Mechanisms of transcription factor selectivity

Abstract

The initiation of transcription is regulated by transcription factors (TFs) binding to DNA response elements (REs). How do TFs recognize specific binding sites among the many similar ones available in the genome? Recent research has illustrated that even a single nucleotide substitution can alter the selective binding of TFs to coregulators, that prior binding events can lead to selective DNA binding, and that selectivity is influenced by the availability of binding sites in the genome. Here, we combine structural insights with recent genomics screens to address the problem of TF-DNA interaction specificity. The emerging picture of selective binding site sequence recognition and TF activation involves three major factors: the cellular network, protein and DNA as dynamic conformational ensembles and the tight packing of multiple TFs and coregulators on stretches of regulatory DNA. The classification of TF recognition mechanisms based on these factors impacts our understanding of how transcription initiation is regulated.

Figure 1.

The sequence degeneracy of the REs listed in Table 1 is shown using a logo representation (http://weblogo.berkeley.edu) [75]. Although the functions of the REs are different, the corresponding sequences and binding affinities can be very similar. For example, the dissociation constants range from 7.1 to 11.0 nM for PUMA-BS2, Noxa, and p53AIP1 (apoptosis), whereas the dissociation constants for growth arrest RE such as cyclin G, 14-3-3σ and p21-3′ are between 7.8 and 12.0 nM. The sequences are also very similar between the two groups, with 1–4 bp difference from the consensus for apoptosis, and 0–3 for growth arrest.

Figure 2.

Three proposed mechanisms of TF selectivity. The classification is based on a conformational ensemble framework. (a) All REs are exposed and available for binding to TFs. The TF selectively binds an RE whose conformation is complementary (here in green). The TF-binding site conformation is allosterically determined by the prior binding events (not shown) of factors whose concentrations are controlled by the cellular network. Once the TF binds to an RE, transcription is initiated (or repressed). (b) All REs are available and the TF can bind to any (or all) REs. The REs allosterically enhance a TF population favored to bind to a specific cofactor. Each RE elicits a slightly different conformation of the binding site (different shapes in the upper part of the TF). The cofactor binds to the binding site conformation, which is complementary. When the cofactor binds, transcription is initiated (or repressed). Here, selectivity is determined by post binding events. (c) Chromatin unavailable REs become exposed through the enhanceosome (e.g. acetylation).

Figure 3.

Achieving selectivity via the combinatorial assembly mechanism. An RE can be recognized by two TFs; however, although the TF-binding sites are similar, the sizes of the TFs differ. (a) The binding of large TFs fit snuggly with the top cofactor, thereby binding the small TFs fit tightly with a cofactor of another shape. The cofactor of the first would be loose on the second and the cofactor of the second would overlap the TFs of the first. Thus, different TF surfaces enforce selective cofactor recruitment. Red TFs match red REs; purple TFs match purple REs. The spacing between the REs is the same in both cases. (b) Selective binding is enforced via different spacing between the REs. At the top, the spacing between the green and blue REs is short, leading to selective binding by small TFs. At the bottom, the spacing is longer, leading to a preferential binding of larger TFs. The larger TFs cannot bind to the top REs owing to steric hindrance; binding of the smaller TFs at the bottom is also unfavorable, leading to lower stability and a lack of cooperativity.

Figure I.

The free energy landscape and population shift that occurs following binding. On the left-hand side, the TF protein (in pale pink) is complexed with REs (in pink, blue or green). The REs allosterically alter the conformation of the protein, as seen in the changes on the surface of the protein. The complex with the RE (in blue) is the most stable. Via conformational selection [,–18], a regulatory protein factor (in purple) binds to the TF whose conformation is most complementary (the one bound to the pink RE). Upon binding the landscape shifts and the complex of the protein, when bound to the RE (in pink), is the most stable.