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Fig. 4. Gel-shift and footprint assays define two Brn3a-binding sites in the
TrkA minimal enhancer. (A) Illustration of six, overlapping, 100 bp
fragments covering TrkA minimal enhancer and (B) gel-shift using a
GST-Brn3a POU-domain fusion protein indicating that only the first and sixth
fragments can bind Brn3a. (C,D) DNAse I footprint assays to define the
Brn3a-binding sequences in the TrkA minimal enhancer. The 5'
protected sequence is 5'-TCTAAGAGATCTATTAATTTCTC-3' (C) and the
3' protected sequence is
5'-TCACCTAACTTATTCCAAGTGACATGCACACCCTCTTAA-3' (D). (E,F, left
panels) Gel-shift assays showing that the protected sequences in (C,D) compete
with the first and sixth 100 bp fragments in (A,B) for GST-Brn3a POU-domain
fusion-protein binding. (E,F, top panels) Protected sequences from (C,D) share
(red boxes) an A/T-rich core sequence. The mutant sequences used in the
competitive gel-shift assays (left panels) and the following transgenic
analysis (Figs 5,
6) are shown in red. (E,F,
right panels) Competitive gel-shift assays using either the wild-type or
mutated Brn3a-binding sites, showing that mutated Brn3a-binding sites do not
bind the GST-Brn3a POU-domain fusion protein (lane 8) and, unlike wild-type
sites (lanes 1-4), do not compete with wild-type sites for binding (lanes
5-7). Arrows in E,F indicate the DNA-protein complexes.
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