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RNA regulatory networks diversified through curvature of the PUF protein scaffold

Author

Listed:
  • Daniel Wilinski

    (University of Wisconsin)

  • Chen Qiu

    (Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health)

  • Christopher P. Lapointe

    (University of Wisconsin)

  • Markus Nevil

    (University of Wisconsin)

  • Zachary T. Campbell

    (University of Wisconsin)

  • Traci M. Tanaka Hall

    (Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health)

  • Marvin Wickens

    (University of Wisconsin)

Abstract

Proteins bind and control mRNAs, directing their localization, translation and stability. Members of the PUF family of RNA-binding proteins control multiple mRNAs in a single cell, and play key roles in development, stem cell maintenance and memory formation. Here we identified the mRNA targets of a S. cerevisiae PUF protein, Puf5p, by ultraviolet-crosslinking-affinity purification and high-throughput sequencing (HITS-CLIP). The binding sites recognized by Puf5p are diverse, with variable spacer lengths between two specific sequences. Each length of site correlates with a distinct biological function. Crystal structures of Puf5p–RNA complexes reveal that the protein scaffold presents an exceptionally flat and extended interaction surface relative to other PUF proteins. In complexes with RNAs of different lengths, the protein is unchanged. A single PUF protein repeat is sufficient to induce broadening of specificity. Changes in protein architecture, such as alterations in curvature, may lead to evolution of mRNA regulatory networks.

Suggested Citation

  • Daniel Wilinski & Chen Qiu & Christopher P. Lapointe & Markus Nevil & Zachary T. Campbell & Traci M. Tanaka Hall & Marvin Wickens, 2015. "RNA regulatory networks diversified through curvature of the PUF protein scaffold," Nature Communications, Nature, vol. 6(1), pages 1-11, November.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms9213
    DOI: 10.1038/ncomms9213
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    Cited by:

    1. Chen Qiu & Sarah L. Crittenden & Brian H. Carrick & Lucas B. Dillard & Stephany J. Costa Dos Santos & Venkata P. Dandey & Robert C. Dutcher & Elizabeth G. Viverette & Robert N. Wine & Jennifer Woodwor, 2025. "A higher order PUF complex is central to regulation of C. elegans germline stem cells," Nature Communications, Nature, vol. 16(1), pages 1-18, December.

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