Polyadenylation site

Figure 37-13. Mechanisms of alternative processing of mRNA precursors. This form of RNA processing involves the selective inclusion or exclusion of exons, the use of alternative 5 donor or 3 acceptor sites, and the use of different polyadenylation sites.

In addition to affecting the efficiency of promoter utilization, eukaryotic cells employ alternative RNA processing to control gene expression. This can result when alternative promoters, intron-exon splice sites, or polyadenylation sites are used. Occasionally, heterogeneity within a cell results, but more commonly the same primary transcript is processed differendy in different tissues. A few examples of each of these types of regulation are presented below. 

In vitro experiments show that correct modification of the 3 -end requires at least three protein factors the CPSF protein, the poly-A polymerase and the poly-A binding protein. The CPSF protein (CPSF cleavage and polyadenylation specificity factor) binds to the AAUAA signal and brings the poly-A polymerase to the polyadenylation site. The poly-A polymerase is supported by the poly-A binding protein. The latter binds to the poly-A sequence and is required for the transition from the phase of synthesis of short poly-A sequences to the formation of mature poly-A sequences (ca. 200 A-residues). 

Fig. 1.46. Alternative polyadenylation in the expression of calcitonin genes of rat. The primary transcript of the calcitonin gene possesses two polyadenylation sites. One site is nsed in the processing of RNA in the thyroid, another site in the brain, and yet another in nerve tissne. The translation of the two mRNAs creates two pre-hormones, from which two different polypeptide hormones (calcitonin and the calcitonin-related peptide", or CGRP) are created via proteolysis.

RNA is removed during processing. Pol II extends the primary transcript well beyond the cleavage and polyadenylation site ("extra RNA") before terminating transcription. Termination signals for Pol II have not yet been defined. 

Carswell, S. and Alwine, J.C. (1989) Efficiency of utilization of the simian virus 40 late polyadenylation site effects of upstream sequences. Mol. Cell, 9,4248 1258. 

Certain pre-mRNAs contain more than one set of signal sequences for 3 end cleavage and polyadenylation. In some cases, the location of the alternative polyadenylation sites is such that, depending on the site chosen, particular exons may be lost or retained in the subsequent splicing reactions (Fig. 7). Here the effect is to change the coding capacity of the final mRNA so that different proteins are produced depending on the polyadenylation site used. In other... 

Stability of ATiR mRNA depends on specific binding motifs for polyso-mal proteins in the 3 UTR immediately upstream of the polyadenylation tract (Nickenig et al. 2001). There are two putative polyadenylation sites in the 3 UTR... 

The initiation codon, usually an AUG, signals the start of translation, and a termination codon marks the end of the translated region. In the analysis of prokaryotic DNA sequences, the signals include the transcriptional and translational initiation sites, the ribosome-binding site, and the transcriptional and translational termination sites. Due to the interrupted nature of the eukaryotic genes, the signals include the translation initiation sites, the intron/exon boundaries (splice sites), translational termination sites, and the polyadenylation sites. 

Matis, S., Xu, Y., Shah, M Guan, X., Einstein, J. R., Mural, R. Uberbacher, E. (1996). Detection of RNA polymerase II promoters and polyadenylation sites in human DNA sequence. Comput Chem 20,135-40. 

The gene for this antibody contains two polyadenylation sites, one after the last two exons (which code for a hydrophobic amino acid sequence) and one before these exons. 

Adenovirus has a single promoter for all RNA made late in the cycle of infection. The primary transcripts terminate at five major polyadenylation sites. Each termination site influences the splicing pattern by allowing particular in-trons or intron termini to be present or not. The five sets are not used with equal frequency, with the result that most mRNAs encoding various genes are not the same. This is the primary mechanism for determining the relative amounts of the different structural proteins synthesized late in the adenovirus life cycle. 

Methoxyethyl (2 -MOE) RNA has been used to inhibit human telomerase in immortal human prostate DU 145 cell lysate. IC50 values of 5-10 nM were obtained, and inhibition of telomerase activity persisted for up to seven days after a single dose of 2 -MOE RNA. A fully modified 2 -MOE oligonucleotide targeted to the 3 -polyadenylation site of E-selectin was found to inhibit polyadenylation at that site, and redirect it to one of 2 upstream cryptic sites. 

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