Comparative analysis of these enhancers revealed the presence of multiple conserved elements within them, and many of these correspond to consensus DNA-binding motifs for different TFs, including Hb [ 13, 14] and Cas [ 3].
In parallel, experimental approaches were developed [ 4], which allowed identification of binding motifs for many different transcription factors.
The flexibility might be necessary for the DH domain to accommodate binding motifs from different interaction partners.
Some of the peptide residues are buried in the MHC groove and act as anchor residues, which define binding motifs specific for different MHC alleles.
KorA carried a binding motif for coenzyme A, and KorB carried binding motifs for Fe-S cluster and thiamine pyrophosphate.
Besides the HABMs and USP domain [27, 28], we identified binding motifs for TRAF2 and TRAF3 in USP17.
While binding motifs for SGF-1 were detected in an OCR 6-kb upstream of the Fibrohexamerin gene in both the silk gland and BmE cells, an Awh-binding motif was detected only in the OCR of the silk gland.
Four of the silk gland-specific OCRs harbored the binding motifs for the TFs Awh, sna, optix, and eip74ef29,30, respectively.
Sequence analysis of the promoter region reveals a GC-rich sequence without a TATA motif and with putative binding motifs for CREB, c-myb, and AP-1 factors.
DREME is capable for finding binding motifs for cofactor TFs.
