SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress @cellcellpress.bsky.social @mitchguttman.bsky.social www.cell.com/cell/fulltex...

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @cp-cell.bsky.social, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment. www.sciencedirect.com/science/arti...

Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment. www.nature.com/articles/s41...

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics

ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

nature.com

Great thread on our paper from Jan👇

@erzbergerlab.bsky.social · 2y ago

Our latest paper, a fantastic collaboration with the Mendell Lab, is out. Great work by Xiaoqiang Zhu and Victor Cruz. We uncover how tRNA structural features in the ribosomal P-site modulate co-translational mRNA decay by the CCR4-NOT complex. #RNAsky #RNAbiology #translation #ribosome #cryoEM 1/5

A report made counterintuitive claims that PRC2 binds → more RNA than PTBP1 & hnRNPU → RNAs that do not exist in the cell We found a simple explanation: the authors ignore most RNA in the sample, leading to inflated background & misleading conclusions. www.biorxiv.org/content/10.1...

Failing to account for RNA quantity inflates background and leads to the misleading appearance that PRC2 and GFP bind to RNA in vivo

We recently published biochemical and quantitative evidence that challenges the widespread claims that PRC2 binds directly to many RNAs in vivo . A recent preprint performs a re-analysis of some of ou...

biorxiv.org

Leonid Mirny and I wrote this for all interested in chromosomes: "The chromosome folding problem and how cells solve it" www.cell.com/action/showP...