Dr. Daniel Ibrahim

(030) 8413 1516

Chromatin Biology of Gene Regulatory Domains

Daniel Ibrahim leads a team within the Research Group Development and Disease at the MPI-MG and the BIH Center for Regenerative Therapies. We are interested in understanding how gene regulatory elements activate their target genes in mammalian genomes and connect a molecular understanding of chromatin structure and function to gene expression in development and disease scenarios. We combine advanced methods in genome engineering with latest DNA-sequencing techniques to profile the regulatory genome.


We apply and develop various genome engineering methods in mESCs to understand how the genomic variants affect gene regulation. We engineer large structural variations and create complex alleles using CRISPR-Cas9 and recombinase-mediated cassette exchange (RMCE) for high-throughput insertion of transgenes.

We adapted latest advances in synthetic biology to assemble BAC-sized transgenes from synthetic DNA and integrate these into mESCs. With this setup, we now design large transgenes in silico, assemble them from short DNA fragments in yeast, and integrate them site-specifically into the mouse genome.

We combine these advanced genome engineering techniques with latest functional genomics methods to investigate how chromatin and gene expression is affected by the engineered genome.

3D chromatin structure and function

We are interested in the connection between 3D chromatin folding and gene regulation, in particular the relevance of Topologically Associated Domains (TADs) for separating the gene regulatory activity. By using CRISPR-Cas9 genome engineering in mESCs, we generated a series mouse lines carrying highly complex alleles with rearranged TADs or deleted CTCF sites at the Sox9 locus. We found that while rearrangement of TADs through Structural Variations can force gene misexpression and disease, disruption of TADs through deletion of multiple CTCF sites has only mild effects on gene expression (Despang et al (2019), Franke*, Ibrahim* et al (2016)).

We are currently investigating the mechanisms underlying enhancer-promoter interaction within TADs at several model loci (e.g. Sox9, Ihh) using ESC differentiation and mouse embryos as model systems. By combining assembly of synthetic DNA and genome-engineering in mESCs with gene regulation in development and cell differentiation, we aim to understand how extended regulatory domains control gene expression.

Gene Regulation and Disease

By applying a deep understanding of gene regulation to mutations found in congenital disease, we are interested in elucidating molecular disease-mechanisms as a foundation for future therapies. In the past, we have successfully described novel disease mechanisms for coding and noncoding mutations. For example we described how missense mutations (Ibrahim et al, 2013, Hernandez-Miranda et al 2018) and alanine-repeat expansions (Basu et al 2020) in transcription factors change the function of the regulatory proteins. By re-engineering disease-causing structural variations, we were able to show how disease-causing structural variations change the 3D-chromatin structure, ultimately leading to gene misexpression and disease. This work is done in collaboration with the BIH Center for Regenerative Therapies.


Selected Publications

3D-Chromatin Structure

Ibrahim, D.M., and S. Mundlos (2020) "The role of 3D chromatin domains in gene regulation: a multi- facetted view on genome organization" Curr Opin Genet Dev, 61, 1–8. doi:10.1016/j.gde.2020.02.015 

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* (2019). "Functional dissection of the Sox9-Kcnj2 locus identifies nonessential and instructive roles of TAD architecture." Nat Genet 51(8): 1263-1271

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 (2016). "Formation of new chromatin domains determines pathogenicity of genomic duplications." Nature 538(7624): 265-269.

Transcription Factors

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) "Unblending of Transcriptional Condensates in Human Repeat Expansion Disease". Cell. 181(5): 1062 - 1079.e30  doi:10.1016/j.cell.2020.04.018. §senior author  

Hernandez-Miranda, L. R., D. M. Ibrahim*, P. L. Ruffault*, M. Larrosa, K. Balueva, T. Muller, W. Weerd, I. Stolte-Dijkstra, R. M. W. Hostra, J. F. Brunet, G. Fortin, S. Mundlos and C. Birchmeier (2018). "Mutation in LBX1/Lbx1 precludes transcription factor cooperativity and causes congenital hypoventilation in humans and mice." Proc Natl Acad Sci U S A: 201813520.

Ibrahim, D. M., P. Hansen, C. Rodelsperger, A. C. Stiege, S. C. Doelken, D. Horn, M. Jager, C. Janetzki, P. Krawitz, G. Leschik, F. Wagner, T. Scheuer, M. Schmidt-von Kegler, P. Seemann, B. Timmermann, P. N. Robinson, S. Mundlos and J. Hecht (2013). "Distinct global shifts in genomic binding profiles of limb malformation-associated HOXD13 mutations." Genome Res 23(12): 2091-2102.            


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