Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in @NatureGenet describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.

RT @ElowitzLab: “What’s past is prologue” — excited about chromatin recording by synthetically engineering recruitment of adenine methyltra….

Introducing Grok Imagine.

RT @MichalRabani: How embryos stay “on time” as they grow?.Happy to share our recent publication: Quantitative modeling of mRNA degradation….

RT @LilingWanLab: (1/n) Excited to share our new preprint! We uncover that RNA actively promotes nucleation and function of pathogenic cond….

RT @jimmykguo: Happy to share our new SPIDR method for mapping RBPs at scale out in @CellCellPress!.

This work was led by co-first authors Jimmy Guo (@jimmykguo) and Erica Wolin with support from amazing teams from our lab @caltech and the Jovanovic lab @Columbia and @Jayquerido with financial support from @NIH @NSF @genome_gov @GenomeTDCC.

We used SPIDR to identify mTOR-dependent changes and observed that 4EBP1 showed a dramatic increase in binding upon mTOR inhibition specifically at mRNAs containing a TOP-motif, suggesting a new model for how translational repression is selectively achieved upon mTOR inhibition.

We identified an interaction between LARP1 and 18S rRNA located within the mRNA channel entry site on the 40S small ribosomal subunit and @Jayquerido resolved this structure at 2.8 Å using single-particle cryo-EM.

Single nucleotide binding maps generated by SPIDR can map known RNP structures at atomic resolution and identify novel components within RNP structures.

We show that SPIDR generates high quality data across a diverse range of RBPs, including transcription, splicing, translation, and miRNA biogenesis, all within a single experiment.

SPIDR uses a simplified split-and-pool based strategy to increase the throughput of CLIP by two orders of magnitude. SPIDR enables the rapid generation of consortium-level datasets within any molecular biology lab without the need for specialized training or equipment.

Many proteins bind RNA, yet we still don’t know what RNAs most bind because methods map one RBP at a time. In @CellCellPress, with the Jovanovic lab, we describe SPIDR – a method for mapping the RNA binding sites of dozens of RBPs in a single experiment.

RT @brangwynnelab: Excited that our nucleolus mapping paper just came out today in Nature! Truly an amazing study from even more amazing du….

RT @IgorUlitsky: Stop the doom scrolling! A new 🗞️ from my lab, describing one of our flagship projects of many years we are super excited….

RT @LabSantoro: Very excited to share our latest work in @MolecularCell showing NPM1 stabilizing the association of nucleolus associated do….

RT @belmont_andrew: Happy to share our recent work showing bulk transport of speckle material between nuclear speckles within dynamic, mult….

RT @disney_lab: We've designed an RNA-targeted small molecule that reduces toxic 4R tau protein linked to FTDP-17. This orally bioavailable….

RT @IgorUlitsky: New preprint 📜 from @AlanMonziani in the lab – EPB41L4A-AS1 long noncoding RNA acts in both cis- and trans-acting transcri….

RT @yodai_takei: Excited to share our new paper out in @Nature revealing cell-type specific nuclear organization and its link to gene regul….

RT @mitchguttman: Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper….

This work was led by co-first authors Drew Perez (@AndrewPerez9201) and Isabel Goronzy (@uclacaltechmstp student) and our amazing team @caltech, and funding from @genome_gov @GenomeTDCC.