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

  1. Anita Adami
  2. Raquel Garza
  3. Fereshteh Dorazehi
  4. Christopher H. Douse
  5. Johan Jakobsson
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Abstract

This 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) 1 .

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  1. Version published to 10.1101/2025.10.24.684366 on bioRxiv