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However, further work will be required to determine whether competition or co-association occurs during binding of these RBPs to individual transcripts.
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Under altered redox conditions in the PCC, rbcL may bind to rbcL, and prevent the binding of stablizing RBPs (like MRL1 and RLSB) leading to decreased rbcL transcripts.
The study of mRNA/protein complexes in vivo is often hampered by the rapidity of the interactions and by nonspecific binding of abundant RBPs.
The binding of these transcripts by various RNA-binding proteins (RBPs) may impair the ability of these RBPs to interact with their respective RNA targets.
This is of interest as the stability of specific transcripts is determined, in part, by the binding of RBPs to cis-acting sequences such as AREs connecting these target mRNAs to core degradation pathways49,50.
Therefore, the functional interactions between PUF and miRNAs may well be very mRNA target-specific because many additional factors and combinatorial binding of RBPs and miRNAs may have an impact on its final fait.
Our motif discovery approach is based on biophysical modeling of the binding of RBPs to target RNAs.
The predicted effects of APA may also affect gene expression through the distinct binding of RBPs to alternate 3′ UTRs.
Reproducible binding of RBPs in intronic regions has proven to be predictive of a role in pre-mRNA processing for multiple proteins.
The binding of RBPs to mRNAs affects numerous steps of an mRNA's lifecycle, including alternative splicing (Blencowe 2006; Glisovic et al. 2008).
RNA transcripts are tethered to regulatory factors, and the combinatorial binding of RBPs to transcripts coordinates different steps of RNA processing (Hogan et al., 2008; Licatalosi and Darnell, 2010; Maniatis and Reed, 2002).
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