Experimental and computational approaches for single-cell enhancer perturbation assay

Shiqi Xie, Gary C. Hon

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations


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)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages19
StatePublished - 2019

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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