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Title: RNA regulatory networks diversified through curvature of the PUF protein scaffold

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.

Authors:
 [1];  [2];  [1];  [1];  [1];  [2];  [1]
  1. Univ. of Wisconsin, Madison, WI (United States). Dept. of Biochemistry
  2. National Institutes of Health, Research Triangle Park, NC (United States). Epigenetics and Stem Cell Biology Lab.
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1214654
Grant/Contract Number:  
AC02-06CH11357; W-31-109-ENG-38
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 6; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Wilinski, Daniel, Qiu, Chen, Lapointe, Christopher P., Nevil, Markus, Campbell, Zachary T., Tanaka Hall, Traci M., and Wickens, Marvin. RNA regulatory networks diversified through curvature of the PUF protein scaffold. United States: N. p., 2015. Web. doi:10.1038/ncomms9213.
Wilinski, Daniel, Qiu, Chen, Lapointe, Christopher P., Nevil, Markus, Campbell, Zachary T., Tanaka Hall, Traci M., & Wickens, Marvin. RNA regulatory networks diversified through curvature of the PUF protein scaffold. United States. doi:10.1038/ncomms9213.
Wilinski, Daniel, Qiu, Chen, Lapointe, Christopher P., Nevil, Markus, Campbell, Zachary T., Tanaka Hall, Traci M., and Wickens, Marvin. Mon . "RNA regulatory networks diversified through curvature of the PUF protein scaffold". United States. doi:10.1038/ncomms9213. https://www.osti.gov/servlets/purl/1214654.
@article{osti_1214654,
title = {RNA regulatory networks diversified through curvature of the PUF protein scaffold},
author = {Wilinski, Daniel and Qiu, Chen and Lapointe, Christopher P. and Nevil, Markus and Campbell, Zachary T. and Tanaka Hall, Traci M. and Wickens, Marvin},
abstractNote = {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.},
doi = {10.1038/ncomms9213},
journal = {Nature Communications},
number = ,
volume = 6,
place = {United States},
year = {2015},
month = {9}
}

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Cited by: 19 works
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    Works referencing / citing this record:

    A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity
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    Toward Identifying Subnetworks from FBF Binding Landscapes in Caenorhabditis Spermatogenic or Oogenic Germlines
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