A framework for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells

Abstract

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. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=197 SRC="FIGDIR/small/684366v2_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@154560aorg.highwire.dtl.DTLVardef@1dce192org.highwire.dtl.DTLVardef@5d7097org.highwire.dtl.DTLVardef@8aea84_HPS_FORMAT_FIGEXP M_FIG C_FIG