the Molecular Biology Core Facility at the Paterson Institute (Manchester) and Cell Services at London Research Insitute for analysis and help. We thank B. Chabot for CB3 cells, and members of the Svejstrup laboratory, P. Verrijjzer and T. H. Jensen for comments on the manuscript. P.C. is a senior research assistant at the Belgian National Foundation for Scientific Research (FNRS).

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P.C. and A.B.D.-S. performed experiments, and S.M. and M.S. did mass spectrometry analyses. P.E., H.H., M.H. and J.S. performed bioinformatic analyses. P.C.and J.Q.S. designed the study, analysed the experimental data and wrote the paper. All authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Jesper Q. Svejstrup.

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The authors declare no competing financial interests.

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Close, P., East, P., Dirac-Svejstrup, A. et al. DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. Nature 484, 386–389 (2012). https://doi.org/10.1038/nature10925

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