Analysis of T-DNA insertion site distribution patterns in Arabidopsis thaliana reveals special features of genes without insertions

Genomics. 2006 May;87(5):645-52. doi: 10.1016/j.ygeno.2005.12.010. Epub 2006 Feb 20.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Codon, Terminator
  • DNA Transposable Elements
  • DNA, Bacterial / genetics*
  • Gene Expression Profiling
  • Genes, Plant
  • Genome, Plant
  • Mutagenesis, Insertional
  • Poly A
  • Protein Biosynthesis
  • Pseudogenes
  • Restriction Mapping
  • Sequence Tagged Sites
  • Transcription Initiation Site


  • Codon, Terminator
  • DNA Transposable Elements
  • DNA, Bacterial
  • T-DNA
  • Poly A