title: High-throughput discovery of post-transcriptional cis-regulatory elements.
abstract: BACKGROUND
  Post-transcriptional gene regulation controls the amount of protein produced from an individual mRNA by altering rates of decay and translation. Many sequence elements that direct post-transcriptional regulation have been found; in mammals, most such elements are located within the 3' untranslated regions (3'UTRs). Comparative genomic studies demonstrate that mammalian 3'UTRs contain extensive conserved sequence tracts, yet only a small fraction corresponds to recognized elements, implying that many additional novel elements exist. Despite a variety of computational, molecular, and biochemical approaches, identifying functional 3'UTRs elements remains difficult.
  
  
  RESULTS
  We created a high-throughput cell-based screen that enables identification of functional post-transcriptional 3'UTR regulatory elements. Our system exploits integrated single-copy reporters, which are expressed and processed as endogenous genes. We screened many thousands of short random sequences for their regulatory potential. Control sequences with known effects were captured effectively using our approach, establishing that our methodology was robust. We found hundreds of functional sequences, which we validated in traditional reporter assays, including verifying their regulatory impact in native sequence contexts. Although 3'UTRs are typically considered repressive, most of the functional elements were activating, including ones that were preferentially conserved. Additionally, we adapted our screening approach to examine the effect of elements on RNA abundance, revealing that most elements act by altering mRNA stability.
  
  
  CONCLUSIONS
  We developed and used a high-throughput approach to discover hundreds of post-transcriptional cis-regulatory elements. These results imply that most human 3'UTRs contain many previously unrecognized cis-regulatory elements, many of which are activating, and that the post-transcriptional fate of an mRNA is largely due to the actions of many individual cis-regulatory elements within its 3'UTR.
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, 445 Biotech, Ithaca, NY, 14853, USA. erinwissink@gmail.com.|Present address: Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA. erinwissink@gmail.com.
authors.forename: Erin M
authors.initials: EM
authors.lastname: Wissink
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, 445 Biotech, Ithaca, NY, 14853, USA. eaf9@cornell.edu.
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Fogarty
authors.affiliation: Department of Molecular Biology and Genetics, Cornell University, 445 Biotech, Ithaca, NY, 14853, USA. agrimson@cornell.edu.
authors.forename: Andrew
authors.initials: A
authors.lastname: Grimson
mesh_terms: D020413:3' Untranslated Regions; D005786:Gene Expression Regulation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012323:RNA Processing, Post-Transcriptional; D020871:RNA Stability; D050436:Regulatory Elements, Transcriptional
chemical_list: D020413:3' Untranslated Regions