Identification, characterization, and molecular phylogeny
of U12-dependent introns in the Arabidopsis thaliana genome
Wei Zhu and Volker Brendel (Nucleic Acid Research 31: 4561-4572)
ABSTRACT
U12-dependent introns are spliced by the minor U12-type
spliceosome and occur in a variety of eukaryotic organisms, including Arabidopsis.
In this study, a set of putative U12-dependent introns was compiled from
a large collection of cDNA/EST-confirmed introns in the Arabidopsis
thaliana genome by means of high-throughput bioinformatic analysis combined
with manual scrutiny. A total of 165 U12-type introns were identified based
upon stringent criteria. This number of sequences well exceeds the total
number of U12-type introns previously reported for plants and allows more
thorough statistical analysis of U12-type signals. Of particular note is
the discovery that the distance between the branch site adenosine and the
acceptor site ranges from 10 nt to 39 nt, significantly longer than the
previously postulated limit of 21 bp. Further analysis indicates that, in
addition to the spacing constraint, the sequence context of the potential
acceptor site may have an important role in 3'-splice site selection. Several
alternative splicing events involving U12-type introns were also captured
in this study, providing evidence that U12-dependent acceptor sites can
also be recognized by the U2-type spliceosome. Furthermore, phylogenetic analysis
suggests that both U12-type AT-AC and U12-type GT-AG introns occurred in
Na+/H+ antiporters in a progenitor of animals and
plants.
Supporting Materials
© 2006 Shannon D. Schlueter