Sometimes it feels like DNA and protein get all the attention.There are numerous ways to detect DNA-protein interactions or to analyze chromatin states (CHIP-seq, FAIRE-seq, Cut & Run) and to detect protein-protein interactions (yeast-two hybrid, Co-IP, BioID),  and that’s just to name a few. But what if you want to study RNA-protein interactions? The characterization of RNA-protein interactions has lagged behind, likely due to limitations of current means to detect RNA-protein interactions. To address this need, the Khavari lab at Stanford created the RNA-protein interaction detection (RaPID) method. RaPID borrows the E. coli biotin ligase BirA* from BioID and allows a researcher to identify proteins that bind an RNA motif of interest in living cells.

Every few months we highlight a subset of the new plasmids in the repository through our hot plasmids articles. These articles provide brief summaries of recent plasmid deposits and we hope they'll make it easier for you to find and use the plasmids you need. If you'd ever like to write about a recent plasmid deposit please sign up here.

This post was contributed by guest blogger Behnam Nabet, a postdoctoral fellow at Dana-Farber Cancer Institute.

Targeted Protein Degradation

In the Bradner and Gray labs, we synthesize compounds that enable selective removal of proteins-of-interest from the proteome. Rather than inhibiting protein function, these so-called “small molecule degraders” recruit the proteasome to destroy targeted proteins. We previously developed small molecule degraders that achieve selective degradation of endogenous proteins (notably, BRD2/3/4, CDK9, TRIM24, FLT3, BTK, and ALK) by linking small molecules that bind these target proteins to other small molecules that bind an E3 ligase. These bifunctional degraders co-opt E3 ligases such as cereblon (CRBN) or von Hippel-Lindau (VHL) to bring the endogenous degradation machinery into close proximity with the target protein, leading to polyubiquitination of the target protein and proteasomal degradation. Remarkably, small molecule degraders provide distinct advantages over pharmacological inhibitors including rapidly depleting a protein-of-interest, increasing target selectivity, overcoming resistance to inhibitors, and inducing prolonged biological effects.

Knowing where bacteria are located within their host is often key to understanding their role in both health and disease. To observe bacteria in action, researchers have developed in vivo bacterial reporters that use fluorophores and luciferases to track bacteria in real time, but each of these reporters has its drawbacks. Acoustic reporter genes (ARGs) overcome these limitations by using gas vesicle reporters that are detectable by an inexpensive and widely available imaging platform: ultrasound.

How many times have you looked at a diagram depicting transcription, or DNA repair, or replication, or any number of CRISPR applications and thought “OK, but how does this work in the context of chromatin?” Though it’s true that adding histones and chromatin architecture to every diagram portraying some aspect of eukaryotic DNA would become busy and potentially detract from the process being depicted, we can’t forget that those other components are still there in real life.  Certainly referring to any DNA within the context of a nucleus as “linear” is a misnomer. The DNA packed into our chromosomes is very much 3-dimensional, as you can see by this post’s chromatin illustrations from Leah Bury of Microscopic Art.