7/7 Big thanks goes out to my supervisor @larsplus.bsky.social, and all people involved in this work and my PhD journey: @robert-froemel.bsky.social @joebowness.bsky.social, Aina Bernal & Chelsea Szu-Tu.
6/7 Focusing on Trp53 and Cebpa 🧬: Trp53 low-affinity motif enhancers track TF expression near-linearly; high-affinity motifs are less sensitive (hinting at cofactor limits). Cebpa-associated enhancers show clear nonlinear responses.
4/7 Method note 🧪: lentiviral delivery makes the assay robust and transferable to primary or hard-to-transfect cells. We validated it with high per-cell capture rates and high concordance between single-cell and bulk activity estimates.
3/7 Two key things we can do with single-cell readouts that bulk can’t 🎯: (1) directly compare activity and quantify specificity of many enhancers in one experiment, and (2) relate enhancer output to TF mRNA levels in numerous cell states—asking how TF levels shape enhancer function.
5/7 Using single-cell lentiMPRA together with synthetic enhancer designs 🧩, we can probe how motif affinity shapes enhancer responses along endogenous TF expression gradients 📈.
2/7 Why this matters: The same enhancer can behave very differently across cell states depending on TF availability or chromatin context. That complicates understanding enhancers in differentiation, disease-variant settings, and designing cell type-specific regulatory elements for gene therapy 🚑.
The main project of my PhD 🧬🔬 is out: we developed single-cell lentiMPRA, a lentivirus-based method to measure enhancer activity and transcriptomes at single-cell resolution. We then applied sc-lentiMPRA to fully synthetic enhancers 🧩...
🔗 doi.org/10.64898/202...
Researchers from the @crg.eu, the @irbbarcelona.org, and the DKFZ have discovered that the reservoir of blood stem cells shrinks with #age. It becomes increasingly dominated by stem cells that produce pro-inflammatory immune cells.
t1p.de/kjf02 👇
Now, synthetic enhancers with single cells - great work by @juruehle.bsky.social : www.biorxiv.org/content/10.6...
Out @nature.com: Clonal tracing with somatic epimutations
🧬 Single cell methylome encodes cell state & clonal identity
🔨 EPI-Clone reads out both (+mutations, +RNA) at scale
🩸 Clonal expansions of HSCs are universal from age 50, not driven by CH mutations
doi.org/10.1038/s415...
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