The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity.

Cis-acting Elements involved in mRNA stability

An mRNA sequence not only encodes proteins but also contains various cis-acting regions, which either alone or with the help of trans-acting proteins, regulate mRNA stability. The 5' end of an mRNA has a 7-methylguanylate (m⁷G) cap, and the 3' end has a poly-A tail, both of which protect mRNA from exonucleases. A poly-A tail shorter than 15-20 nucleotides can lead to decapping and subsequent degradation of the mRNA; therefore, the length of the poly-A tail is important for the stability of mRNA. The 5' and 3' untranslated regions (UTR) of mRNA contain various sequences that act as binding sites for proteins involved in mRNA degradation and stability. The 5' UTR contains binding regions for proteins that promote decapping or removal of the 5' m⁷G cap. The 3' UTR in some mRNAs, especially those with a half-life ofless than 30 minutes, carriesmultiple “AUUUA” repeats, known as AU-rich sequences. When mRNA-destabilizing proteins bind to these AU-rich sequences, they promote rapid deadenylation and degradation of the mRNA. On the other hand, when mRNA-stabilizing proteins are present, they compete with the destabilizing proteins for binding to the AU-rich sequences and decrease the degradation rate of the mRNA. Some other mRNAs also carry specific recognition sequences for endonucleases.

Major Pathways of m-RNA degradation

The most common mechanisms of mRNA degradation involve the removal of the 3' end poly-A tail and 5' m⁷G cap. Deadenylation, removal of adenines from the poly-A tail, can lead to degradation of mRNA by two different mechanisms. The first mechanism involves the shortening of the poly-A tail to less than 15-20 nucleotides, which destabilizes the association between the mRNA and its binding proteins. This exposes the 5' m⁷G cap to the decapping enzymes, DCP1 and DCP2. The decapped and unprotected 5' end of the mRNA then can be degraded with the help of the 5' to 3' exonuclease, XRN1. Another mechanism of degradation involves complete removal of the 3' poly-A tail by deadenylases and the subsequent degradation of the unprotected 3' end by the cytoplasmic exosome complex in the 3' to 5' direction. The 5' to 3' mRNA degradation is a major pathway in yeast, while the 3' to 5' mRNA degradation is a major one in mammalian cells; however, mRNA can also be degraded by both mechanisms at the same time. In some mRNAs, deadenylation is not a prerequisite for degradation. One mechanism involves the decapping of the 5' end followed by 5' to 3' mRNA degradation using exonuclease XRN1. The other less observed degradation pathway involves an internal cleavage of the mRNA using endonucleases. The nascent unprotected ends of the broken mRNA then can be easily degraded in 5' to 3' and 3' to 5' directions with the help of XRN1 and the exosome complex, respectively.