In bacteria, transcription and translation take place simultaneously. In eukaryotes, transcription takes place in the nucleus and the pre-mRNAs are then processed before moving to the cytoplasm for translation, allowing opportunities for gene control after transcription. Consequently, posttranscriptional gene regulation assumes an important role in eukaryotic cells. A common level of gene regulation in eukaryotes is RNA processing and degradation.

GENE REGULATION THROUGH RNA PROCESSING Alternative splicing allows a pre-mRNA to be spliced in multiple ways, generating different proteins in different tissues or at different times in development (see Chapter 10). Many eukaryotic genes undergo alternative splicing, and the regulation of splicing is an important means of controlling gene expression in eukaryotic cells.

An example of regulation by alternative mRNA splicing is sex determination in fruit flies (see Sex Determination in Drosophila melanogaster in Section 4.1). Sex differentiation in Drosophila arises from a cascade of gene regulation. In XX fly embryos, a female-specific promoter is activated early in development and stimulates the transcription of the sex-lethal (Sxl) gene (Figure 12.19). The protein encoded by Sxl regulates the splicing of the pre-mRNA transcribed from another gene called transformer (tra). The splicing of tra pre-mRNA results in the production of Tra protein (see Figure 12.19). Together with another protein (Tra-2), Tra stimulates the female-specific splicing of pre-mRNA from yet another gene called doublesex (dsx). This event produces a female-specific Dsx protein, which causes the embryo to develop female characteristics.

In XY fly embryos, the promoter that transcribes the Sxl gene in females is inactive, so no Sxl protein is produced. In the absence of Sxl protein, tra pre-mRNA is spliced at a different 3′ splice site to produce a nonfunctional form of Tra protein (Figure 12.20). In turn, the presence of this nonfunctional Tra in males causes dsx pre-mRNAs to be spliced differently from that in females, and a male-specific Dsx protein is produced (see Figure 12.19). This event causes the development of male-specific traits.

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THE DEGRADATION OF RNA The amount of a protein that is synthesized depends on the amount of corresponding mRNA available for translation. The amount of available mRNA, in turn, depends on both the rate of mRNA synthesis and the rate of mRNA degradation. Eukaryotic mRNAs are generally more stable than bacterial mRNAs, which typically last only a few minutes before being degraded. Nonetheless, there is great variability in the stability of eukaryotic mRNAs: some mRNAs persist for only a few minutes, whereas others last for hours, days, or even months. These variations can produce large differences in the amount of protein that is synthesized.

Various factors, including the 5′ cap and the poly(A) tail (see Chapter 10), affect the stability of eukaryotic mRNA. Poly(A)-binding proteins (PABPs) normally bind to the poly(A) tail and contribute to its stability-enhancing effect. The presence of these proteins at the 3′ end of the mRNA protects the 5′ cap. When the poly(A) tail has been shortened below a critical limit, the 5′ cap is removed, and the mRNA is degraded by the removal of nucleotides from the 5′ end. These observations suggest that the 5′ cap and the 3′ poly(A) tail of eukaryotic mRNA physically interact with each other, most likely by the poly(A) tail bending around so that the PABPs make contact with the 5′ cap.

Much of RNA degradation in eukaryotes takes place in specialized complexes called P bodies. P bodies help control the expression of genes by regulating which RNA molecules are degraded and which are sequestered for later release. RNA degradation facilitated by small interfering RNAs (see next section) can also take place within P bodies.

Other parts of eukaryotic mRNA, including sequences in the 5′ untranslated region (5′ UTR), the coding region, and the 3′ UTR, also affect mRNA stability. Some short-lived eukaryotic mRNAs have one or more copies of the consensus sequence 5′—AUUUAUAA—3′, referred to as the AU-rich element, in the 3′ UTR. The mRNAs containing AU-rich elements are degraded by a mechanism in which microRNAs (see next section) take part.