title: Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae.
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.
authors: Mallory A
authors: MA
authors: Freeberg
authors: Ting
authors: T
authors: Han
authors: James J
authors: JJ
authors: Moresco
authors: Andy
authors: A
authors: Kong
authors: Yu-Cheng
authors: YC
authors: Yang
authors: Zhi John
authors: ZJ
authors: Lu
authors: John R
authors: JR
authors: Yates
authors: John K
authors: JK
authors: Kim
mesh_terms: D020413:3' Untranslated Regions; D001665:Binding Sites; D003432:Cross-Linking Reagents; D011485:Protein Binding; D059370:RNA Folding; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D003432:Cross-Linking Reagents; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins