Alu RNAs are transcribed from the repetitive Alu elements and can be found as free Alu RNAs or embedded in messenger RNAs (mRNAs), notably, in the untranslated regions (UTR), which are known to modulate the stability of mRNAs or their translation efficiency. A protein partner of Alu RNAs is the heterodimer SRP9/14 of the Signal Recognition Particle (SRP). Therefore, SRP9/14 could bind to embedded Alu RNAs and thus regulate mRNA expression. We developed a method to study this interaction, using two fusion proteins and in vivo crosslinking. We used as a positive control an isoform of TRF2 mRNA (Telomeric Repeat Binding Factor 2), which binds SRP9/14 in vitro via its Alu sequence. We were able to precipitate Alu-containing RNAs specifically with both proteins, when compared to mutant and negative control proteins. However, both wild-type and mutant proteins precipitated TRF2 mRNAs, which either contained or lacked the Alu sequence, suggesting that the proteins might not bind the Alu sequence of this specific mRNA in vivo. Further optimization of the isolation of RNA-protein complexes will lead us to a genome-wide identification of Alu-containing mRNAs bound by SRP9/14. Analysis of the effects of SRP9/14 binding on stability and/or transcription of Alu-containing mRNAs will provide us with a better understanding of the function of Alu sequences in mRNAs.