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Series GSE126320 Query DataSets for GSE126320
Status Public on Aug 21, 2019
Title Identification of Functional Regulatory Elements in the Human Genome Using Pooled CRISPR Screens
Organisms Homo sapiens; Expression vector lentiGuide-Puro
Experiment type Other
Summary Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function. However, protein-coding genes comprise <2% of the sequence space in the human genome leaving a substantial portion of the genome uninterrogated. Noncoding regions of the genome harbor important regulatory elements (e.g. promoters, enhancers, suppressors) that influence cellular processes but high-throughput methods for evaluating their essentiality have yet to be established. Here, we describe a CRISPR-based screening approach that facilitates the functional profiling of thousands of noncoding regulatory elements in parallel. We selected the tumor suppressor p53 as a model system and designed a pooled CRISPR library targeting thousands of p53 binding sites throughout the genome. Following transduction into dCas9-KRAB-expressing cells we identified several regulatory elements that influence cell proliferation. Moreover, we uncovered multiple elements that are required for the p53-mediated DNA damage response. Surprisingly, many of these elements are located deep within intergenic regions of the genome that have no prior functional annotations. This work diversifies the applications for pooled CRISPR screens and provides a framework for future functional studies focused on noncoding regulatory elements.
 
Overall design Pooled CRISPR screens targeting p53-regulated genes and p53 binding sites in human renal adenocarcinoma cells (769P)
 
Contributor(s) Toohey SM, Younger ST
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Submission date Feb 08, 2019
Last update date Aug 23, 2019
Contact name Scott T Younger
E-mail(s) styounger@cmh.edu
Organization name Children's Mercy Kansas City
Street address 2401 Gillham Road
City Kansas City
State/province MO
ZIP/Postal code 64108
Country USA
 
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL26170 Illumina MiSeq (Expression vector lentiGuide-Puro)
Samples (29)
GSM3596291 lentiGuide-Puro-pDNA-Gene-Library
GSM3596292 lentiGuide-Puro-pDNA-Peak-Library
GSM3596293 CRISPRko-Gene-ETP-A
Relations
BioProject PRJNA521541
SRA SRP184733

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE126320_CRISPRi-Peak.txt.gz 312.1 Kb (ftp)(http) TXT
GSE126320_CRISPRko-Gene.txt.gz 43.5 Kb (ftp)(http) TXT
GSE126320_CRISPRko-Peak.txt.gz 299.8 Kb (ftp)(http) TXT
GSE126320_RAW.tar 150.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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