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Elsevier, Genomics, 5(87), p. 645-652, 2006

DOI: 10.1016/j.ygeno.2005.12.010

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

Journal article published in 2006 by Yong Li ORCID, Mario G. Rosso, Bekir Ülker, Bekir Ulker, Bernd Weisshaar ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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.