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TRACER database

The TRACER (Transposase and Recombinase-Associated Chromosomal Engineering Resource) database is a central resource describing mice and embryos carrying a transgenic insertion generated by a Sleeping Beauty transposon-based system (Ruf et al., 2011).

The transgenes used comprise different features. The transposons currently used most frequently (SB9 and SB8) contain:

A “regulatory sensor”

A “regulatory sensor”

A LacZ gene driven by a minimal promoter. This promoter has no activity by itself but responds to the activities of the surrounding transcriptional regulatory elements around (warning: these elements can be quite far from the insertion site). For many insertions, the associated LacZ expression is described, in mid-gestation (E11-12) mouse embryos is described and annotated.

A tool for ”recombineering”

A tool for ”recombineering”

A loxP site, which can be used to initiate in vivo chromosomal rearrangements such as deletions, duplications or inversions when combined with another loxP (Hérault et al., 1998; Spitz et al., 2005; Wu et al., 2007)

As such, the insertions provide information about the surrounding regulatory landscape(s) and, for the ones available, can be used for in vivo CRE-mediated chromosomal re-engineering.

Dynamic remobilisation

Dynamic remobilisation

Importantly, the transgenes are flanked by the inverted repeats of a Sleeping Beauty transposon. Accordingly, each one can be “remobilized”, by breeding to a transgenic line expressing SB-transposase expressing transgenic line (Ruf et al., 2011). The remobilisation rate varies depending on the insertion site, but is usually very high (10-50%). In addition, since Sleeping Beauty is biased for “local hopping”, the new insertions are frequently observed (~ 15-30%) within 1 to 2 Mb from their starting site.

Information or mice (alive or cryopreserved) can be requested via email or directly through the EMBL TRACER database

References

Hérault, Y., Rassoulzadegan, M., Cuzin, F., and Duboule, D. (1998). Engineering chromosomes in mice through targeted meiotic recombination (TAMERE). Nat Genet 20, 381–384.

Ruf, S., Symmons, O., Uslu, V.V., Dolle, D., Hot, C., Ettwiller, L., and Spitz, F. (2011). Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet 43, 379–386.

Spitz, F., Herkenne, C., Morris, M.A., and Duboule, D. (2005). Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat Genet 37, 889–893.

Wu, Ying, Wu, and Capecchi (2007). Toward simpler and faster genome-wide mutagenesis in mice. Nat Genet.

Searches: General Visual

Search SB lines Assembly: NCBIM37 / mm9
Genomic
--- chromosome
(hold 'Ctrl' for multiple)
--- position
(1000, >1000, <1000 or
a range, eg, 100-500.
Zeros can be in K or M,
case-insensitive,
eg, 100K-5m)
SB name/Gene Name/Ensembl Gene ID
--- SB name
(wildcard * supported,
Eg, 1*, or *1 or 1*1)
--- gene name
--- Ensembl gene id
--- Extend
base pair range
from gene start/end
default: 0.5M
Expression Domains/Stages
--- domain
(hold 'Ctrl' for multiple)
--- stage
(hold 'Ctrl' for multiple)
--- expression
Using AND OR to join main search categories
Insertions
Chromosomes: 12345678910111213141516171819XY
? Using the visual search

Using the visual search

Click on one of the chromosome boxex of your interest to display the insertions along its karyotype.

To search for insertions, you can:

Move along the chromosome:
click on the red range box and drag.

Change the size of the range box:
click on the range box and point your cursor to its lower right corner (the shape of the cursor should have now become double-arrow) and drag.

Dear TRACER database users:

If you cannot find a line of your interest, you are welcome to add your wishes here through this interface.


Please choose to enter the required data:
By position:
Chromosome *
Chromosome start *
Chromosome end *
By gene name
Gene Symbol *
Distance to gene (in base pairs or KB, MB. Eg. 1000 or 500K or 2M or 5.5M) *

Contact email * Firstname * Lastname *

To contact us by email, please select the option which best describes your issues

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