Fine-tuning transcriptional activity of transcriptional regulatory factors by DNA-sequence induced selective use of coregulators
Final Report Abstract
Despite having essentially the same genome, the cells of our body perform very different functions. This is because different parts of the information encoded in our genome, in the form of genes, are activated in individual cells. For example, muscle cells activate genes important for movement whereas immune cells activate other genes to deal with infections. Importantly, genes are not simply turned on but need to be activated at the right level. A failure to activate genes at the right level can have adverse effects. For instance, for Down syndrome where an extra copy of a chromosome and the affiliated increase in gene dose for genes encoded on this chromosome result in developmental defects. The activation of genes is controlled by transcription factors, which are proteins that bind to regions of the genome that contain their recognition DNA sequence to regulate the expression of genes. We studied gene regulation by a transcription factor called the glucocorticoid receptor. This receptor is activated by the release of stress hormones, which in turn results in the activation of various genes. These hormones are released by the body in response to stress, for example when glucose levels in the blood are too low. In addition, the hormones that activate the glucocorticoid receptor can be synthesized in the lab and are broadly used in the clinic to treat diseases caused by an overactive immune system. The first aim of our study was to understand mechanisms that specify which genes are activated by the glucocorticoid receptor. A key to this is to figure out mechanisms that specify where in the genome the glucocorticoid receptor binds because this determines which genes are regulated. To our surprise, we found that binding close to the start site of genes is disfavored with most of the binding of the glucocorticoid receptor occurring at sites that are further away. One reason for the lack of binding is that the recognition DNA sequence for the glucocorticoid receptor is depleted near the start site of genes. However this only explains a fraction of the lack of binding of the glucocorticoid receptor near the start site of genes and despite our efforts, the mechanistic cause for this depletion remains a mystery. What we did discover in the course of this study was a yet unknown recognition DNA sequence that is bound by the glucocorticoid receptor in conjunction with another transcription factor. This can explain binding at genomic regions that do not contain the previously known recognition DNA sequence. The second aim of our study was to study and identify mechanisms that influence how much of a given gene is produced in response to glucocorticoid receptor activation by stress hormones. Here we found that the recognition sequence of the glucocorticoid receptor is not simply passive Velcro that facilitates binding. Rather, we found that subtle variations in the sequence directly flanking the recognition DNA sequence can influence the structure of the associated glucocorticoid receptor. Our data indicates that these subtle structural changes influence the activity of the glucocorticoid receptor. Given that the recognition DNA sequence of the glucocorticoid receptor differs from gene to gene, the sequence-induced subtle structural changes could explain the different levels of activation we observe for individual genes. Furthermore, we find evidence that proteins, so-called coactivators, that assist in the activation of genes, cooperate with the glucocorticoid receptor in a gene-specific manner. Interestingly, the ability of the coactivator we studied to cooperate with the glucocorticoid receptor also depended on the recognition DNA sequence. Together, these findings suggest that differences between genes in the level of activation by the glucocorticoid receptor might be a consequence of sequence-induced structural changes that allow or restrict the cooperation with coactivators to fine-tune the expression of individual genes.
Publications
- Identification and characterization of BATF3 as a context-specific coactivator of the glucocorticoid receptor. PLoS ONE. 2017 Jul 14;12(7):e0181219
Petra Birth, Stefanie Schöne, Ulrich Stelzl, Sebastiaan H. Meijsing
(See online at https://doi.org/10.1371/journal.pone.0181219) - (2015) ChIP-exo signal associated with DNA-binding motifs provide insights into the genomic binding of the glucocorticoid receptor and cooperating transcription factors. Genome Research Feb 26, 25(6): 825-835
Starick SR, Ibn-Salem J, Jurk, M, Hernandez C, Love MI, Chung HR, Vingron M, Thomas- Chollier M, Meijsing SH
(See online at https://doi.org/10.1101/gr.185157.114) - (2016). Sequences flanking the core binding site modulate the structure and activity of the glucocorticoid receptor. Nature Communications. 2016 Sep 1;7:12621
Schöne S, Jurk M, Helabad MB, Dror I, Lebars I, Kieffer B, Imhof P, Rohs R, Thomas- Chollier M, Vingron M, Meijsing SH
(See online at https://doi.org/10.1038/ncomms12621) - (2017). Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation. Nucleic Acids Res. 28;45(4):1805-1819
Love MI, Huska MR, Jurk M, Schöpflin R, Starick SR, Schwahn K, Cooper SB, Yamamoto KR, Thomas-Chollier M, Vingron M, Meijsing SH
(See online at https://doi.org/10.1093/nar/gkw1163)
