A framework for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells
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This protocol describes a workflow for transcriptional silencing of transposable elements (TEs) in human induced pluripotent stem cells (hiPSCs). It illustrates how to design gRNAs to target TE families or unique TE loci and how to validate the efficiency and specificity of large-scale CRISPRi-based silencing using a multiome approach that combines bulk RNA sequencing, CUT&RUN epigenetic profiling, and proteomics. This unique framework optimizes performance and interpretation of in vitro functional studies based on transcriptional manipulation of TEs in hiPSC models.
For complete details on the use and execution of this protocol, please refer to Adami et al . (2025) 1 .
