In the completed periods of DNA access we have successfully established a system that enables us to interrogate a large number of sequence motifs for their ability to recruit transcription factors to a defined genomic locus. Our experimental setup enableed us to monitor different motifs in parallel and since we use single molecule footprinting a s readout we obtain a quantitative overview of the TF engagements. We were furthermore able to monitor TF binding as a function of nucleosomes presence and positioning. The latter is a critical addition as it allows to ask, in the context of the cell, how motif engagement changes depending on position relative to the complex and context dependent interface of the 140 bp that are covered by the nucleosome (Grand, Pregnaloto et al., Molecular Cell 2024). We furthermore identified how the important TF and tumor suppressor p53 engages with chromatin and how its cofactor TRIM24 reads out local histone modifications to modulated p53 function in a chromatin dependent manner (Isbel et al. NSMB 2023). By generating genetic deletions of a family of Methyl DNA Binding Domain proteins (MBDs) and contrasting the epigenome and transcriptome changes with those when we remove DNA methylation we were able to demonstrate that MBDs do nod function in repressing methylated promoters in stem and differentiated cells (Kaluscha, Domcke et al. Nature Genetics, 2022). We have in addition summarized the research field and challenges that we try to address within DNAaccess in a review article (Isbel et al. Nature Review Genetics 2022). We furthermore identified and reported the contribution of different ISWI subunit to guiding binding of CTCF revealing a novel function for DNA accessibility in nuclear organization (Iurlaro, Masoni et al., Nature Genetics, 2024). We have furthermore combined machine learning with inducible expression of lineage driving transcription factors to decode the chromatin and motif syntax for key e-box binding transcription factors (Durdu et al., Molecular Cell 2025) and provided a general computational and experimental framework to decode chromatin sensitivity.
