@MathiasEder91

PhD student at the Netherlands Cancer Institute | Cyclist, Footballer

Joined April 2022
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New preprint by our lab -- Revealing the functional landscape of a large genomic locus by highly multiplexed local hopping of a reporter: biorxiv.org/content/10.1101/…. Even a 'simple' genomic locus such as the mouse Sox2 locus still holds surprises...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. By relocating promoter-reporter constructs into >1,000 alternative...

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Have you ever wondered about how the genomic position of regulatory elements impact their functional output? Check out our latest pre-print from the @bvanssteensellab. biorxiv.org/content/10.1101/…

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

Genes are often activated by enhancers located at large genomic distances. The importance of this positioning is poorly understood. By relocating promoter-reporter constructs into >1,000 alternative...

biorxiv.org
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7/8 We repeated the reporter hopping in a Sox2 deletion background. We observe an expansion of the region permissive for reporter activity, extending beyond the original TAD boundaries. This demonstrates that the Sox2 gene constrains the realm of influence of the SCR.
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8/8 Finally, we wondered why the Sox2 gene is such a good competitor compared to our Sox2 reporter. We included the Sox2 coding sequence and 3’ UTR in a set of new reporters, and found that this boosts reporter expression and strengthens the competition with the Sox2 gene.
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6/8 CRISPR deletion of Sox2 in clones with the reporter at 3 different positions, led to substantial upregulation of the reporters. Reporters located closest to Sox2 (-116kb) show higher maximum activation than reporters closer to the SCR (-39kb).
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7/8 We repeated the reporter hopping in a Sox2 deletion background. We observe an expansion of the region permissive for reporter activity, extending beyond the original TAD boundaries. This demonstrates that the Sox2 gene constrains the realm of influence of the SCR.
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I wrote a blog post about my PhD project at the @bvansteensellab. Give it a read! chromatingenomics.wordpress.…

Developing specific reporters for dozens of transcription factors in parallel

Introduction to the TF reporter project In each cell type, transcription factors – or TFs – play a pivotal role by controlling the activity of the ~25,000 genes in our genome. TFs are a…

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See also Lise's explanation on our Open Science blog: chromatingenomics.wordpress.…

Investigating LAD biology by a random scrambling approach

Lamina-associated domains (LADs) are large chromatin domains tethered at the nuclear lamina (NL). Their biology has been investigated for over a decade, especially in the BvS lab. We and others hav…

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New preprint from our lab: LAD scrambling to figure out how they interact with the nuclear lamina. biorxiv.org/content/10.1101/…

Genome - nuclear lamina interactions are multivalent and cooperative

Lamina-associated domains (LADs) are megabase-sized genomic regions that interact with the nuclear lamina (NL). It is not yet understood how their interactions with the NL are encoded in their DNA....

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