We have performed TFBS enrichment analysis to establish the fact that the promoter regions of the genes having similar expression profile are bound by the same transcription factors.
A growing wealth of ChIP-chip and ChIP-seq data makes it possible to identify genes related by common epigenetic mark or bound by the same transcription factor.
As an example, the word w= CATAAT might be bound by the same transcription factor as the words CTTAAT and ATTATG, the former having one substitution, the latter being on the reverse strand.
We can for instance mention the participation of loci to the same transcription factory [ 22, 25, 26], their synchronisation during replication [ 27], or the fact that they bind to a common protein, such as CTCF [ 28].
Remarkably, although all ETS transcription factors bind the same DNA consensus sequence and overlapping tissue expression is observed, individual ETS transcription factors play unique roles in the development of HSCs.
The fact that some BORIS isoproteins can bind the CST promoter and activate transcription while others can bind the same promoter but do not display transcriptional activity (Fig. 8) suggests that BORIS isoforms, similarly to CREM, can perform opposing functions with the same DNA target.
The full-length proteins encoded by Zfy1 and Zfy2 are predicted to be zinc-finger transcription factors that bind the same DNA target sequences (Grants et al., 2010; Taylor-Harris et al., 1995); this suggests that Zfy1 may contribute to the impaired fertility of XY females.
Both complexes bind the same genes in C. elegans despite their opposing effects on transcription (Pferdehirt et al. 2011).
A typical case study for motif discovery has been the analysis of sequences (e.g. promoters) from genes showing similar expression patterns and likely to be bound by the same set of transcription factors, in order to identify their putative binding sites that should appear to be overrepresented in the sequences.
In the nucleoplasm, several pluripotency factors often bind to the same genomic regions, designated multiple transcription factor loci (MTLs) (Chen et al. 2008).
