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mathiaseder.bsky.social

@mathiaseder.bsky.social
99 followers 84 following 19 posts
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mathiaseder.bsky.social @mathiaseder.bsky.social · 23/03/2026
5 - We also looked at the effect of inserting CBS sites (without promoter) in the locus. Between gene and enhancer, CBS insertions consistently reduce Sox2 expression in an orientation-dependent manner, further suggesting a polarity in the loop extrusion process.
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mathiaseder.bsky.social @mathiaseder.bsky.social · 23/03/2026
4 - Inverting only the CBS upstream of the reporter did not recapitulate the effects that we observed when the entire CBS–promoter construct was inverted, indicating that reporter activation depends on the combined orientation of the CBS and the promoter.
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mathiaseder.bsky.social @mathiaseder.bsky.social · 23/03/2026
3 - We found that a CBS that is naturally located upstream of the Sox2 promoter endows this P with a strong orientation-dependent activation, anywhere within the gene-enhancer interval. Adding three CBSs enhances the orientation bias, suggesting a quantitative effect of CTCF on regulatory output.
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mathiaseder.bsky.social @mathiaseder.bsky.social · 23/03/2026
2 - We previously designed a Sox2 reporter containing the Sox2 promoter followed by a blue fluorescent protein (mTurquoise2). To test the effect of CBSs on the reporter, we added CBSs upstream of the promoter in either the forward or reverse motif orientation.
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mathiaseder.bsky.social @mathiaseder.bsky.social · 19/09/2025
5/ We found that this competition is partly encoded in the Sox2 coding sequence (CDS) – a 1kb exon. Addition of the CDS to the reporter increases reporter expression and competition with the Sox2 gene. This effect seems to be mediated by the CDS-DNA sequence rather than the produced RNA or protein.
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mathiaseder.bsky.social @mathiaseder.bsky.social · 19/09/2025
4/ Strikingly, deleting the endogenous Sox2 gene expands this landscape—yet the original Sox2 site remains a “sweet spot” for activation. Genes can thus act as gatekeepers, restricting their enhancer’s influence.
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mathiaseder.bsky.social @mathiaseder.bsky.social · 19/09/2025
3/ These maps depict a sharply confined activation landscape. Interestingly, reporter expression is highest at the enhancer and around the endogenous gene whereas it turns silent upstream of the gene and downstream of the enhancer.
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mathiaseder.bsky.social @mathiaseder.bsky.social · 19/09/2025
2/ By “loading” our transposon with a fluorescent Sox2 reporter, relocating it, and sorting cells by reporter expression, we generated high-resolution activity maps.
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mathiaseder.bsky.social @mathiaseder.bsky.social · 19/09/2025
1/ Using a transposon-based approach, we systematically studied the positional relationship between the mouse Sox2 gene and its enhancer (SCR). In a single experiment, we can map >2000 unique genomic positions.
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