It is clear that the field of mRNA decay is approaching the end of its beginning. Tremendous progress has been made toward understanding mRNA sequences that regulate mRNA stability and the enzymatic activities that mediate mRNA decay. The few examples provided in this review illustrate the complexity that will arise when all of the mRNA decay pathways and their targets are considered collectively. Indeed, future advances will depend on elucidating the complicated, multifactorial webs of regulatory events that coordinate the half-lives of cellular mRNAs depending on the stage of organismal development, the type of tissue, and the environmental conditions under which individual cells exist.
Genetic and biochemical approaches have identified the deadenylases, decapping enzymes, and exonucleases that catalyze mRNA decay. Within the next several years, we should have catalogued and characterized most if not all of the endonucleases. Sequence comparison has not been very successful in identifying endonucleases that act on mRNAs, thus their identification will require careful application of biochemical and molecular biological approaches. Identification of the targets and cleavage sites of these enzymes will be possible though the application of RNA-Seq. Together with improvements in computational approaches to RNA structure determinations, the knowledge gained from such studies will play a crucial role in defining the molecular code that directs particular transcripts to regulated decay processes, and should also provide insights into the mechanisms responsible for generating many of the poorly characterized small RNAs.
Given the advent of high-throughput proteomic and sequencing technologies, it is also becoming possible to identify the constituents of individual mRNPs: RIP-SEQ can be used to deep sequence mRNAs that co-immunoprecipitate with a particular protein as well as ncRNAs that could regulate at least some of the mRNAs; mass spectrometry can be used to identify proteins in these complexes and their post-translational modifications. Once established, it then becomes important to uncover how the sequences and structures of mRNAs, including their post-transcriptional modifications (consider, e.g., the terminal-U transferases that promote exosome-mediated mRNA decay), and their associated proteins and ncRNAs interact dynamically in response to signal transduction pathways to determine mRNA half-lives.
Integrating the many mRNA-specific regulatory pathways with those pathways that modulate the half-lives of multiple mRNAs will be a daunting task requiring sophisticated mathematical modeling. The complexity of such a task is compounded by the direct participation of nuclear receptors, indicating that mRNA half-lives could be regulated by cell environment, age and type. After understanding how mRNA decay is regulated by intracellular signal transduction at the single-cell level, it becomes important to evaluate intracellular signal transduction-mediated regulation at the organ and, ultimately, organismal levels, the latter of which will undoubtedly require considerations of age, gender and diet. As an added caveat, while mRNAs largely function to produce proteins, growing support for the idea that they can also serve as sinks for regulatory proteins and antisense ncRNAs such as microRNAs by functioning as “competing cellular RNAs, or ceRNAs100
, indicates that the regulation of mRNA decay may cast a very broad net and affect as yet unappreciated cellular processes.
In the end, it is hoped that new insights into how mRNA decay is regulated will uncover new therapies to treat inherited and acquired diseases (BOX 5
). Developing such therapies is at a forefront of a number of biotechnology companies and academic laboratories.
BOX 5. mRNA degradation and disease
Many diseases are due to the misregulation of mRNA decay (for a review see53
). For example, the level of the UPF3X NMD factor is downregulated in patients with syndromic or non-syndromic intellectual disability who harbor mutations in the UPF3X gene, which as its name implies is X-linked; as a consequence, the elevated level of the UPF3 NMD factor appears to compensate for the lack of UPF3X and lessens the disability110,111
Another recent example involves the von Hippel-Lindau (VHL) tumor suppressor that is inactivated in patients with VHL disease, an autosomally dominant cancer, or clear-cell renal carcinoma. VHL was found to regulate the stability of the ARE-containing mRNA that encodes vascular endothelial growth factor (and undoubtedly other ARE-containing mRNAs) by targeting at least some isoforms of AUF1 for ubiquitination and proteasome-mediated destruction112
It follows from this and many other studies that the targeted decay of particular mRNAs using, e.g., small interfering (si)RNA is at the forefront of developing therapies. siRNA-based disease treatments are challenging considering difficulties in delivering siRNAs to tissues and the inherent instability of siRNAs once delivered. In a recent approach holding promise, the arginine-glycine-aspartate tripeptide that mimics cell adhesion proteins and binds integrins has been used to “functionalize” siRNA nanoparticles that target mRNA encoding the signal transducer and activator of transcription (STAT)1, which upregulates genes in response to signals by type I, type II or type III inteferons113
. The nanoparticles were found to be resistant to serum-mediated degradation, effectively taken up by tissues, and effectively delivered to the joints of rheumatoid-arthritic mice so as to alleviate disease113