Gene Regulation in Cell Differentiation and Disease

• When 3D genome changes cause disease: the impact of structural variations in congenital disease and cancer.
  Weischenfeldt J, Ibrahim DM.Curr Opin Genet Dev. doi: 10.1016/j.gde.2023.102048. PMID: 37156210 (2023)
• Unblending of Transcriptional Condensates in Human Repeat Expansion Disease Basu, S.*,  S.D. Mackowiak*, H. Niskanen, D. Knezevic, V. Asimi, S. Grosswendt, H. Geertsema, S. Ali, Salaheddine, I. Jerković, H. Ewers, S. Mundlos, A. Meissner, D. M. Ibrahim^§ and D. Hnisz (2020) Cell. 181(5): 1062 - 1079.e30      doi:10.1016/j.cell.2020.04.018. 
• Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture 
  Despang, A., R. Schopflin, M. Franke, S. Ali, I. Jerkovic, C. Paliou, W. L. Chan, B. Timmermann, L. Wittler, M. Vingron, S. Mundlos* and D M. Ibrahim*  . Nat Genet 51, 1263-1271, doi:10.1038/s41588-019-0466-z (2019).
• Three-dimensional chromatin in disease: What holds us together and what drives us apart?
  Ibrahim DM, Mundlos S. Curr Opin Cell Biol. doi: 10.1016/j.ceb.2020.01.003. PMID: 32036200 (2020)
• Formation of new chromatin domains determines pathogenicity of genomic duplications
  Franke, M.*, D.M. Ibrahim*, G. Andrey, W. Schwarzer, V. Heinrich, R. Schopflin, K. Kraft, R. Kempfer, I. Jerkovic, W. L. Chan, M. Spielmann, B. Timmermann, L. Wittler, I. Kurth, P. Cambiaso, O. Zuffardi, G. Houge, L. Lambie, F. Brancati, A. Pombo, M. Vingron, F. Spitz and S. Mundlos. Naturedoi:10.1038/nature19800 (2016)

• DFG SPP22.02
• ERC Starting Grant SYNREG

Synthetic Regulatory Genomics

We established a synthetic biology derived workflow to studying gene regulation. Through combination of methods from microbiology with integrase-based genome engineering for mESCs and human iPSCs we can synthesize computer-designed DNA sequences of dozens to hundreds of kb and integrate them site-specific into the mESCs and human iPSCs. With this, we can effectively write large genomic regions. By combining this genome engineering approach with cell, organoid, and in vivo model systems we characterize and investigate how gene regulatory information is encoded in the regulatory genome. We are interested how synergy between enhancers and the intervening inter-enhancer sequence controls gene expression levels and gene expression patterns.

High-Throughput Genome Engineering

Within a gene regulatory domain usually many enhancers and multiple promoters co-exist. Yet enhancers only activate some promoters, or the other way round promoters allow only activation by some enhancers. Long-standing anecdotal evidence as well as more recent systematic studies emphasized that promoter must be capable of discriminating between enhancers. How this is achieved, however, is unknown, mainly because it requires systematic, high-throughput integration of transgenes at specific genomic loci. 

In this project we adapted a Recombinase Mediated Cassette Exchange (RMCE) to investigate how different promoters respond to the regulatory elements at different genomic positions. The results will help to better understand the effects of patient mutations, evaluate detrimental effects of transgene insertions and optimize novel transgene designs.

Programming gene expression in hiPSC-derived organoids

By transfering the genome engineering technologies we pioneer in mESC to human iPS cells and hIPSC-derived organoids. Our aim is to develop new transgenic approahces that mimick the normal gene regulatory mechanisms in order to drive cell-type specifc gene expression. Through programming gene expression in human cells and hope to pave the way for a new transgenic approaches.

Functional and Computational Genomics

We generate chromatin profiles using ChIP-, ATAC-, RNA-seq as well as Hi-C to characterize the regulatory geneome in disease-relevant cell types of the heart, bone and other tissues. To better understand the regulatory factors governing these cell types we perform computatntional and functional analyses of the regulatory regions. 

3D Genomics and gene regulation

Annotation of functional gene regulatory elements has motivated the understanding of the genome’s spatial organisation. Cell-type specific gene expression is controlled by regulatory elements, such as enhancers, insulators, or boundaries, located at large genomic distances from their target genes. Thus, the physical interaction within the 3D nuclear space has emerged to be an important factor regulating gene expression.

Our work described how the genome partitioned into spatially separated units called Topologically Associating Domains (TADs) that encompass a gene and all its relevant cis-regulatory elements. Through analysis of patients with structural variations we could provide 

first direct evidence for the connection between TADs and gene regulatory domains. This work had direct clinical impact through development of new diagnostic strategies for previously unsolved cases with rare genetic disease, which is now a widely accepted mutation mechanism.