In this and the previous chapter, we have seen that in eukaryotic cells, mRNAs are synthesized and processed in the nucleus, transported through nuclear pore complexes to the cytoplasm, and then, in some cases, transported to specific areas of the cytoplasm before being translated by ribosomes. Each of these fundamental processes is carried out by complex macromolecular machines composed of scores of proteins and in many cases RNAs as well. The complexity of these macromolecular machines ensures accuracy in finding promoters and splice sites in long DNA and RNA sequences and provides various avenues for regulating the synthesis of a polypeptide chain. Much remains to be learned about the structure, operation, and regulation of complex machines such as spliceosomes and the cleavage/polyadenylation apparatus.

Recent examples of the regulation of pre-mRNA splicing raise the question of how extracellular signals might control such events, especially in the nervous systems of vertebrates. A case in point is the remarkable situation in the chick inner ear, in which multiple isoforms of the Ca²⁺-activated K⁺ channel called Slo are produced by alternative RNA splicing. Cell-cell interactions appear to inform cells of their position in the cochlea, leading to alternative splicing of Slo pre-mRNA. The challenging task facing researchers is to discover how such cell-cell interactions regulate the activity of RNA-processing factors.

The mechanism of mRNP transport through nuclear pore complexes poses many intriguing questions. Future research is likely to reveal additional activities of hnRNP and nuclear mRNP proteins and clarify their mechanisms of action. For instance, there is a small gene family encoding proteins homologous to the large subunit of the mRNP exporter. What are the functions of these related proteins? Do they participate in the transport of overlapping sets of mRNPs? Some hnRNP proteins contain nuclear-retention signals that prevent nuclear export when fused to hnRNP proteins with nuclear-export signals. How are these hnRNP proteins selectively removed from processed mRNAs in the nucleus, allowing the mRNAs to be transported to the cytoplasm?

The localization of certain mRNAs to specific subcellular locations is fundamental to the development of multicellular organisms. During development, as we will see in Chapter 21, an individual cell frequently divides into two daughter cells that function differently from each other. In the language of developmental biology, the two daughter cells are said to have different developmental fates. In many cases, this difference in developmental fate results from the localization of an mRNA to one region of the cell before mitosis so that after cell division, it is present in one daughter cell and not the other. Much exciting work remains to be done to fully understand the molecular mechanisms controlling mRNA localization that are so critical for the normal development of multicellular organisms.

Some of the most exciting and unanticipated discoveries in molecular cell biology in recent years have concerned the existence and function of miRNAs and the process of RNA interference. RNA interference (RNAi) provides molecular cell biologists with a powerful method for studying gene function. The discovery of hundreds of miRNAs in humans and other organisms suggests that multiple significant examples of translational control by this mechanism await characterization. Recent studies in S. pombe and plants link similar short nuclear RNAs to the control of DNA methylation and the formation of heterochromatin. Will similar processes control gene expression through the assembly of heterochromatin in humans and other animals? What other regulatory processes might be directed by other kinds of small RNAs? Because control by these mechanisms depends on base pairing between miRNAs and target mRNAs or genes, genomic and bioinformatic methods will probably suggest genes that may be controlled by them. What other processes, in addition to translation control, mRNA degradation, and heterochromatin assembly, might be controlled by miRNAs?

These are just a few of the fascinating questions concerning RNA processing, post-transcriptional control, and nuclear transport that will challenge molecular cell biologists in the coming decades. The astounding discoveries of entirely unanticipated mechanisms of gene control by miRNAs remind us that many more surprises are likely in the future.