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We found a clear enrichment of DNA binding motifs of multiple transcription factors that were previously described to be involved in prostate cancer, including the androgen receptor (AR).
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Consistent with their findings, VAS was able to find overlaps between the SNP and open chromatin signals in various normal brain cells and the presence of binding motifs for multiple transcription factors around that region.We also made a number of additional interesting observations based on the VAS results.
In both instances, binding motifs for multiple proteins were identified, many of which are specific to transcription factors.
To further analyze the multiple binding motifs of OsSMF1 with different intensities, we assayed their binding specificities to recombinant OsSMF1 by electrophoretic mobility shift assay (EMSA) using biotinylated double-stranded oligonucleotide probes corresponding to each motif.
CM were synthesized that had defined lengths and contained aa corresponding to binding motifs of MHC class II molecules relevant in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE), specifically HLA-DRB1∗1501 and HLA-DRB5∗0101, which are related to MS, and H2-IAs associated with EAE in SJL mice.
Fig. 2 Identification of binding motifs of recombinant OsSMF1 from E. coli by Q9-PBM.
Here, we used the Q9-PBM to determine the binding motifs of OsSMF1.
We first attempted to identify the binding motifs of the OsSMF1 protein using a Q9-PBM.
It can detect alternative binding motifs as well as binding motifs of potential co-factors.
Myb repeats are classically considered to be DNA binding motifs, and multiple copies of these domains are often found in transcription factors (reviewed in ref (33)).
Motif cc_3 corresponds to the DNA binding motif of the FixK transcription factor.
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