Originally, introns were described as non-coding sequences inter- spersed with exons
in primary transcripts. Spliceosomal U2 introns are ubiquitous in nuclear transcriptomes.
Alternative splicing can in- crease proteome diversity and provide means for (post)transcriptional
regulation. Some intron RNAs accumulate to perform crucial functions in response to,
e.g., nutrient exhaustion. U2 intron excision requires a ribonucleoprotein complex,
the U2 spliceosome, and involves highly coordinated RNA-RNA interactions with the
intron’s 5’-donor- and 3’-ac- ceptor G’s at opposite splice sites, and the branch-point
A. However, continual generation of new U2 introns is a vexing mystery. Stwintrons
consist of nested U2 introns excised by consecutive splicing reactions. In a [D1,2]
stwintron, an internal intron is integrated in the 5’-donor of an external intron
between the first and second nucleotide. Using the principle of nested U2 introns,
we have identified many dozens of gen- uine [D1,2] stwintrons in Hypoxylon sp. CO27-5
and EC38. The large majority of them were sequence-unique but located at gene positions
also occupied by [D1,2]’s in other Hypoxylaceae, suggesting a common ancestry. Conversely,
25 [D1,2]’s were sequence-similar and unique to Hypoxylon CO27-5/EC38. A striking
distinction between these groups of stwintrons involves the density of a terminal
symmetry sequence (40–50 nt), which is considerably higher in most sequence-similar
“sister” stwintrons. Moreover, we found canonical introns which are sequence-similar
to the termini of sister stwintrons but lack the latter’s central spacer separating
the terminal inverted repeats (TIR). Conse- quently, these new canonical introns only
consist of TIRs, predicted to form a relatively stable hairpin secondary structure
bringing the do- nor- and acceptor G’s in very close proximity. Sister stwintrons
would duplicate as [D1,2] stwintrons but occasionally give rise to highly sym- metrical
introns, which propagate as canonical introns. The TIR seems key to the inferred (stw)intron
propagation.
