Gene expression is a combination of many processes, including transcription, pre-mRNA processing, nucleocytoplasmic transport of mRNA, translation, mRNA decay, and protein modification and decay.
Many changes in the programs of gene expression occur during development, differentiation, and aging.
These alterations are reflected at both the mRNA and protein levels.
While altered gene expression at the levels of transcription and protein turnover has been appreciated for some time, mRNA decay is now emerging as an important control point and a major contributor to gene expression as well.
Continuing identification of the protein factors and cofactors, and mRNA instability elements, responsible for mRNA decay are allowing us to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation.
Most mRNAs within the total population are relatively stable.
However, mRNAs encoding many oncoproteins, cytokines, and signal transduction components are labile, probably to ensure that their levels are maintained within critical levels and to allow rapid changes in their levels in response to stimuli.
Their instability is determined by A + U-rich elements (AREs), found in the 3'-UTRs. AREs represent the best-characterized and most widespread family of instability sequences.
They generally promote rapid deadenylation-dependent degradation, though there are a few exceptions.
For example, the initial event in the degradation of the chemokine GRO-mRNA is endonucleolytic cleavage within its ARE.
There is no strict sequence conservation among AREs, but they have been grouped into three classes based upon sequence similarities; class I: one or more AUUUA pentamers within a U-rich region; class II:
Tandem repeats of AUUUA; and class III: non-AUUUA but U-rich. mRNAs containing class I and III sequences often encode oncoproteins.
mRNAs containing class II sequences often encode cytokines and chemokines.
These differences might promote binding by different proteins to allow independent regulation of cytokines and proto-oncogenes.
Recent evidence also indicates that AREs can adopt higher order structures.
One attractive hypothesis is that RNA structural differences may allow differential regulation of ARE-containing transcripts.
Since AREs promote rapid deadenylation and decapping in cell-free systems, future work will undoubtedly uncover interactions between ARE-BPs and deadenylases, such as PARN, and decapping activities. ARE-mRNA stabilization can occur under conditions of cellular stress, like heat shock and UV exposure, T cell activation and monocyte adhesion.
The available evidence indicates that the Hu family of ELAV-like proteins is required for ARE-mRNA stabilization during stress conditions.
One likely hypothesis is that competition among ARE-BPs may establish whether an ARE-mRNA is stabilized or destabilized as a means of regulating mRNA turnover.
Thus, ARE binding by an ELAV-like protein might preempt binding by AUF1, KSRP, and/or TTP.
Additionally, alterations in the higher order structure of an ARE-RNA might influence the repertoire of ARE-BPs that can bind the ARE and, thus, influence stabilization versus destabilization.
A common theme is that RNA-binding proteins recognize specific sequence elements to target a mRNA for degradation.
Thus, specific protein-RNA interactions allow mRNA-specific degradation, and these interactions are frequently subject to regulatory control.
Talking about senescence the ARE-BP HuR, an ELAV-like protein, binds to the ARE-mRNA encoding the cell cycle inhibitor p21CIP1 and stabilizes it.
Under conditions of cellular stress, increased cytoplasmic HuR levels stabilize p21 mRNA to inhibit cell division.
These observations prompted the Gorospe laboratory to investigate the role of HuR in expression of proliferative genes during replicative senescence.
Two model systems of senescence were employed: serial passage of WI-38 human diploid fibroblasts; and IDH4 human fibroblasts, in which inducible expression of the SV40 large T antigen can reverse its normal limited life span.
In both systems, aged cells expressed less total HuR (both cytoplasmic and nuclear) and lower levels of mRNAs encoding proliferative proteins (e.g. cyclins A and B1, c-Fos, and DP-1).
The lower levels of HuR allowed faster decay of these mRNAs.
Consistent with this observation was the finding that extracts of aged cells contained less HuR-dependent ARE-RNA-binding activity compared to young cells.
Importantly, manipulating HuR levels could directly modify the aging phenotype of each cell type.
For example, ectopic overexpression of HuR converted aged cells to a younger phenotype, including elevated cdk activity, proliferation, and 3H-incorporation.
By contrast, lowering HuR expression using antisense converted young cells to an aged phenotype, including diminished cdk activity, proliferation, and 3H-incorporation.
Interestingly, levels of the ARE-BP AUF1 also decline with age, which could affect ARE-directed mRNA decay as well.
How might HuR levels be regulated in an age-dependent fashion?
Some tantalizing clues come from recent work demonstrating that the AMP-activated kinase (AMPK) can regulate cytoplasmic levels of HuR.
AMPK is a sensor of metabolic stresses that cause ATP depletion.
In low levels of ATP, AMPK is activated, and cytoplasmic HuR levels decline.
That results in reduced p21, cyclins A and B1 due to increased decay of their mRNAs.
Cell division declines as well.
This is again consistent with the notion that ARE-mRNAs encoding proliferative proteins are more susceptible to degradation when HuR levels decline.
Senescence is also a potent inducer of AMPK, which might explain why HuR levels decline in an age-dependent fashion.
Taken together, these studies suggest a model by which mRNA decay rates are determined by a balance between stabilization and rapid degradation (Fig. 1).
As levels of HuR decline with age, the balance shifts toward more rapid degradation.
Thus, HuR and other ARE-BPs may act in concert to globally regulate age-related changes in gene expression.
Fig.1. Model of age-related changes in ARE-directed mRNA decay. In young cells, mRNA destabilizing ARE-BPs, such as AUF1, KSRP, and TTP, and the stabilizing ELAV-like proteins, such as HuR, provide a balance of mRNA degradation and stabilization. As cells age, HuR levels decline, shifting the balance to mRNA degradation. Many ARE-mRNAs encoding proteins that contribute to proliferation, thus, decline which contributes to the phenotype of senescence.