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. 2007 Jan 18:2:103-20.

3'UTR-located ALU elements: donors of potential miRNA target sites and mediators of network miRNA-based regulatory interactions

Evelina Daskalova  1 , Vesselin Baev, Ventsislav Rusinov, Ivan Minkov
Affiliations

3'UTR-located ALU elements: donors of potential miRNA target sites and mediators of network miRNA-based regulatory interactions

Evelina Daskalova et al. Evol Bioinform Online. .

Abstract

Recent research data reveal complex, network-based interactions between mobile elements and regulatory systems of eukaryotic cells. In this article, we focus on regulatory interactions between Alu elements and micro RNAs (miRNAs). Our results show that the majority of the Alu sequences inserted in 3'UTRs of analyzed human genes carry strong potential target sites for at least 53 different miRNAs. Thus, 3'UTR-located Alu elements may play the role of mobile regulatory modules that supply binding sites for miRNA regulation. Their abundance and ability to distribute a set of certain miRNA target sites may have an important role in establishment, extension, network organization, and, as we suppose - in the regulation and environment-dependent activation/inactivation of some elements of the miRNA regulatory system, as well as for a larger scale RNA-based regulatory interactions. The Alu-miRNA connection may be crucial especially for the primate/human evolution.

Keywords: retroelements; Alu elements; eukaryotic regulatory networks; evolution; miRNAs.

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Figures

Figure 1
Figure 1
Mobile elements (MEs) and their relation to cellular regulatory processes. The connection between ret-roelements and miRNAs is the objective of current study.
Figure 2
Figure 2
Distribution of target sites on the 3′UTR of the protein chemokine ligand 5 (NM_002985). It carries 2 Alu insertions in direct orientation: AluYc1 and AluS that have occupied 53,5% f the 3′UTR length. All six probable target sites with proper structure (red lines) map in the two Alu inserts. All the rest are ‘cryptic target sites’ with sequence complementarity to relevant miRNAs but without proper structure (green lines).
Figure 3
Figure 3
Structures of some miRNA/mRNA duplexes at target sites localized in Alu insertions. 3′ end of miRNA is shown at the top of the figures, 5′—at the bottom. miRNAs are colored in red, mRNA targets – in black. (a) – (e) – target sites in antisense Alu insertions. over page: (f) – (j) target sites in sense Alu insertions.
Figure 3
Figure 3
Structures of some miRNA/mRNA duplexes at target sites localized in Alu insertions. 3′ end of miRNA is shown at the top of the figures, 5′—at the bottom. miRNAs are colored in red, mRNA targets – in black. (a) – (e) – target sites in antisense Alu insertions. over page: (f) – (j) target sites in sense Alu insertions.
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