Transcriptional regulation of common essential genes in mammalian chromatin

• Applicant: Dr. Ralph Grand
• Subject Area: General Genetics and Functional Genome Biology
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 556634773

Each cell in our body needs to express genes that encode for fundamental cellular processes such as metabolism. Despite the general relevance of these common essential genes (CEGs), our understanding of their regulation remains limited. This is likely due to the redundant regulatory mechanisms that ensure CEG expression across cell types, and the essential nature of regulatory factors. However, with the rising awareness that abnormal CEG expression can contribute to disease, a comprehensive understanding of their regulation is pressing.Genes are controlled by regulatory regions that are read by combinations of sequence-specific transcription factors (TFs) to establish gene expression patterns. In mammalian cells, this occurs in the context of chromatin, where nucleosomes can impact TF access to DNA. Extensive profiling of chromatin and regulatory proteins, and in vitro biochemistry and structural analysis, have generated genome-wide location maps and atomic resolution images of chromatin and regulatory factors. However, these snapshots struggle to define how TFs and cofactors cooperate to modulate chromatin and transcription in the cell. Thus, fundamental questions remain about how TF combinations and cofactors control CEG activity in mammalian cells.To dissect the interplay between these regulatory layers in the cell requires a reductionist system to identify the factors and define their contributions to gene activation. My discovery of BANP as one of the most potent transcriptional activators in the human genome that also modulates chromatin provides such a tractable system. Using BANP as an entry point, we will define the role of TF cooperativity and cofactors in regulating CEG activity in murine embryonic stem cells. We will generate combinatorial inducible degron cell lines for TFs that co-bind with BANP, which enables to measure primary changes in TF binding, chromatin, and gene activity following rapid depletion, to explore how TF combinatorics modulate CEG activity. We will further explore how TF binding is translated into gene activity through the action of cofactors by identifying BANP cofactors using proteomics and a CRISPR knockout screen and tagging them with inducible degrons to investigate their function. This will generate a comprehensive understanding of how BANP interprets regulatory regions embedded in chromatin to modulate CEG gene activity. Furthermore, it will help to interpret disease-associated mutations in regulatory sequences and factors, with the potential to aid in diagnosis and treatment.

• DFG Programme: Research Grants