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

Nat Commun. 2021 May 20;12(1):2969. doi: 10.1038/s41467-021-23213-w.

Abstract

Chromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites / genetics
  • CRISPR-Cas Systems / genetics*
  • Cell Line, Tumor
  • Chromatin / metabolism*
  • Chromatin Immunoprecipitation Sequencing*
  • Epigenesis, Genetic
  • Epigenomics / methods
  • Gene Expression Regulation, Neoplastic
  • Gene Knockdown Techniques
  • Gene Regulatory Networks
  • High-Throughput Screening Assays / methods*
  • Humans
  • Neoplasms / genetics*
  • RNA, Guide, CRISPR-Cas Systems / genetics
  • Single-Cell Analysis / methods
  • Transcription Factors / metabolism

Substances

  • Chromatin
  • RNA, Guide, CRISPR-Cas Systems
  • Transcription Factors