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Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling.

作者信息

Yan Rachel E, Corman Alba, Katgara Lyla, Wang Xiao, Xue Xinhe, Gajic Zoran Z, Sam Richard, Farid Michael, Friedman Samuel M, Choo Jungwook, Raimondi Ivan, Ganesan Shridar, Katsevich Eugene, Greenfield Jeffrey P, Dahmane Nadia, Sanjana Neville E

机构信息

New York Genome Center, New York, NY, USA.

Department of Biology, New York University, New York, NY, USA.

出版信息

Nat Biotechnol. 2024 Nov 21. doi: 10.1038/s41587-024-02475-x.

DOI:10.1038/s41587-024-02475-x
PMID:39572737
Abstract

Pooled single-cell CRISPR screens have profiled either gene expression or chromatin accessibility but not both modalities. Here we develop MultiPerturb-seq, a high-throughput CRISPR screening platform with joint single-nucleus chromatin accessibility, transcriptome and guide RNA capture using combinatorial indexing combined with droplet microfluidics to scale throughput and integrate all three modalities. We identify key differentiation genes in a rare pediatric cancer and establish ZNHIT1 as a potential target for cancer reprogramming therapy.

摘要

相似文献

[1]
Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling.

Nat Biotechnol. 2024-11-21

[2]
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[3]
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[4]
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[5]
Pooled CRISPR screening with single-cell transcriptome readout.

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[6]
Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens.

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[7]
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility.

Nat Biotechnol. 2019-6-24

[8]
High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer.

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[9]
scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing.

Genome Biol. 2024-4-8

[10]
Massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing.

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引用本文的文献

[1]
Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics.

Nat Methods. 2025-5-26

[2]
Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes.

Science. 2025-4-4

本文引用的文献

[1]
In vitro culture of cynomolgus monkey embryos from blastocyst to early organogenesis.

Nat Protoc. 2024-12

[2]
CRISPR/Cas9-mediated deletion of a GA-repeat in human GPM6B leads to disruption of neural cell differentiation from NT2 cells.

Sci Rep. 2024-1-25

[3]
Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis.

Trends Genet. 2024-2

[4]
Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens.

Science. 2023-5-19

[5]
ISSAAC-seq enables sensitive and flexible multimodal profiling of chromatin accessibility and gene expression in single cells.

Nat Methods. 2022-10

[6]
Chromatin accessibility profiling by ATAC-seq.

Nat Protoc. 2022-6

[7]
Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC.

Nat Biotechnol. 2022-3

[8]
Tagmentation-based single-cell genomics.

Genome Res. 2021-10

[9]
CellProfiler 4: improvements in speed, utility and usability.

BMC Bioinformatics. 2021-9-10

[10]
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.

Nat Biotechnol. 2021-10

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