Transposons for Functional Genomics

Provided by Jonathan Clarke, Sean Walsh, Mike Bevan and Jonathan Jones
The John Innes Centre Genome Lab supports the utilization of transposon insertions, developed by GARNET, for functional genomics applications. Four populations of Arabidopsis lines containing transposon insertions were generated by GARNET and are freely available from NASC. The transposon lines offer resources for forward and reverse genetic screens in the Columbia-0 and Landsberg erecta ecotypes. Special features include: inducible over-expression, gene traps for expression analysis and enhancer traps for mis-expression in addition to simple knock out mutants.

The transposon insertion sites have been sequenced, integrating the transposon lines with the gene models. These may be viewed at ATIdb or NASC AtEmsembl. Gene expression patterns identified within the GARNET Gene Trap (GGT) collection have been integrated into ATIdb. Patterns can be searched and retrieved using a simple Ontology at ATIdb Gene Traps.

The John Innes Centre Genome Lab will shortly be releasing lines via NASC for the remobilization of SM lines and the inducible over-expression of SM lines. Full support including protocols and advice will be available.

A new insertion site verification service for transposon and T-DNA lines will be available shortly to screen putative insertions within defined genes and isolate homozygous lines. The long term goal of this service will be to establish unigene knockout sets for the community.

GARNET Collections
1. The SM collection of single copy dSpm insertions, produced by Dr. Jonathan Clarke (GARNET) from the SLAT collection of Prof. Jonathan Jones (Sainsbury laboratory BBSRC grant 83/GAT9113 - GAIT; EU grant BI04CT95183 - AIMS). (Columbia-0)

2.The ACTIVATE (AT) collection, produced by Dr. Jonathan Clarke and Dr. George Coupland at the JIC (BBSRC grant PAG01523 - PAGA; EU grant BIO4CT95183 - AIMS), which was generated by the mobilization of an Activation Ds transposable element. (Landsberg erecta)

3.The GARNET Gene Traps (GGT) collection, produced by Dr. Jonathan Clarke and Prof. Mike Bevan at the JIC (BBSRC grant FGT11378; EU grant QLG2CT1999-00351 - EXOTIC), which was generated by the mobilization of a Gene-Trap Ds transposable element. (Landsberg erecta)

4.The GARNET Mis Expression Enhancer Traps (GMT) collection produced by Dr Jonathan Clarke at the JIC and Dr. Ian Moore at Oxford University (BBSRC grant FGT11321), which was generated by the mobilization of Mis-expression Enhancer Trap Ds transposable element. (Landsberg erecta)

For further details of the lines and applications contact Jonathan Clarke
For ATIdb enquiries contact Sean Walsh