Looking forward to feedback from the community. We want to move into new applications (SynBio, genAI, . ), reach out if interested!.

Stay tuned, we have some exciting collaborations in the works (@lucapinello lab), applying EXTRA-seq to test cell type specificity & the dynamic range of synthetically created sequences.

We evaluated combinatorial E-P modifications, finding a new role for the TATA box, which acts as a 'noise suppressor' to prevent expression from weak (1 TFBS) "enhancers". With increasing E strength it switches to activation thus expanding the dynamic range.

It also allows testing "out-of context" enhancer activities and what enhancer-native molecular features correlate with expression.

We sys compare it to plasmid-based MPRAs and deep learning models (Enformer @deepmind), finding new bio insights & suggesting ways to improve predictions. We resolve expression differences down to distinct TF configurations on DNA, highlighting shortcomings of MPRAs and DL tools.

EXTRA-seq can be targeted to endogenous loci, allowing us to measure "near-native" gene expression as a function of dozens of newly introduced E-P genotypes (over 2kb apart).

Finally out! We present EXTRA-seq, a new EXTended Reporter Assay to quantify endogenous enhancer-promoter communication at kb scale!.A 🧵about what it can do:.

Enjoyed presenting at #NGSB24! Thanks to the entire OC for putting together a fantastic meeting! So many exciting new avenues for SynBio, from DNA synthesis, cell-free systems, designing regulatory systems, all the way to improving AI and exploring new applications!.

RT @ArttuJolma: (1/8) Thrilled to reveal the results of the Codebook Project, an international effort to identify accurate DNA-binding moti….

Check out this preprint from @AntoniGralak a very talented PhD in the @BartDeplancke lab, developing methyl-SMiLE-seq and applying it to study poorly characterized human TFs as part of the Codebook Consortium! 1/5 linked preprints across exp. platforms.

It's finally out! Massive team effort by the Codebook Consortium to characterize binding specificities of poorly studied human TFs. Preprint below highlights results of the benchmarking (1/5 preprints). Glad I was able to contribute as part of @BartDeplancke lab, w @AntoniGralak.

highly recommend!.

We believe that context-only TFs are critical in establishing cooperative environments with high TF concentrations in enhancers marked by cell type-specific pioneers/activators. Such environments increase the odds that regulatory elements can engage in productive communication.

Moreover, such communicating enhancers display elevated levels of TF occupancy that is no longer reflective of TFBS strength, supporting the notion of a ‘high' TF concentration environment.

Context-only TFs are associated with higher levels of BRD4, thus indicating that their ‘activity-boosting’ ability may relate to an overall increase in TF recruitment. Indeed, context-only TFBSs are enriched in genetically-linked enhancers that resemble Super Enhancers.

This cooperativity is not explained by the formation of canonical TF heterodimers: context-only TFs are found in peak shoulders, on average ~200bp away from the causal SNP.

By contrasting episomal and genome-integrated STARR-seq assays of syn enhs w 1-5 TFBSs, we show that these ‘context-only’ TFs cannot independently establish endogenous activity, BUT when added to cell type-specific TFs (like those found at SNPs), they boost enhancer activity.

To recap, we asked why some SNPs found in enhancers result in molecular changes, while others do not. We found that beyond the usual TF suspects enriched directly at the SNPs, there is also a class of TFs specifically enriched in the context of causal SNPs.

Excited to have our work out now in @NatureGenetics. @BartDeplancke . Few important changes compared to the preprint! see 🧵 below.

Excited to share our latest tool at #NGSB24, leveraging synthetic enhancers to learn what deep learning models get right & wrong about how the non-coding genome controls gene expression. Pre-print coming soon!.