Panos Oikonomou, Hani Goodarzi, Saeed Tavazoie
Post-transcriptional 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 catalogue of functional regulatory elements embedded in 3′-untranslated regions (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, non-coding, 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 post-transcriptional fates of human transcripts. This combined experimental/computational strategy can be used to systematically characterize the vast landscape of post-transcriptional regulatory elements controlling physiological and pathological cellular state transitions.
Panos Oikonomou, Hani Goodarzi, Saeed Tavazoie. Systematic identification of regulatory elements in conserved 3′-untranslated regions of human transcripts. 2014-04-10. https://doi.org/10.1016/j.celrep.2014.03.001
Two independently generated C3U libraries of 16,332 conserved human 34-nt 3′-UTR elements were tested in pooled Flp-In-293 cells. FACS expression bins and high-throughput sequencing of reporter-insert amplicons were used to identify elements enriched in high- or low-DIR populations.
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