title: Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts.
abstract: Posttranscriptional regulatory programs governing diverse aspects of RNA biology remain largely uncharacterized. Understanding the functional roles of RNA cis-regulatory elements is essential for decoding complex programs that underlie the dynamic regulation of transcript stability, splicing, localization, and translation. Here, we describe a combined experimental/computational technology to reveal a catalog of functional regulatory elements embedded in 3' UTRs of human transcripts. We used a bidirectional reporter system coupled with flow cytometry and high-throughput sequencing to measure the effect of short, noncoding, vertebrate-conserved RNA sequences on transcript stability and translation. Information-theoretic motif analysis of the resulting sequence-to-gene-expression mapping revealed linear and structural RNA cis-regulatory elements that positively and negatively modulate the posttranscriptional fates of human transcripts. This combined experimental/computational strategy can be used to systematically characterize the vast landscape of posttranscriptional regulatory elements controlling physiological and pathological cellular state transitions.
authors.affiliation: Joint Centers for Systems Biology, Columbia University, New York, NY 10032, USA.
authors.forename: Panos
authors.initials: P
authors.lastname: Oikonomou
authors.affiliation: Joint Centers for Systems Biology, Columbia University, New York, NY 10032, USA.
authors.forename: Hani
authors.initials: H
authors.lastname: Goodarzi
authors.affiliation: Joint Centers for Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biology, Columbia University, New York, NY 10032, USA; Department of Systems Biology, Columbia University, New York, NY 10032, USA. Electronic address: st2744@columbia.edu.
authors.forename: Saeed
authors.initials: S
authors.lastname: Tavazoie
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D051379:Mice; D009690:Nucleic Acid Conformation; D012313:RNA / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D012313:RNA