Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions.
Large collections of sequence-indexed T-DNA insertion mutants are invaluable resources for plant functional genomics. Flanking sequence tag (FST) data from these collections indicated that T-DNA insertions are not randomly distributed in the Arabidopsis thaliana genome and that there are still a fairly high number of annotated genes without T-DNA insertions. We have analyzed FST data from the FLAGdb, GABI-Kat, and SIGnAL mutant populations. The lack of detectable transcriptional activity and the absence of suitable restriction sites were among the reasons genes are not covered by insertions. Additionally, a refined analysis of FSTs to genes with annotated noncoding regions showed that transcription initiation and polyadenylation site regions of genes are favored targets for T-DNA integration. These findings have implications for the use of T-DNA in saturation mutagenesis and for our chances to find a useful knockout allele for every gene.
Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany.
Yong
Y
Li
Mario G
MG
Rosso
Bekir
B
Ulker
Bernd
B
Weisshaar
D017360:Arabidopsis / Q000235:genetics*; D018388:Codon, Terminator; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics*; D020869:Gene Expression Profiling; D017343:Genes, Plant; D018745:Genome, Plant; D016254:Mutagenesis, Insertional; D011061:Poly A; D014176:Protein Biosynthesis; D011544:Pseudogenes; D015183:Restriction Mapping; D016324:Sequence Tagged Sites; D024363:Transcription Initiation Site
D018388:Codon, Terminator; D004251:DNA Transposable Elements; D004269:DNA, Bacterial; C036483:T-DNA; D011061:Poly A