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Open Access Research

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

Mallory A Freeberg12, Ting Han13, James J Moresco4, Andy Kong12, Yu-Cheng Yang5, Zhi John Lu5, John R Yates and John K Kim1*

  • * Corresponding author: John K Kim jnkim@umich.edu

  • † Equal contributors

Author affiliations

1 Life Sciences Institute, Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-2216, USA

2 Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2216, USA

3 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109-2216, USA

4 Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA

5 MOE Key Lab of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China 10008

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Citation and License

Genome Biology 2013, 14:R13  doi:10.1186/gb-2013-14-2-r13

Published: 14 February 2013

Abstract

Background

Protein-RNA interactions are integral components of nearly every aspect of biology, including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions.

Results

Here, we describe the gPAR-CLIP (global photoactivatable-ribonucleoside-enhanced crosslinking and immunopurification) approach for capturing regions of the untranslated, polyadenylated transcriptome bound by RNA-binding proteins (RBPs) in budding yeast. We report over 13,000 RBP crosslinking sites in untranslated regions (UTRs) covering 72% of protein-coding transcripts encoded in the genome, confirming 3' UTRs as major sites for RBP interaction. Comparative genomic analyses reveal that RBP crosslinking sites are highly conserved, and RNA folding predictions indicate that secondary structural elements are constrained by protein binding and may serve as generalizable modes of RNA recognition. Finally, 38% of 3' UTR crosslinking sites show changes in RBP occupancy upon glucose or nitrogen deprivation, with major impacts on metabolic pathways as well as mitochondrial and ribosomal gene expression.

Conclusions

Our study offers an unprecedented view of the pervasiveness and dynamics of protein-RNA interactions in vivo.