After my first public report at the Double Helix 70’s celebration (bit.ly/4iONi3M) on Oct 2023 and a bioRxiv on June 2024, FOOtprinting by dsDNA DeamInasE (FOODIE), the major effort of my CPL/PKU group, delayed by the pandemic, has been yearmarked by today issue of PNAS

🎇🎄Some holiday reading: Overdue TWEETORIAL on the latest preprint from our lab. 🎇🎄 In this work, superstar postdoc Xinhe Xue combined 2 kinds of pooled CRISPR screens to pinpoint noncoding regulatory elements and the transcription factors that activate these elements.

We finally posted a manuscript describing this tool predicting accurate 3D DNA mechanics from sequence and its applications to probe mechanical selection in diverse eukaryotic genomes. Led by Jonghan Park of Yonsei U with awesome help from collaborators biorxiv.org/content/10.110…

Real-time visualization of reconstituted transcription reveals RNA polymerase II activation mechanisms at single promoters biorxiv.org/cgi/content/sh… #biorxiv_biochem

The first #cryoEM structure of a Mediator complex subunit in complex with a transactivation domain nature.com/articles/s4146…

🧵 1/ New preprint! How do transcription factors (TFs) use intrinsically disordered regions (IDRs) to find their target sites? biorxiv.org/content/10.110… #TranscriptionFactors #IDPs #SingleMolecule #Biophysics

Plasmid-based reporter assays are the bedrock of regulatory genomics. But a basic question has gone unanswered for decades: Do chromatin architectures form on plasmids transfected into mammalian cells—and does it matter? We finally have answers. biorxiv.org/content/10.110…

So you want to change transgene expression: just change your promoter, right? Changing the promoter increases RNA and thus protein levels. What more could be happening? [1/n] Well, promoters don’t just set RNA levels; they uniquely transform how RNAs are transmitted into protein

Very excited to share a preprint from my time as a postdoc with Baranello Lab at Karolinska Institutet which will provide the foundation for my lab’s future work investigating how oncoproteins can affect the diffusion of their targets. Here’s what we found: 1/11 bit.ly/3TTl50B

We are pleased to present a new preprint from the lab, led by Paul Batty. We discovered a structural dependency within the SAGA complex, which is critical for regulating the stability of its histone acetyl transferase, KAT2A (1/n) biorxiv.org/content/10.110…

I'm glad that I had a chance to contribute to this wide-ranging article discussing the myriad ways ML is being used in genomics: nature.com/articles/d4158…

Which mutations rewire function of regulatory DNA? Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models. Led by @EESetiz 1/N 🧵👇