All mRNA functions, starting with biogenesis, co-transcriptional processing, nuclear export, subcellular distribution, translation and ending with decay, involve association with RNA-binding proteins forming discrete ribonucleo-protein (RNP) complexes [1], [2].
In the former, the 3'UTR plays a central role in mRNA 3' processing and polyadenylation, whereas in the latter cis-elements in the 3'UTR are bound by trans-acting factors which modulate mRNA stability, nuclear export, subcellular localization, and translation efficiency [24] [27].
Recent advances in RNA research have revealed that the 3'UTR plays a prominent role in regulating the stability, subcellular localization, and translation of its parent mRNA via sequence-specific interactions with trans-acting factors including small RNAs and proteins [5].
The ability to identify mRNA targets directly, without relying on a change in their levels in response to perturbation of a specific miRNA, makes it possible to systematically investigate other possible miRNA-directed effects on their expression, including, for example, effects on subcellular localization or translation.
The 3' UTR contains cis-regulatory elements important for mRNA stability, degradation, subcellular localization and translation.
Cellular mRNAs are partitioned into two subcellular compartments for translation: the cytosol and the endoplasmic reticulum (ER).
Sequences in UTRs may control translation, subcellular localization, and transcript stability through a variety of mechanisms (e.g., Mignone et al. 2002).
Additionally, many of the factors identified in the screen have been previously implicated in controlling the subcellular distributions and translation of maternal mRNAs in the oocyte and early embryo.
In fact, they contain cis-regulatory elements, such as AU-rich elements (ARE), microRNA binding sites, etc. (Khabar, 2005; Bartel, 2009), which can affect transcript stability, degradation, subcellular localization and translation.
RBPs act on many kinds of RNA, such as ribosomal RNA (rRNA), transfer RNA (tRNA), small interfering RNA and microRNA, particularly at different stages of the messenger RNA (mRNA) life-cycle from splicing, polyadenylation, various modifications and subcellular localization to translation [ 1].
