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The export factor Yra1 modulates mRNA 3′ end processing

Nature Structural & Molecular Biology volume 18, pages 1164–1171 (2011)Cite this article

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Abstract

The Saccharomyces cerevisiae mRNA export adaptor Yra1 binds the Pcf11 subunit of cleavage-polyadenylation factor CF1A that links export to 3′ end formation. We found that an unexpected consequence of this interaction is that Yra1 influences cleavage-polyadenylation. Yra1 competes with the CF1A subunit Clp1 for binding to Pcf11, and excess Yra1 inhibits 3′ processing in vitro. Release of Yra1 at the 3′ ends of genes coincides with recruitment of Clp1, and depletion of Yra1 enhances Clp1 recruitment within some genes. These results suggest that CF1A is not necessarily recruited as a complete unit; instead, Clp1 can be incorporated co-transcriptionally in a process regulated by Yra1. Yra1 depletion causes widespread changes in poly(A) site choice, particularly at sites where the efficiency element is divergently positioned. We propose that one way Yra1 modulates cleavage-polyadenylation is by influencing co-transcriptional assembly of the CF1A 3′ processing factor.

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Figure 1: Yra1 influences the cleavage-polyadenylation apparatus.
Figure 2: Distinct ChIP profiles for export and 3′ processing factors.
Figure 3: Yra1 depletion enhances Clp1 recruitment on long genes.
Figure 4: Yra1 depletion affects alternative poly(A) site choice at ACT1.
Figure 5: Widespread effects of Yra1 depletion on alternative poly(A) site choice within 3′ UTRs.
Figure 6: Yra1 depletion alters use of poly(A) sites within genes and at ncRNAs.
Figure 7: Positioning of the consensus efficiency element differs between Yra1-sensitive and Yra1-insensitive poly(A) sites.

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Acknowledgements

This work was supported by US National Institutes of Health grant GM58613 to D.B. We thank C. Moore (Tufts University) for GAL7 plasmids and advice on processing extracts, R. Zhao (University of Colorado) for recombinant Sub2, C. Wang and M. Covarrubias (City of Hope Functional Genomics Core) for array hybridization, J. Dover and J. Castoe for Illumina sequencing, and T. Blumenthal and J. Hesselberth (University of Colorado) for helpful comments.

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  1. Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA

    Sara A Johnson, Hyunmin Kim, Benjamin Erickson & David L Bentley

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Contributions

S.A.J., B.E. and D.L.B. designed and conducted the experiments. H.K. wrote the software and carried out the informatics. S.A.J., H.K. and D.L.B. wrote the paper.

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Correspondence to David L Bentley.

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Supplementary Figures 1–5, Supplementary Table 1 and Supplementary Methods (PDF 6697 kb)

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Gene lists used in this study (XLS 153 kb)

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Johnson, S., Kim, H., Erickson, B. et al. The export factor Yra1 modulates mRNA 3′ end processing. Nat Struct Mol Biol 18, 1164–1171 (2011). https://doi.org/10.1038/nsmb.2126

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