Systematic mapping of functional enhancer-promoter connections with CRISPR interference

By C. Fulco, Mathias Munschauer, Rockwell Anyoha, Glen Munson, S. Grossman, Elizabeth M. Perez, Michael Kane, B. Cleary, Eric S. Lander, J. Engreitz. Science, 2016

607 citations recorded by the source corpus.

CRISPR screens illuminate enhancer function The noncoding regions around a gene that control the transcription of the protein-coding region are difficult to identify. Leveraging a CRISPR interference system (CRISPRi), Fulco et al. identified enhancer-promoter connections to map specific noncoding regions affecting gene regulation for the GATA1 and MYC loci (see the Perspective by Einstein and Yeo). Going forward, such CRISPRi-mapping can be used to evaluate promoter-enhancer screens functionally in an unbiased way. Science, this issue p. 769; see also p. 705 Functional mapping of noncoding elements with CRISPR interference may predict enhancer function. Gene expression in mammals is regulated by noncoding elements that can affect physiology and disease, yet the functions and target genes of most noncoding elements remain unknown. We present a high-throughput approach that uses clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi) to discover regulatory elements and identify their target genes. We assess >1 megabase of sequence in the vicinity of two essential transcription factors, MYC and GATA1, and identify nine distal enhancers that control gene expression and cellular proliferation. Quantitative features of chromatin state and chromosome conformation distinguish the seven enhancers that regulate MYC from other elements that do not, suggesting a strategy for predicting enhancer–promoter connectivity. This CRISPRi-based approach can be applied to dissect transcriptional networks and interpret the contributions of noncoding genetic variation to human disease.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b61f77b35610e6488e31c9c651b3cfcd6cfca1da

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Citations in the corpus

Genome-wide Programmable Transcriptional Memory by CRISPR-based Epigenome Editing (2021, background): “CRISPRoff targeting of enhancer elements Finally, we explored the potential utility of CRISPRoff for silencing promoter-distal elements by targeting enhancers that control the expression of the PVT1 long noncoding RNA (Cho et al., 2018; Fulco et al., 2016).”
The chromatin accessibility landscape of primary human cancers (2018, background): “As expected, the histogram of distances between a peak and its target gene decays sharply with distance (39) (Fig.”
Genome-wide enhancer maps link risk variants to disease genes (2021, methodology): “We generated cell lines expressing KRAB-dCas9-IRES-BFP under the control of a doxycycline-inducible promoter (Addgene, 85449) and the reverse tetracycline transactivator (rtTA) and a neomycin resistance gene under the control of an EF1α promoter (ClonTech), as previously described 12 .”
CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells (2016, positive): “By catalyzing repressive chromatin modifications around the TSS and serving as a transcriptional roadblock, CRISPRi tests a broad range of lncRNA gene functions including the production of cis- and trans-acting RNA transcripts (4), cis-mediated regulation related to lncRNA transcription itself (26–2”
Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation (2018, background): “We identify 1,801 differentially accessible regions across these CMP clusters, including two previously validated erythroid enhancers (Fulco et al., 2016) regulating GATA1 expression (Figures S3I and S3J).”
Activity-by-Contact model of enhancer-promoter regulation from thousands of CRISPR perturbations (2019, methodology): “(KRAB-dCas9 has previously been shown to repress many promoters and enhancers, and affects elements within ~200–500 bp of the gRNA; Supplementary Note 1) 7–9 .”