As a control for binding specificity, we also tested the ability of PARP-1 to bind to AMP-agarose beads.
The binding specificity was also evaluated by measuring the uptake of 111In-DTPA-11B6 in hK2-negative DU145 xenografts expressing low levels of hK2 (n = 3) at 48 h post-injection, which are considered to be hK2-negative when compared to other PCa tumours.
This high degree of binding specificity is also observed when we compared the Ubx and Hth binding sites identified in the imaginal discs with the sites bound by a group of transcription factors analyzed by ChIP-chip in embryos [49], [50].
To determine the binding specificity, we also generated mutated TRE1 and TRE2 for the competition assay.
Concurrently, alternative probes with improved binding specificity are also being developed [ 118].
To control binding specificity, we also used p53−/− or PHD1-silenced HCT116 cells and performed an IP with an unrelated IgG control antibody.
Within each TF family, DNA binding specificity has also diverged considerably, with many families having 2 10 different subclasses displaying different primary binding specificities (Berger et al., 2008; Wei et al., 2010; Jolma et al., 2013).
To corroborate these findings, binding specificity was also assessed by rosette-formation using different human cell lines (28) (Fig. 5 B, C ). Bead-IgG1 complexes set the standard (100% rosettes) for each cell type.
The observed changes in binding specificity are also consistent with crystal structures for the ETS-family members (see Figure 5; Kodandapani et al, 1996; Batchelor et al, 1998; Mo et al, 1998; Mo et al, 2000; Garvie et al, 2001; Pufall et al, 2005; Wang et al, 2005; Lamber et al, 2008; Agarkar et al, 2010).
