Following our success in describing the changes in the global binding of transcription factors in stem cells (Domcke, Bardet et al., Nature 2015) we collaborated with the Taipale lab to define in vitro the sensitivity of several hundred human transcription factors to DNA methylation and in vivo for selected cases in presence or absence of DNA methylation and hydroxymethylation. This identified a surprisingly large number of factors that are slightly attracted to methylated cytosines within their target motif (Yin et al., Science 2017).
We successfully established novel protocols to monitor TF binding using a combination of footprinting enzymes. As a proof of concept we have used these approaches to quantitatively describe the turnover of RNA polymerase at paused genes (Krebs et al., Molecular Cell 2017).
These approaches have also contributed to a study where we defined the contribution of CGs to the output of promoters (Hartl et al., Genome Research, 2019).
One key technology development within ReadMe was the successful establishment of a protocol that enables comprehensive monitoring of DNA bound proteins. This has been achieved recently and a proof of concept paper showing the ulitity of the approach will be published in the coming weeks (Ginno et al., Nature Communications, 2018). More recently we have published the first comprehensive genomic map of DNA methylation in our genome using a sophisticated approach of genetic deletion and time-course monitoring of DNA methylation changes (Ginno et al., Nature Communication, 2020). In addition we have generated neurons that lack DNA methylation enabling us to identify several methylation sensitive transcription factors that operate in neurons and have identified a factor that activates endogenous retrovirus in the absence of DNA methylation (Kaluscha et al., in prepation. We furthermore have identified a totally novel transcription factor important for CpG island regulation yet highly sensitive to DNA methylation (Grand et al., under review).
Thus ReadMe has reached its experimental milestones and achieved several novel insights. In addition to above and upcoming publications we have communicated these results through several presentations at international scientific meetings (including virtual meetings during the pandemic) and seminar visits in institutes. Selected achievements are further promoted on the internet and on social media using the twitter account of the FIM as well as that of the Schübeler lab.
