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Eukaryotic transcription factors activate gene expression with their DNA-binding domains and activation domains. DNA- binding domains bind the genome by recognizing structurally related DNA sequences; they are structured, conserved, and predictable from protein sequences. Activation domains recruit chromatin modifiers, coactivator complexes, or basal tran- scriptional machinery via structurally diverse protein-protein interactions. Activation domains and DNA-binding domains have been called independent, modular units, but there are many departures from modularity, including interactions be- tween these regions and overlap in function. Compared to DNA-binding domains, activation domains are poorly under- stood because they are poorly conserved, intrinsically disor- dered, and difficult to predict from protein sequences. This review, organized around commonly asked questions, de- scribes recent progress that the field has made in under- standing the sequence features that control activation domains and predicting them from sequence.
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Identification of plant transcriptional activation domains
Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.
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- PAR ID:
- 10588571
- Publisher / Repository:
- Nature
- Date Published:
- Journal Name:
- Nature
- Volume:
- 632
- Issue:
- 8023
- ISSN:
- 0028-0836
- Page Range / eLocation ID:
- 166 to 173
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1038/s41586-024-07707-3
