Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay

Shiqi Xie, Gary Hon

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Transcriptional enhancers drive cell-type-specific gene expression patterns, and thus play key roles in development and disease. Large-scale consortia have extensively cataloged >one million putative enhancers encoded in the human genome. But few enhancers have been endogenously tested for function. For almost all enhancers, it remains unknown what genes they target and how much they contribute to target gene expression. We have previously developed a method called Mosaic-seq, which enables the high-throughput interrogation of enhancer activity by performing pooled CRISPRi-based epigenetic suppression of enhancers with a single-cell transcriptomic readout. Here, we describe an optimized version of this method, Mosaic-seq2. We have made several key improvements that have significantly simplified the library preparation process and increased the overall sensitivity and throughput of the method.

Original languageEnglish (US)
Pages (from-to)203-221
Number of pages19
JournalMethods in molecular biology (Clifton, N.J.)
Volume1935
DOIs
StatePublished - Jan 1 2019

Fingerprint

Gene Expression
Human Genome
Epigenomics
Libraries
Genes

Keywords

  • CRISPRi
  • Enhancer
  • Single-cell perturbation
  • Single-cell RNA-seq

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay. / Xie, Shiqi; Hon, Gary.

In: Methods in molecular biology (Clifton, N.J.), Vol. 1935, 01.01.2019, p. 203-221.

Research output: Contribution to journalArticle

@article{17c4d7e0872c4afe8f45911497f6c764,
title = "Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay",
abstract = "Transcriptional enhancers drive cell-type-specific gene expression patterns, and thus play key roles in development and disease. Large-scale consortia have extensively cataloged >one million putative enhancers encoded in the human genome. But few enhancers have been endogenously tested for function. For almost all enhancers, it remains unknown what genes they target and how much they contribute to target gene expression. We have previously developed a method called Mosaic-seq, which enables the high-throughput interrogation of enhancer activity by performing pooled CRISPRi-based epigenetic suppression of enhancers with a single-cell transcriptomic readout. Here, we describe an optimized version of this method, Mosaic-seq2. We have made several key improvements that have significantly simplified the library preparation process and increased the overall sensitivity and throughput of the method.",
keywords = "CRISPRi, Enhancer, Single-cell perturbation, Single-cell RNA-seq",
author = "Shiqi Xie and Gary Hon",
year = "2019",
month = "1",
day = "1",
doi = "10.1007/978-1-4939-9057-3_14",
language = "English (US)",
volume = "1935",
pages = "203--221",
journal = "Methods in molecular biology (Clifton, N.J.)",
issn = "1064-3745",
publisher = "Humana Press",

}

TY - JOUR

T1 - Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay

AU - Xie, Shiqi

AU - Hon, Gary

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Transcriptional enhancers drive cell-type-specific gene expression patterns, and thus play key roles in development and disease. Large-scale consortia have extensively cataloged >one million putative enhancers encoded in the human genome. But few enhancers have been endogenously tested for function. For almost all enhancers, it remains unknown what genes they target and how much they contribute to target gene expression. We have previously developed a method called Mosaic-seq, which enables the high-throughput interrogation of enhancer activity by performing pooled CRISPRi-based epigenetic suppression of enhancers with a single-cell transcriptomic readout. Here, we describe an optimized version of this method, Mosaic-seq2. We have made several key improvements that have significantly simplified the library preparation process and increased the overall sensitivity and throughput of the method.

AB - Transcriptional enhancers drive cell-type-specific gene expression patterns, and thus play key roles in development and disease. Large-scale consortia have extensively cataloged >one million putative enhancers encoded in the human genome. But few enhancers have been endogenously tested for function. For almost all enhancers, it remains unknown what genes they target and how much they contribute to target gene expression. We have previously developed a method called Mosaic-seq, which enables the high-throughput interrogation of enhancer activity by performing pooled CRISPRi-based epigenetic suppression of enhancers with a single-cell transcriptomic readout. Here, we describe an optimized version of this method, Mosaic-seq2. We have made several key improvements that have significantly simplified the library preparation process and increased the overall sensitivity and throughput of the method.

KW - CRISPRi

KW - Enhancer

KW - Single-cell perturbation

KW - Single-cell RNA-seq

UR - http://www.scopus.com/inward/record.url?scp=85061481816&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85061481816&partnerID=8YFLogxK

U2 - 10.1007/978-1-4939-9057-3_14

DO - 10.1007/978-1-4939-9057-3_14

M3 - Article

C2 - 30758829

AN - SCOPUS:85061481816

VL - 1935

SP - 203

EP - 221

JO - Methods in molecular biology (Clifton, N.J.)

JF - Methods in molecular biology (Clifton, N.J.)

SN - 1064-3745

ER -