Mathias Eder

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/10.110…. Even a 'simple' genomic locus such as the mouse Sox2 locus still holds surprises...

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.

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.

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/10.110…

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.

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).

I wrote a blog post about my PhD project at the @bvansteensellab. Give it a read! chromatingenomics.wordpress.com/2024/01/16/dev…

See also Lise's explanation on our Open Science blog: chromatingenomics.wordpress.com/2023/11/29/inv…

New preprint from our lab: LAD scrambling to figure out how they interact with the nuclear lamina. biorxiv.org/content/10.110…