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The regulation of genes is done for an important part by transcription factors. But which genes a transcription factor transcribes is strongly dependent on where it is. This allows a transcription factor to regulate different genes in different tissues. The big question is: How does it do this? Now researchers from the Netherlands and Germany showed that the unique composition of a transcription factor complex is determining which DNA-sequency it binds.
It was already known that which genes a transcription factor transcribes depends at least partly on the accessibility of the DNA. In addition, it was known that for regulating gene transcription, transcription factors often interact with other transcription factors. But how this interaction exactly result in the specific gene transcription was unknown.
In order to study this the researchers analysed the transcription factor FRUITFULL. During development FRUITFULL is present in specific tissue types. Two of these are the inflorescence meristem and the pistil. The researchers observed in each of these tissues where FRUITFULL binds to the DNA. This overlapped partly, but for a large part not. In each tissue FRUITFULL was regulating the transcription of a unique set of genes.
Like each lock has its own unique key
Subsequently the researchers analysed with which transcription factors FRUITFULL forms a complex, in the inflorescence meristem, and with which in the pistil. This showed that in the inflorescence meristem FRUITFULL is working together with SOC1. While in the pistil FRUITFULL works with AG, SEP1, SEP2, and SEP3. In addition, the researchers noticed that in both the inflorescence meristem and the pistil FRUITFULL is also interacting with other transcription factors.
Using the FRUITFULL-transcription factor dimers, the researchers analysed which DNA sequences they bind. This showed that, although each FRUITFULL-transcription factor dimer binds a CArG-box like motif, the specific DNA-sequence was for each FRUITFULL-transcription factor dimer unique. The researchers translated the DNA sequence to its three-dimensional form. This showed that each FRUITFULL-transcription factor dimer preferred a specific form.
These results suggest a unique form for each FRUITFULL-transcription factor dimer, one that exactly fits its preferred DNA sequence. Just like each lock has its own unique key. Working together with other transcription factors enables FRUITFULL to regulate a specific set of genes in each tissue.
Literature
van Mourik, H., Chen, P., Smaczniak, C., Boeren, S., Kaufmann, K., Bemer, M., Angenent, G. C., and Muio, J. M. (2023) Dual specificity and target gene selection by the MADS-domain protein FRUITFULL. Nature. Plants https://doi.org/10.1038/s41477-023-01351-x
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