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

By Anita Adami, MSc, Raquel Garza, PhD and Johan Jakobsson, PhD
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Output Details

Description
The published protocol describes the workflow for transcriptional silencing of transposable elements (TEs) in human induced pluripotent stem cells (hiPSCs). The protocol illustrates how to design gRNAs to target families of TEs (or a unique TE locus) 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 protocol offers a unique framework to perform and interpret in vitro functional studies based on TEs transcriptional manipulation in hiPSC models. For complete details on the use and execution of this protocol, please refer to Adami et al. (2025).
Identifier (DOI)
10.1101/2025.10.24.684366
Tags
  • CRISPRi dCas9
  • hiPSCs (Human induced pluripotent stem cells)
  • Transposable elements
Team
Team Jakobsson
Program
Collaborative Research Network
Theme
Neuro-Immune Interactions

Meet the Authors

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