Identification, characterization and molecular phylogeny of U12-dependent introns in the Arabidopsis thaliana genome.

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 a 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 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.

[1]  J. Thompson,et al.  Multiple sequence alignment with Clustal X. , 1998, Trends in biochemical sciences.

[2]  P. Sharp,et al.  Evolutionary fates and origins of U12-type introns. , 1998, Molecular cell.

[3]  Sudhir Kumar,et al.  MEGA2: molecular evolutionary genetics analysis software , 2001, Bioinform..

[4]  Jackson Ij,et al.  A reappraisal of non-consensus mRNA splice sites. , 1991 .

[5]  Daniel R. Gallie,et al.  A look beyond transcription : mechanisms determining mRNA stability and translation in plants , 1998 .

[6]  Claudia Schneider,et al.  A novel U2 and U11/U12 snRNP protein that associates with the pre‐mRNA branch site , 2001, The EMBO journal.

[7]  A. Krainer,et al.  U1-Mediated Exon Definition Interactions Between AT-AC and GT-AG Introns , 1996, Science.

[8]  R. Padgett,et al.  Role of the 3′ Splice Site in U12-Dependent Intron Splicing , 2001, Molecular and Cellular Biology.

[9]  Christopher B. Burge,et al.  Classification of Introns: U2-Type or U12-Type , 1997, Cell.

[10]  M. Montagu,et al.  Non–canonical introns are at least 109 years old , 1996, Nature Genetics.

[11]  J. Steitz,et al.  Initial recognition of U12-dependent introns requires both U11/5' splice-site and U12/branchpoint interactions. , 1999, Genes & development.

[12]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.

[13]  Adrian R. Krainer,et al.  AT-AC Pre-mRNA Splicing Mechanisms and Conservation of Minor Introns in Voltage-Gated Ion Channel Genes , 1999, Molecular and Cellular Biology.

[14]  V. Brendel,et al.  Refined Annotation of the Arabidopsis Genome by Complete Expressed Sequence Tag Mapping1 , 2003, Plant Physiology.

[15]  A. Krainer,et al.  Functions of SR proteins in the U 12-dependent ATAC pre-mRNA Service Email , 2001 .

[16]  C. Will,et al.  Identification of both shared and distinct proteins in the major and minor spliceosomes. , 1999, Science.

[17]  R. Padgett,et al.  The intramolecular stem-loop structure of U6 snRNA can functionally replace the U6atac snRNA stem-loop. , 2001, RNA.

[18]  Abhijit A. Patel,et al.  The splicing of U12‐type introns can be a rate‐limiting step in gene expression , 2002, The EMBO journal.

[19]  A. Krainer,et al.  Splicing of a divergent subclass of AT-AC introns requires the major spliceosomal snRNAs. , 1997, RNA.

[20]  P. Sharp,et al.  Splicing of precursors to mRNAs by the spliceosomes , 1993 .

[21]  Woan-Yuh Tarn,et al.  Highly Diverged U4 and U6 Small Nuclear RNAs Required for Splicing Rare AT-AC Introns , 1996, Science.

[22]  Christopher W. J. Smith,et al.  Mutually exclusive splicing of α-tropomyosin exons enforced by an unusual lariat branch point location: Implications for constitutive splicing , 1989, Cell.

[23]  R. Padgett,et al.  Conserved sequences in a class of rare eukaryotic nuclear introns with non-consensus splice sites. , 1994, Journal of molecular biology.

[24]  Woan-Yuh Tarn,et al.  A Novel Spliceosome Containing U11, U12, and U5 snRNPs Excises a Minor Class (AT–AC) Intron In Vitro , 1996, Cell.

[25]  C. Will,et al.  Human U4/U6.U5 and U4atac/U6atac.U5 Tri-snRNPs Exhibit Similar Protein Compositions , 2002, Molecular and Cellular Biology.

[26]  K. Hokamp,et al.  A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. , 2003, Genome research.

[27]  I. Jackson,et al.  A reappraisal of non-consensus mRNA splice sites. , 1991, Nucleic acids research.

[28]  M. Moore,et al.  The human Prp8 protein is a component of both U2- and U12-dependent spliceosomes. , 1999, RNA.

[29]  R. Padgett,et al.  Requirement of U12 snRNA for in Vivo Splicing of a Minor Class of Eukaryotic Nuclear Pre-mRNA Introns , 1996, Science.

[30]  S. Yokoi,et al.  Differential Expression and Function of Arabidopsis Thaliana Antiporters in the Salt Stress Response , 2002 .

[31]  R. Padgett,et al.  Conservation of functional features of U6atac and U12 snRNAs between vertebrates and higher plants. , 1999, RNA.

[32]  R. Durbin,et al.  A computational scan for U12-dependent introns in the human genome sequence. , 2001, Nucleic acids research.

[33]  Michael P. Cummings,et al.  MEGA (Molecular Evolutionary Genetics Analysis) , 2004 .

[34]  R. Padgett,et al.  Alternative splicing of U12-dependent introns in vivo responds to purine-rich enhancers. , 2001, RNA.

[35]  R. Padgett,et al.  Terminal intron dinucleotide sequences do not distinguish between U2- and U12-dependent introns. , 1997, Molecular cell.

[36]  S. Karlin,et al.  Over- and under-representation of short oligonucleotides in DNA sequences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Wei Zhu,et al.  Optimal spliced alignment of homologous cDNA to a genomic DNA template , 2000, Bioinform..