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We've used the fragment based protocol of MED-SuMo which exploits the whole PDB on the basis that similar protein surfaces might bind the same fragment.
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Again, it was clear that mCbx7 was enriched in the chromatin precipitated through mCbx8 (Fig. 5B), implying that mCbx7 and mCbx8 bind simultaneously to the same fragment of chromatin.
PNGaseF treatment revealed a truncated fragment of 101L-moPrP bound to heparin whereas the same fragment present in the 101P-moPrP expressing cells was not detected (Figure 5B).
If they bound to the same colonies, or to the same fragment or fraction of DNA, the possibility of false positives is virtually eliminated.
Both yeast one-hybrid analysis and co-expression of reporter and effector genes demonstrated that two proteins, TaWRKY and TaRAV, which can specially bind to TaeIF5A1 promoter fragments containing the W-box, but failed in binding to the same fragments containing the mutated core sequence "T TTT".
The same fragment occurs in 37.3% of all compound records.
Five independent clones contained the same fragment.
By contrast, FREX employs two copies of the same fragment.
M PEAK relies on the fact that multiple probes will bind the same chromatin fragment if the probes are designed to be close together along the genomic sequence, with maximal binding seen where the probe sequence and the binding element overlap.
YHNN and QYHH both bound to the same protein fragments (residues 419 447) at the subunit interface of β-Gal (Figure S6 in File S1).
We also found that the coIP of the differentially tagged Ku70 or Ku80 subunits was not the result of different heterodimers being bound to opposing ends of the same DNA fragment because the interaction was not eliminated by treatment of the WCEs with the combination of DNaseI and Benzonase nuclease prior to immunoprecipitation.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com