Question

In this paper regarding a polymorphism within the AQP7 gene and its potential effects on one's metabolic profile, the authors use a luciferase assay to confirm that the alleles of this SNP have a definite impact on the expression of AQP7 in the presence of CEBPB, but the SNP itself falls outside the predicted CEBPB binding sequence: enter image description here

The only thing I can imagine is a second transcription factor that cooperates with CEBPB has a binding sequence that overlaps this SNP, but I see no mention of such a thing in this paper. If this SNP truly affects the binding of CEBPB, then wouldn't the corresponding binding sequence have to extend through this SNP?

Edit:

To quote the paper, A gel shift assay was then performed to investigate whether the A-953G SNP affects C/EBP binding. Compared with the radiolabeled oligonucleotide carrying the 953A, the one carrying the -953G variant showed a 30+/-7% reduced binding to C/EBP

And here is the gel shift assay:


As far as I can tell, even if the scientists had reason to believe that this SNP affected CEBP binding in this region, it shouldn't be beyond science for someone to hypothesize how that is.

Answer 1

The student's question addresses how a SNP can affect gene expression without being direct within a transcription factor's binding site. The given SNP influences the binding affinity of CEBPB, and the effects are confirmed with a luciferase assay and gel shift assays.

Step-by-step explanation:

The question pertains to a phenomenon where a single nucleotide polymorphism (SNP) affects the expression of the AQP7 gene despite not being located within the predicted binding region for the transcription factor CEBPB. It is possible that the SNP affects the binding affinity of CEBPB indirectly or that there is an unrecognized interaction with other transcription factors. The use of a luciferase assay in the study demonstrates that different alleles of this SNP indeed have disparate impacts on the expression levels of AQP7, suggesting functional consequences due to the SNP's position. Gel shift assays further confirm the influence of different SNP variants on the protein-DNA binding dynamics. Understanding the precise molecular mechanisms behind these observations requires more in-depth research, potentially exploring the wider genomic context and interactions with other regulatory elements or proteins.