Downstream

 Nucleotide sequence elements located downstream from protein-coding sequences are defined by the direction of transcription. They are primarily involved in termination of transcription and in messenger RNA (mRNA) processing, in particular, polyadenylation. Prokaryotic terminators typically have runs of T at the termination point, preceded by complementary symmetrical sequences, which provide the potential for formation of hairpin structures at the ends of the mRNA (1). The hairpins presumably cause transcription to pause, a phenomenon known as attenuation, before the complete arrest.

 The mechanism of transcription termination in eukaryotes is not fully understood (2, 3). There are usually many alternative locations for the termination points for the same gene, within a downstream region as large as several thousand bases. It appears that, in a manner similar to that in prokaryotic terminators, transcription elongation in eukaryotes first slows down, due to formation of secondary structure in the mRNA, and then terminates within a nearby U-rich sequence (3). At the noncoding 3′-end of newly formed eukaryotic RNA transcripts several polyadenylation signals usually exist with the consensus sequence AAUAAA. One of these sites (but not always the same in different rounds of transcription of the same gene) is somehow selected for the RNA cleavage, which occurs about 20 bases downstream from the site, and for subsequent polyadenylation of 3′-end of the mRNA. Polyadenylation of mRNA is also known in prokaryotes, although it is not as site specific or extensive as in eukaryotes (4).

The eukaryotic downstream sequences—in particular those located within 3′-ends of the RNA transcripts—are also involved in many external functions. For example, they can act in trans and control the efficiency of the, stability, and compartmentalization of an mRNA (5) .

References

1. K. S. Wilson and P. von Hippel (1995) Proc. Natl. Acad. Sci. USA 92, 8793–8797. 

2. N. J. Proudfoot (1988) Trends Biochem. Genet. 14, 105–110. 

3. O. Resnekov et al. (1988) Gene 72, 91–104. 

4. N. Sarkar (1997) Ann. Rev. Biochem. 66, 173–197. 

5. C. J. Decker and R. Parker (1995) Curr. Opin. Cell Biol. 7, 386–392.