Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens

Noa Liscovitch-Brauer; Antonino Montalbano; Jiale Deng; Alejandro Méndez-Mancilla; Hans Hermann Wessels; Nicholas G. Moss; Chia Yu Kung; Akash Sookdeo; Xinyi Guo; Evan Geller; Suma Jaini; Peter Smibert; Neville E. Sanjana

doi:10.1038/s41587-021-00902-x

Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens

Noa Liscovitch-Brauer, Antonino Montalbano, Jiale Deng, Alejandro Méndez-Mancilla, Hans Hermann Wessels, Nicholas G. Moss, Chia Yu Kung, Akash Sookdeo, Xinyi Guo, Evan Geller, Suma Jaini, Peter Smibert, Neville E. Sanjana

Research output: Contribution to journal › Article › peer-review

50 Scopus citations

Abstract

CRISPR screens have been used to connect genetic perturbations with changes in gene expression and phenotypes. Here we describe a CRISPR-based, single-cell combinatorial indexing assay for transposase-accessible chromatin (CRISPR–sciATAC) to link genetic perturbations to genome-wide chromatin accessibility in a large number of cells. In human myelogenous leukemia cells, we apply CRISPR–sciATAC to target 105 chromatin-related genes, generating chromatin accessibility data for ~30,000 single cells. We correlate the loss of specific chromatin remodelers with changes in accessibility globally and at the binding sites of individual transcription factors (TFs). For example, we show that loss of the H3K27 methyltransferase EZH2 increases accessibility at heterochromatic regions involved in embryonic development and triggers expression of genes in the HOXA and HOXD clusters. At a subset of regulatory sites, we also analyze changes in nucleosome spacing following the loss of chromatin remodelers. CRISPR–sciATAC is a high-throughput, single-cell method for studying the effect of genetic perturbations on chromatin in normal and disease states.

Original language	English
Pages (from-to)	1270-1277
Number of pages	8
Journal	Nature Biotechnology
Volume	39
Issue number	10
DOIs	https://doi.org/10.1038/s41587-021-00902-x
State	Published - Oct 2021
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.

Funding

We thank the entire Sanjana laboratory for support and advice. We thank J. Morris for help with eQTL resources, M. Zaran and R. Satija for computational resources and the NYGC Sequencing Platform and NYU Biology Genomics Core for sequencing resources. BL21(DE3) cells transformed with pET-PfuX7 were kindly provided by J. Gregory. N.L.-B. is supported by a postdoctoral fellowship from the Human Frontier Science Program Organization (no. LT000672/2019-L), an EMBO long-term fellowship (no. ALTF 826-2018) and the Weizmann Institute of Science National Postdoctoral Award Program for Advancing Women in Science. N.E.S. is supported by NYU and NYGC startup funds, NIH/NHGRI (nos. R00HG008171 and DP2HG010099), NIH/NCI (no. R01CA218668), DARPA (no. D18AP00053), the Sidney Kimmel Foundation, the Melanoma Research Alliance and the Brain and Behavior Foundation.

Funders	Funder number
Human Frontier Science Program Organization	LT000672/2019-L
Weizmann Institute of Science National Postdoctoral Award Program for Advancing Women in Science
National Institutes of Health
National Human Genome Research Institute	R00HG008171, DP2HG010099
National Cancer Institute	R01CA218668
Defense Advanced Research Projects Agency	D18AP00053
Brain and Behavior Research Foundation
European Molecular Biology Organization	ALTF 826-2018
Melanoma Research Alliance
New York University
Sidney Kimmel Foundation
New York Genome Center
Human Frontier Science Program

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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Cite this

Liscovitch-Brauer, N., Montalbano, A., Deng, J., Méndez-Mancilla, A., Wessels, H. H., Moss, N. G., Kung, C. Y., Sookdeo, A., Guo, X., Geller, E., Jaini, S., Smibert, P., & Sanjana, N. E. (2021). Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens. Nature Biotechnology, 39(10), 1270-1277. https://doi.org/10.1038/s41587-021-00902-x

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abstract = "CRISPR screens have been used to connect genetic perturbations with changes in gene expression and phenotypes. Here we describe a CRISPR-based, single-cell combinatorial indexing assay for transposase-accessible chromatin (CRISPR–sciATAC) to link genetic perturbations to genome-wide chromatin accessibility in a large number of cells. In human myelogenous leukemia cells, we apply CRISPR–sciATAC to target 105 chromatin-related genes, generating chromatin accessibility data for ~30,000 single cells. We correlate the loss of specific chromatin remodelers with changes in accessibility globally and at the binding sites of individual transcription factors (TFs). For example, we show that loss of the H3K27 methyltransferase EZH2 increases accessibility at heterochromatic regions involved in embryonic development and triggers expression of genes in the HOXA and HOXD clusters. At a subset of regulatory sites, we also analyze changes in nucleosome spacing following the loss of chromatin remodelers. CRISPR–sciATAC is a high-throughput, single-cell method for studying the effect of genetic perturbations on chromatin in normal and disease states.",

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Liscovitch-Brauer, N, Montalbano, A, Deng, J, Méndez-Mancilla, A, Wessels, HH, Moss, NG, Kung, CY, Sookdeo, A, Guo, X, Geller, E, Jaini, S, Smibert, P & Sanjana, NE 2021, 'Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens', Nature Biotechnology, vol. 39, no. 10, pp. 1270-1277. https://doi.org/10.1038/s41587-021-00902-x

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AU - Smibert, Peter

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Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens

Abstract

Bibliographical note

Funding

UN SDGs

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