Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures

Abstract

Primary, secondary and higher-order structures of downstream elements of mammalian pre-mRNA polyadenylation signals [poly(A) signals] are re viewed. We have carried out a detailed analysis on our database of 244 human pre-mRNA poly(A) signals in order to characterize elements in their downstream regions. We suggest that the downstream region of the mammalian pre-mRNA poly(A) signal consists of various simple elements located at different distances from each other. Thus, the downstream region is not described by any precise consensus. Searching our database, we found that approximately 80% of pre-mRNAs with the AAUAAA or AUUAAA core upstream elements contain simple downstream elements, consisting of U-rich and/or 2GU/U tracts, the former occurring approximately 2-fold more often than the latter. Approximately one-third of the pre-mRNAs analyzed here contain sequences that may form G-quadruplexes. A substantial number of these sequences are located immediately downstream of the poly(A) signal. A possible role of G-rich sequences in the polyadenylation process is discussed. A model of the secondary structure of the SV40 late pre-mRNA poly(A) signal downstream region is presented.

Figure 1

The sequences of downstream regions of pre-mRNA poly(A) signals. The four out of five base UREs and 2GU/U elements are indicated by a single line, G-rich tracts are indicated by a double line. The binding site for CstF is indicated by a dotted line. The segments which form the double-helical structure are indicated by a wavy line.

Figure 2

The secondary structure scheme of the core poly(A) signal of the SV40 L pre-mRNA. The secondary structures of the pre-mRNA fragments were determined using the mfold version 3.1 program for RNA folding by Zuker and Turner (http://www.bioinfo.rpi.edu/applications/mfold/). The U-rich downstream element and the AAUAAA hexamer are marked by single and double lines, respectively. The cleavage site is marked by an arrow. The sites attacked by RNase T1 (56) are marked by triangles. Thermodynamic stabilities of the hairpins I, I′, II and II′ are –3.1, –2.5, –4.3 and –2.4 kcal/mol, respectively.

Figure 3

Patterns of pre-mRNA fragments folding into G-quadruplexes. (A) Fragment of human cerebroside sulfotransferase pre-mRNA. (B) Fragment of human glyceraldehyde-3-phosphate dehydrogenase pre-mRNA.