How can we move toward a quantitative, predictive framework for how RBPs bind and regulate their RNA partners? In a new preprint, we show that structural profiling via DMS-MaPseq can be used to measure fractional occupancies of RBPs at single-base resolution. #rnasky www.biorxiv.org/content/10.6...

1/ Happy to share our preprint from the Greenleaf Lab: beCasKAS, our method to directly detect CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning. www.biorxiv.org/content/10.1...

🚀 Our new paper is out @natmethods.nature.com! Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultra–low-background, single-mRNA imaging in live cells. 🔗 www.nature.com/articles/s41... 🧬 www.addgene.org/John_Ngo/

Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)

Interested in synthetic approaches to both understand and manipulate gene expression? We (the Bintu lab) wrote a review that discusses just that - how modern low- and high-throughput approaches can dissect gene regulation at the DNA, RNA, and protein level. www.annualreviews.org/content/jour...

The latest live-cell imaging work from the Boettiger lab measures chromosomal kinetics across genomic scales — it’s moving faster than you think! —, and puts a number on the ‘in vivo’ speed of cohesin loop extrusion itself. www.biorxiv.org/content/10.1...

Proteases might serve as versatile control knobs for gene and cell therapies, but there looms the risk of immunogenicity as we and others have been using viral proteases. We now report a control system based on a an engineered human protease and its clinically approved inhibitor. rdcu.be/d6kVt

Amtrak set an all-time ridership record in FY 2024, carrying 32.8 million riders. Of that, 43% was on Northeast Corridor routes; 44% was on state-supported routes; and 13% was on long-distance routes. Most-used routes: —NEC Regional —Acela —Pacific Surfliner —Empire S —Keystone —Capitol Corridor

In theory, my project will be: 1. Do a screen. 2. Follow up on the interesting biology. In practice, my project will be: 1. Start a screen. 2. Finish the screen.

🧬 Excited to share our new preprint! DMS chemical mapping, a key technique for studying RNA structure. Everyone assumes low DMS reactivity = Watson-Crick , high = non-WC. However, analyzing 7,500 RNA structures containing known 3D structures reveals it's not that simple. doi.org/10.1101/2024...