I'm very new in biology and doing more computational analysis. I'm confused with the type of interactions between Transcription Factors (TF) and target genes.

Is it possible that the same transcription factor interacts differently with the same target gene under different conditions?

e.g., TF1 up-regulates Gene1 under condition 1 while TF1 down-regulates the same gene Gene1 under condition 2 Does the above example take place in biological systems?

I can only think of different TF complexes which are regulating the gene Gene1 under different conditions with different effect. However, it would be great to know if, in case TF1 does not participate in any TF complexes to regulate Gene1 under certain conditions, it is then possible that "TF1" regulates Gene1 differently under different conditions?

  • $\begingroup$ It also depends what you take as "normal expression". Even if you have only an ON and an OFF state for a single interaction, the system can display "upregulation" and "downregulation" of target genes if expression is normally somewhere between completely ON and OFF. $\endgroup$ – VonBeche Aug 3 '17 at 15:37

Short answer - yes but probably somewhat rarely.

Transcription factors aren't necessarily limited to being either repressors or activators. In practice they mostly do one a lot more than the other - e.g. if they have an 'activation' domain then they will mostly activate, but they can still do the opposite, directly or indirectly.

A single TF will often regulate different genes in different directions. This can be due to indirect effects - our activator activates a repressor which then switches off a gene. It can however also happen through direct means - for instance a factor might bind a repressing or activating domain at different locations, or displace different factors.

Most of this variation is probably specific to the target gene, so factors are probably more specific in their effect on a given gene. However, since our factors action depends on other genes,and different genes will be active in different conditions, there's no reason a factor couldn't do different things under different conditions while at the same location - perhaps one condition activates a repressor that binds with it, or a stronger activator that it competes with.

It's a matter of ongoing research, but I would expect this kind of thing to be the exception rather than the rule. In general complex interactions between TFs at a given location seem to be rarer than more or less additive effects.


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