Synthetic Regulatory Genomics

Rewriting large genomic regions to understand gene regulation

We have established a synthetic biology-derived workflow to study gene regulation. By combining methods from microbiology with integrase-based genome engineering, we can synthesize rationally designed DNA sequences of dozens to hundreds of kilobases in size and site-specifically integrate them into mouse ESCs and human iPSCs. This method allows us to write large genomic regions, which we leverage to investigate how gene regulatory information is encoded in our model systems.

Models and applications

We study the function of synthetic regulatory domains in mouse ESCs and embryos, as well as human iPSCs and iPSC-derived organoids. We use these models to understand how cell type-specific gene expression patterns and expression levels are encoded in genomic DNA sequences. Together with our colleagues at the Berlin Institute of Health (BIH), we apply this knowledge to elucidate disease mechanisms and develop technologies that lay the foundation for future gene and cell therapies. 

Enhancer synergy and gene expression levels

Prdm14 is an important transcription factor expressed in pluripotent stem cells. Its activity is controlled by 5 enhancers located in a 85kb regulatory domain. We study how variations of enhancer spacing, positioning and inter-enhancer sequences in the 85kb Prdm14 domain change its expression in mESCs.

Enhancer synergy and gene expression patterns

Indian hedgehog (Ihh) is a developmental gene expressed in developing bones, cells of the gastrointestinal tract and in neurons. Its activity is controlled by a ~100kb regulatory domain with dozens of cell-type specific enhancers. Using our synthetic genomics approach, we create mouse models carrying synthetic variants of the Ihh regulatory domain. We investigate how manipulation of enhancer order and spacing in the 100kb regulatory domain affects the cell type-specific expression of Ihh. 

Differential gene expression within a shared regulatory environment

CDX2 and PDX1 are master transcription factors of tissue development, CDX2 is a master regulator of intestinal development, while PDX1 is crucial for formation of the developmentally closely related pancreas. Though their expression domains are non-overlapping, the genes lie next to each other within a regulatory domain. By leveraging our ability to rationally re-write the CDX2/PDX1 locus, we investigate how differential expression patterns are encoded in a putatively shared regulatory environment. 

Involved Team Members

Milan Antonovic
Silvia Carvalho
Andreas Magg
Hannah Wieler