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Genome-wide CRISPR/Cas9 screens are a high-throughput systematic approach for identifying genes involved in a biological process. These screens provide an alternative to genome-wide RNAi screens, which although highly effective, are affected by low on-target efficacy, non-specific toxicity, and off-target effects. The flaws of RNAi screens are well characterized and strategies exist to control for these faults. However, it’s still unclear if similar pitfalls exist for CRISPR screens and how best to design these screens to controls for flaws. Recently the Bassik Lab at Stanford developed a new genome-wide CRISPR knockout screen to analyze the following unanswered questions about CRISPR screen design.

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.

Kinases: they regulate many proteins, with ~1/3 of human proteins predicted to be phosphorylated on at least one site. Phosphorylation is particularly important for regulating signal transduction and measuring kinase activity at the single-cell level can aid in drawing connections between signaling activity and cell phenotype. One method for monitoring live single-cell kinase activity is FRET, but FRET reporters are challenging to design and difficult to multiplex. The Covert Lab provides an alternative tool with their Kinase Translocation Reporters (KTRs) whose cellular localization serves as a proxy measurement of kinase activity. The key advantage of KTRs is that they are easy to create and simple to multiplex.

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.

One way to define a protein’s purpose is by its protein-protein interactions (PPIs). These interactions are often modeled as binary relationships, i.e. protein A interacts with protein B; but proteins are social biomolecules. They can be part of multiple dynamic and overlapping complexes that have distinct functions. Many existing methods for identifying PPIs, such as affinity purification mass spectrometry (AP-MS), lack the ability to specifically identify proteins that interact with a particular protein  complex as opposed to an individual protein. The Bethune Lab has overcome this limitation by creating Split-BioID, a spatiotemporally controllable version of the proximity-dependent biotinylation technique BioID. The key advantage of Split-BioID is that it allows for the validation of a binary PPI as well as the identification of additional interacting factors.