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Multiplexed and Inducible Gene Modulation in Human Pluripotent Stem Cells by CRISPR Interference and Activation

Dane Z. Hazelbaker, Amanda Beccard, Patrizia Mazzucato, Gabriella Angelini, Angelica Messana, Daisy Lam, Kevin Eggan, View ORCID ProfileLindy E. Barrett
doi: https://doi.org/10.1101/603951
Dane Z. Hazelbaker
aStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Amanda Beccard
aStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Patrizia Mazzucato
aStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Gabriella Angelini
aStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Angelica Messana
aStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Daisy Lam
aStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Kevin Eggan
aStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
bDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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Lindy E. Barrett
aStanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
bDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
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  • ORCID record for Lindy E. Barrett
  • For correspondence: lbarrett@broadinstitute.org
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ABSTRACT

CRISPR-Cas9-mediated gene interference (CRISPRi) and activation (CRISPRa) approaches hold promise for functional genomic studies and genome-wide screens in human pluripotent stem cells (hPSCs). However, in contrast to CRISPR-Cas9 nuclease approaches, the efficiency of CRISPRi/a depends on continued expression of the dead Cas9 (dCas9) effector and guide RNA (gRNA), which can vary substantially depending on transgene design and delivery. Here, we design new fluorescently labeled piggyBac (PB) vectors to deliver robust and stable expression of multiplexed gRNAs. In addition, we generate hPSC lines harboring AAVS1-integrated, inducible and fluorescent dCas9-KRAB and dCas9-VPR transgenes to allow for accurate quantification and tracking of cells that express both the dCas9 effectors and gRNAs. We then employ these systems to target the TCF4 gene and conduct a rigorous assessment of expression levels of the dCas9 effectors, gRNAs and targeted gene. Collectively, these data provide proof-of-principle application of a stable, multiplexed PB gRNA delivery system that can be widely exploited to further enable genome engineering studies in hPSCs. Paired with diverse CRISPR tools including our dual fluorescence CRISPRi/a cell lines, this system would facilitate functional dissection of individual genes and pathways as well as larger-scale screens for studies of development and disease.

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Posted April 09, 2019.
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Multiplexed and Inducible Gene Modulation in Human Pluripotent Stem Cells by CRISPR Interference and Activation
Dane Z. Hazelbaker, Amanda Beccard, Patrizia Mazzucato, Gabriella Angelini, Angelica Messana, Daisy Lam, Kevin Eggan, Lindy E. Barrett
bioRxiv 603951; doi: https://doi.org/10.1101/603951
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Multiplexed and Inducible Gene Modulation in Human Pluripotent Stem Cells by CRISPR Interference and Activation
Dane Z. Hazelbaker, Amanda Beccard, Patrizia Mazzucato, Gabriella Angelini, Angelica Messana, Daisy Lam, Kevin Eggan, Lindy E. Barrett
bioRxiv 603951; doi: https://doi.org/10.1101/603951

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