Splicing does more than it was initially cut out to. As well as removing introns, splicing changes the composition of messenger RNA–protein (mRNP) complexes, which is thought to be important in communicating the nuclear history of the RNA to the cytoplasm. Y14 — a protein that binds RNA in a spliceosome-dependent manner and remains bound to mRNA in the cytoplasm — is a suitable candidate for mediating such molecular imprinting.

To determine whether Y14 binds randomly or specifically to mRNA, Narry Kim, Jeongsik Yong and co-workers microinjected radiolabelled pre-mRNAs into oocytes and, following splicing and nuclear export, separated them into nuclear and cytoplasmic fractions. By mixing these fractions with specific antisense deoxyoligonucleotides and RNase H, the mRNA was cleaved in a sequence-specific manner. An anti-Y14 antibody was then used to show that only specific RNA fragments co-immunoprecipitated with Y14. Further analysis revealed that Y14 binds to a minimum region, ∼20 nucleotides upstream of exon–exon boundaries, that shares no common sequence.

RNase H cleavage patterns were identical within nuclear and cytoplasmic fractions, indicating that Y14 remains bound to mRNA following nuclear export. Another protein, Aly/REF, also binds mRNA in the nucleus, but does not co-immunoprecipitate with mRNA in the cytoplasm. This indicates that at some stage before, during or after nuclear export, Aly/REF dissociates from mRNA, consistent with its role as a nucleo-cytoplasmic shuttling protein.

Why, then, does Y14 remain bound to mRNA in the cytoplasm? A likely explanation is that it acts as a molecular imprint, indicating to the cytoplasm where the introns previously were. Beyond possible roles in nuclear export, or mRNA turnover, localization or transport within the cytoplasm, a particularly attractive theory is that Y14 binding near exon–exon junctions functions in nonsense-mediated decay (NMD), a process whereby transcripts containing premature termination codons are degraded to avoid creating carboxy-terminally truncated proteins. During translation of normal mRNA, Y14 (located upstream of exon–exon junctions) would be removed. As the termination codon of higher eukaryotes usually lies in the last exon of the mRNA, by the time the translating ribosome reaches it, Y14 proteins should have been removed. However, if a nonsense mutation occurs upstream of the final exon–exon junction, the remaining downstream Y14 complexes would identify these transcripts for degradation.