Super Pioneer Transcription Factors: Mechanisms of action and possible applications

In mammals, transcription factor (TF) recruitment to gene regulatory elements is an essential event for transcription regulation. Chromatin compaction and epigenetic modifications can regulate the accessibility of TF binding sites (TFBSs) to their corresponding TFs. Surprisingly, recent studies identified a select class of TFs called Pioneer Transcription Factors (PFs) that could access nucleosome-bound DNA, even in compact chromatin, leading to nucleosome eviction and opening the chromatin. This important finding indicates that epigenetic modifications could, in some cases, result from TF binding instead of controlling it. However, whether PFs can bind to methylated DNA and induce demethylation and transcription activation is largely not known. This is particularly relevant, as DNA methylation does not only affect the accessibility of DNA but also its affinity to TF binding. Using a high throughput approach to investigate PF effect on DNA methylation, we identified “Super Pioneer Transcription Factors" (SPFs) that can bind methylated DNA and induce DNA demethylation, in addition to their known ability to induce nucleosome remodelling. Most SPFs seem to induce TET (Ten-eleven translocation methylcytosine dioxygenase)-dependent active demethylation, except for SOX2 that can inhibit the maintenance of DNA methylation by DNMT1 during replication. These results add more complexity to the relationship between TF binding and epigenetic modifications and imply the need to revise the current view of the role of DNA methylation as a primary event in transcription regulation. Moreover, using CRISPR-based approach, we have demonstrated that synthetic recruitment of SPFs to methylated promoters could demethylate and activate them, providing a proof of principle for the use of SPFs to reactivate aberrantly methylated genes in diseases. Our aims for the extension year are: 1)To investigate the mechanisms underlying SPF-dependent DNA demethylation2)To define common characteristics of the different classes of PFs.3)To provide a proof of concept for the use of SPFs to activate genes with beneficial impact in pathological conditions.