Worm Breeder's Gazette 9(2): 37

These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.

Observations on Tc1 Somatic Excision and Target Sequence

K-S. Ruan and S.W. Emmons

Figure 1

We have cloned and sequenced three empty sites resulting from Tc1 
somatic excision from two sites in the Bergerac strain.  One clone is 
from a 7.0 kbp BamHI fragment, and the other two clones are from a 3.5 
kbp EcoRI fragment isolated from two independent worm DNA preparations.
Sequence comparison of the 7.0 kbp empty site with the corresponding 
Tc1 filled site reveals four extra nucleotides, ATGT, remaining after 
Tc1 excision.  This indicates an imprecise excision at this site.  
Comparison of the two DNA sequences from the 3.5 kbp empty sites with 
their corresponding filled site shows that there are no changes in the 
sequence resulting from excision, indicating a precise excision at 
this site.  These results suggest that there may be a relationship 
between the precision of somatic excision and the location of the Tc1 
insertion site.  Perhaps, the conformation of the DNA at the insertion 
site, or the degree of match between the target site sequence and a 
concensus sequence regulates whether somatic Tc1 excision is precise 
or not.  We are cloning more empty sites to determine if different 
sites continue the trend toward precise excision or imprecise excision.

By inspection of the several Tc1 insertion sites (see table below) 
that have been sequenced by various labs (Rosenzweig, Liao and Hirsh, 
Moerman and Waterston, Eide and Anderson, and Ruan and Emmons) a 
number of target site concensus sequences could be derived.  One that 
we propose here is: TGTA and its complement TACA.  If either DNA 
strand can be used, a match of at least three out of four bases is 
made in all of the target sites.  (A dot above the TA pair indicates 
the Tc1 insertion site.)
A TA base pair near the concensus sequence seems to be strongly 
preferred as the point of Tc1 insertion (Rosenzweig, Liao and Hirsh).  
If one assumes that Tc1 excises by either a blunt end cut or by a two 
base staggered cut (and filling in with AT on the opposite strand), 
becomes part of the extrachromosomal circle.  Either mechanism of 
excision would generate an RsaI site (Ruan and Emmons) and a TGTA 
concensus sequence at the joint of the two Tc1 ends.  Concensus 
sequences that match in the extrachromosomal Tc1 and the target site 
may be cis-acting signals that aid trans-acting factors during Tc1 
[See Figure 1]

Figure 1