Systems Biology of Gene Regulation

What defines the identity of a cell? How is the same genetic code used to build more than 200 different cell types with distinct physiological and morphological properties? These fundamental questions drive our enthusiasm for understanding how information processing is regulated at the level of chromatin modifications and DNA sequence.

A multitude of DNA sequence-dependent and -independent interactions coordinate the spatiotemporal recruitment of transcriptional regulators to the genome and are required for tissue-specific gene expression and cell identity. Interference or lack of specificity in this process results in defective embryonic development and can give rise to various human diseases, including cancer. However, the underlying mechanisms that mediate such precise interactions are not fully explored and the current challenge is to understand how gene regulatory processes are correctly recruited to the genome.

We aim to cover this gap by a) dissecting how interactions between transcriptional or chromatin regulators and the genome are specified, and b) how these interactions impact chromatin and transcription during biological processes. Towards this we combine various experimental and computational strategies, including genome and epigenome engineering, genome-wide studies, proteomics, single-cell measurements and computational modelling. We use mouse embryonic stem cells and their differentiation to neuronal and haematopoietic cells as our main model system. This integrative approach allows us to understand gene regulatory mechanisms in a quantitative and functional manner.

Current topics in the lab are:

Principles and design of epigenetic gene regulatory circuits

DNA sequence-specific transcription factors (TFs) are the key factors that initiate and regulate cell type-specific gene regulation. In addition, various degrees of compaction and chemical modifications of the genome have been identified to provide additional layers of regulation. Correct distribution and interpretation of such “epigenetic” modifications along the genome are highly relevant for gene regulation.

We aim to understand how epigenetic marks are specified and interpreted in a dynamic manner. One major focus is to dissect the mechanisms that guide the specificity of writers, erasers and readers of epigenetic marks to the genome. Based on genome-wide comparisons of numerous epigenetic marks, DNA sequence and transcriptional activity, several correlations and anti-correlations are apparent, which suggest context-dependent crosstalk and feedback between these features. Through applying high-throughput functional analysis and reverse engineering of epigenetic regulatory circuits, we want to dissect the underlying principles that mediate context-dependent regulation and memory in vivo, and apply this knowledge to synthetically regulate the chromatin and transcriptional output of a cell.

Relevant Publications: Butz et al., Nature Genetics 2022;

Chromatin-mediated protein-genome interaction dynamics in living cells

We aim to characterise the minimal building blocks that determine spatiotemporal interactions between regulatory proteins and the (epi-)genome, and how these drive context-dependent regulation of biological processes in the cell. We exploit these natural building blocks to develop engineered chromatin readers (eCR) for mapping protein-chromatin interactions via live imaging, genomics, and proteomics, at high resolution and in a high-throughput fashion. By fusing eCRs to promiscuous biotin-ligases, we have developed ChromID, a novel method to identify the protein network associated with chromatin modifications and DNA damage sites.

Relevant Publications: Villaseñor et al. Nature Biotechnology 2020; Cardoso et al. bioRxiv 2024

Function and regulation of genome-wide DNA methylation patterns

DNA methylation is the paradigm epigenetic modification associated with transcriptional repression and required for genome function. However, the mechanisms that specify deposition and readout of this mark have not been fully understood in vivo. We have previously explored this by studying genome-wide targeting of the writers and readers of this mark. These studies have identified how local context, such as DNA sequence composition, nucleosome positioning or gene activity can influence targeting of these factors to the genome. This knowledge allowed us to predict their binding in different cell types, and furthermore uncovered how mutations in these factors, including the ones identified in ICF or Rett Syndrome patients, result in improper establishment or readout of this relevant epigenetic mark.

Our more recent work revealed how DNA methylation is regulated through the specific activity of the de novo Methyltransferase DNMT3A, revealing its targeting preference to tissue-specific, Polycomb-regulated CpG island promoters. By combining functional genomics with molecular dynamics simulations, we identified the molecular mechanism that drives DNA sequence preferences of the DNMT3A/B enzymes.

Relevant Publications: Baubec et al. Cell 2013; Baubec et al. Nature 2015; Manzo et al. EMBOJ 2017; Mallona et al. NAR 2020

Chromatin regulation and function during cellular differentiation

Chromatin plays an important role during development, however the exact mechanisms at play are not fully understood. We study the function of different chromatin modifications and chromatin regulatory proteins in the context of cellular differentiation. For example we have identified how changes in the composition of the NuRD complex can influence neuronal differentiation, or the role of SETD2 in establishing neuronal gene activity.

Relevant Publications: Schmolka et al., Nature Communications 2023; Ambrosi et al., bioRxiv 2024