In the present thesis, I analyzed DNA-encoded signals that regulate gene expression by modulating transcription factor (TF) binding. Candidate signals in the form of DNA sequence motifs were identified by analysis of ChIP-Seq data, on the assumption that corresponding signals are enriched (enhancing TF binding) or depleted (restricting TF binding) at genomic binding sites. The influence of such signals on the genomic binding of the glucocorticoid receptor (GR), a hormone-activated TF, was the topic of my thesis.
One part focused on signals that enhance genomic binding of GR. Specifically, I studied signals in a cell line where the conventional binding site of GR is rarely found at GR-bound regions raising the question: what are the sequences responsible for GR recruitment in this cell line? The results presented here indicate that recruitment of GR is likely facilitated via interactions with other DNA-bound proteins. Such interactions might either indirectly tether GR to the DNA, or might elevate the local concentration of GR and thereby increase the likelihood of it to bind to DNA directly.
Another part of my thesis focused on the identification and functional characterization of sequence-encoded signals that restrict genomic GR binding. I identified such sequences and found that they indeed interfere with GR binding to the genome. Interestingly, my studies indicate that the mechanisms employed by these sequences to restrict GR binding do not involve changes in DNA accessibility. Rather, my results suggest that interactions with proteins found at specific subnuclear structures, called paraspeckles, are important to restrict GR binding. One possibility is that these sequence motifs serve as anchoring points for subnuclear re-localization of corresponding genomic loci and thereby influence GR binding. Another possibility is that the proteins recruited by these sequence motifs prevent GR interactions with the genome. As a response to external stimuli such genomic regions can be reactivated for TF binding by sponge-like activities of paraspeckles to sequestrate such proteins.
Together, my studies uncovered novel mechanisms that allow or restrict where TFs bind in the genome and thereby increase our understanding of how the information in the genome is decoded to produce the gene-products needed by cells.
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