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

Adami, Anita LU orcid ; Garza, Raquel LU orcid ; Dorazehi, Fereshteh LU orcid ; Douse, Christopher H. LU orcid and Jakobsson, Johan LU orcid (2026) In STAR Protocols 7(1).
Abstract

Here, we present a workflow for transcriptional silencing of transposable elements (TEs) in human induced pluripotent stem cells (hiPSCs). We describe steps for designing guide RNAs (gRNAs) to target TE families or unique TE loci. We also detail procedures for validating the efficiency and specificity of large-scale CRISPRi-based silencing using a multiome approach combining bulk RNA sequencing, CUT&RUN epigenetic profiling, and proteomics. This framework optimizes the 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.

Please use this url to cite or link to this publication:
author
; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
STAR Protocols
volume
7
issue
1
article number
104398
publisher
Cell Press
external identifiers
  • pmid:41758644
  • scopus:105031151803
ISSN
2666-1667
DOI
10.1016/j.xpro.2026.104398
language
English
LU publication?
yes
additional info
Publisher Copyright: © 2026 The Author(s).
id
4fa5c58b-3103-407c-82a8-79643e51eaee
date added to LUP
2026-04-09 13:47:57
date last changed
2026-05-07 17:35:20
@article{4fa5c58b-3103-407c-82a8-79643e51eaee,
  abstract     = {{<p>Here, we present a workflow for transcriptional silencing of transposable elements (TEs) in human induced pluripotent stem cells (hiPSCs). We describe steps for designing guide RNAs (gRNAs) to target TE families or unique TE loci. We also detail procedures for validating the efficiency and specificity of large-scale CRISPRi-based silencing using a multiome approach combining bulk RNA sequencing, CUT&amp;RUN epigenetic profiling, and proteomics. This framework optimizes the 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.</p>}},
  author       = {{Adami, Anita and Garza, Raquel and Dorazehi, Fereshteh and Douse, Christopher H. and Jakobsson, Johan}},
  issn         = {{2666-1667}},
  language     = {{eng}},
  month        = {{03}},
  number       = {{1}},
  publisher    = {{Cell Press}},
  series       = {{STAR Protocols}},
  title        = {{Protocol for efficient CRISPRi-mediated silencing of retrotransposons in human pluripotent stem cells}},
  url          = {{http://dx.doi.org/10.1016/j.xpro.2026.104398}},
  doi          = {{10.1016/j.xpro.2026.104398}},
  volume       = {{7}},
  year         = {{2026}},
}