Studies of local stability in histone, U-snRNA and globin precursor mRNAs around transcription termination sites

Using an efficient algorithm we have carried out extensive studies of the local distributions of significant stem-loop structures around the 3′ termini of histone, U-snRNA and globin precursor mRNAs. We have analyzed statistically about 320 distribution curves from 47 species of histone, 16 species of U-snRNA and 22 globin sequences. Our results show that there are common and significant stem-loop structures near the 3′ ends of histone mRNAs of vertebrates and invertebrates. One of these structures encompasses both of the features known to be essential for 3′ processing: the palindrome and the CAAGAAAGA consensus sequence. Such stem-loop structures are not found in the 3′ termini of yeast and wheat histones, in globin precursor mRNAs or near the 3′ end of U-snRNA of vertebrates. These results are consistent with recent experimental data, in which the terminal stem-loop structure and the CAAGAAAGA spacer within the histone pre-mRNAs are required absolutely for RNA processing. For globin pre-mRNAs a common secondary structure appears to recur approx. 40 bases downstream from the conserved AAUAAA motif. This is also in agreement with experimental data which shows that the sequence downstream of the polyadenylation site is important for 3′ end formation. Our results are also compatible with the suggestion that the 3′ ends of histone and U-snRNA may be generated by related, but distinct, RNA processing mechanisms.