As the title described, it is common that a target gene sequence contains motif that acts as the binding site of transcription factor rather then the upstream regulatory region. Does this affect gene expression? or transcription factor just release followed by subsequent upstream transcription? please share your thoughts.
Transcription factors that bind to the promoter regulates the expression of the corresponding gene. It is a classical case. Transcription factors can also bind to introns within a gene. These regions can be enhancers regulating several genes. This is also a classical case.
You may also think about coding sequence. It has been discovered (using ChIP-seq experiments) that transcription factors bind to exons. In some cases, it has been demonstrated that such regions are also regulatory regions. However, such regions are often excluded by bioinformatic tools focused on regulatory regions. Studies are required to investigate whether coding regions with a regulatory function are distributed throughout the genome.
Pascal Rihet Thank you for respond, I'm facing a condition that a plasmid is already been inserted with a gene of interest, and been proved that can be expressed by transfected host. We tried to replace such gene, however, we discovered that the original gene of interest contained binding motif for the very same transcription factors that drive the response element of promoter. We cannot assure whether such motif is essential for the expression of gene, which we can either introduce or remove such motif to our new replaced gene.
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