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CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these stud... Full description

Journal Title: Nature biotechnology 2017, Vol.35 (6), p.561-568
Main Author: Klann, Tyler S
Other Authors: Black, Joshua B , Chellappan, Malathi , Safi, Alexias , Song, Lingyun , Hilton, Isaac B , Crawford, Gregory E , Reddy, Timothy E , Gersbach, Charles A
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: United States: Nature Publishing Group
ID: ISSN: 1087-0156
Link: https://www.ncbi.nlm.nih.gov/pubmed/28369033
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recordid: cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5462860
title: CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome
format: Article
creator:
  • Klann, Tyler S
  • Black, Joshua B
  • Chellappan, Malathi
  • Safi, Alexias
  • Song, Lingyun
  • Hilton, Isaac B
  • Crawford, Gregory E
  • Reddy, Timothy E
  • Gersbach, Charles A
subjects:
  • Article
  • Chromosome Mapping - methods
  • Clustered Regularly Interspaced Short Palindromic Repeats - genetics
  • CRISPR-Associated Proteins - genetics
  • CRISPR-Cas Systems
  • DNA sequencing
  • Epigenomics - methods
  • Gene Editing - methods
  • Genome, Human - genetics
  • High-Throughput Nucleotide Sequencing - methods
  • Humans
  • Methods
  • Nucleotide sequencing
  • Regulatory Elements, Transcriptional - genetics
  • Sequence Analysis, DNA - methods
ispartof: Nature biotechnology, 2017, Vol.35 (6), p.561-568
description: Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9 repressor and dCas9 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, we carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.
language: eng
source:
identifier: ISSN: 1087-0156
fulltext: no_fulltext
issn:
  • 1087-0156
  • 1546-1696
url: Link


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descriptionLarge genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9 repressor and dCas9 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, we carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.
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subjectArticle ; Chromosome Mapping - methods ; Clustered Regularly Interspaced Short Palindromic Repeats - genetics ; CRISPR-Associated Proteins - genetics ; CRISPR-Cas Systems ; DNA sequencing ; Epigenomics - methods ; Gene Editing - methods ; Genome, Human - genetics ; High-Throughput Nucleotide Sequencing - methods ; Humans ; Methods ; Nucleotide sequencing ; Regulatory Elements, Transcriptional - genetics ; Sequence Analysis, DNA - methods
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abstractLarge genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context. Using dCas9 repressor and dCas9 activator constructs and lentiviral single guide RNA libraries to target DNase I hypersensitive sites surrounding a gene of interest, we carried out both loss- and gain-of-function screens to identify regulatory elements for the β-globin and HER2 loci in human cells. CERES readily identified known and previously unidentified regulatory elements, some of which were dependent on cell type or direction of perturbation. This technology allows the high-throughput functional annotation of putative regulatory elements in their native chromosomal context.
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