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Many RBPs bind to structured elements, and binding is actually based on structural fidelity rather than primary sequence recognition.
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Rev binds to a highly structured element called Rev Response Element (RRE) present in all viral transcripts [2].
The overall dynamics of the system would be considerably different from that of protein-based mechanisms, for example translation is prevented by specific RNA-binding proteins that are known to bind secondary structure elements in UTRs [ 26] Recent experimental studies have identified essentially two classes of mechanisms by which miRNAs are thought to regulate gene expression.
The exposed elements bind to similar exposed elements on other Fn modules, leading to a specific aggregation [11].
Another proposed role is in relation to chromosomal structure, because both DNA gyrase and DNA polymerase I can bind to REP elements [ 64, 65].
Proteins that bind to these elements remain to be isolated.
GT proteins specifically bind to GT elements, and the elements are highly degenerated.
The spacing between the cis elements determines the interactions between DBTFs that bind to those elements.
Heterodimers bind to TH response elements (or T3 responsive element; TRE) in target genes.
In animals, translational control of specific mRNAs frequently involves trans-acting factors that bind to specific recognition elements in the 3'UTR and target eIF4F assembly at the cap structure [ 18].
Transcriptional regulation emerges from the interaction between trans factors (Latin for 'far side of') that bind to cis-regulatory elements (Latin for 'this side of') in the context of a particular chromatin/chromosome structure.
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