Resolving how genetic perturbations act through gene regulatory paths
Perturb-seq measures transcriptional responses to thousands of genetic perturbations, but each gene's response mixes the contributions of many regulatory paths, so how a perturbation acts cannot be resolved from expression alone, however large the model. Here we present REGA-perturb, which supplies this missing information rather than adding model complexity: reference epigenomes define a…
Perturb-seq is a technique that measures transcriptional responses to numerous genetic perturbations. However, each gene's response is a mix of several regulatory paths, making it impossible to determine how a perturbation acts solely based on expression data. To address this issue, researchers have developed REGA-perturb, which provides additional information without increasing model complexity.
Instead of adding more complexity, REGA-perturb uses reference epigenomes to create a scaffold of potential transcription factor (TF)-regulatory element-gene paths. Then, it analyzes perturbation responses pooled through shared latent programs to determine how each path is utilized. This method requires only RNA measurements.
REGA-perturb was tested across three CRISPR interference screens, involving a total of 2.4 million cells. The results showed that the method inferred TF-target relationships with significantly greater accuracy than random, more than four times better than the best existing method. It also successfully separated candidate direct from indirect targets and predicted targets of TFs that were not included in the training data.
Furthermore, REGA-perturb was able to infer perturbation-induced changes in TF activity that were not reflected in TF transcript levels, and resolved perturbation-specific regulatory rewiring where opposing regulatory changes cancel each other out at the expression level.
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