ArticleNature methods2024
Multicenter integrated analysis of noncoding CRISPRi screens.
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Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41citing papers in PubMed
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Who cites it
41 citing papers in PubMed.
- Article
- Dual-line Genome-scale CRISPR Screening Enables Robust Target Gene Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Programmable CRISPRtune dissects the transcriptional repressive activity of MeCP2.bioRxiv : the preprint server for biology · 2026Article
- The Encyclopedia of DNA Elements.bioRxiv : the preprint server for biology · 2026Article
- Region-Level Design and Analysis of CRISPR Perturbation Screens with FRACTEL.bioRxiv : the preprint server for biology · 2026Article
- Segmentally Duplicated Regulatory Elements Undergo Human-Specific Rewiring.Molecular biology and evolution · 2026Article
- High-throughput measurements of protein domain functions using magnetic separation.Nature protocols · 2026Review
- Cardiovascular Genetic Epidemiology in the Genome-Wide Era: From Association Discovery to Mechanistic Dissection and Clinical Translation.Cardiovascular drugs and therapy · 2026Review
- Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- Enhancer hubs govern chromatin topology and Th17 cell identity.bioRxiv : the preprint server for biology · 2026Article
- Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells.bioRxiv : the preprint server for biology · 2026Article
- Reprogramming of neuronal genome function and phenotype by astrocytes.bioRxiv : the preprint server for biology · 2026Article
- Nucleotide-resolution mapping of regulatory elements via allelic readout of tiled base editing.Nature communications · 2026Article
- Integrating natural and engineered genetic variations to decode regulatory influence on blood traits.Cell reports · 2026Article
- Article
- CRISPR-based functional genomic screening in neurodegeneration: mechanistic insights into AD, PD, and ALS.Frontiers in aging neuroscience · 2026Review
- Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells.Stem cell reports · 2025Article
- Segmentally duplicated regulatory elements undergo human-specific rewiring.bioRxiv : the preprint server for biology · 2025Article
- CRISPR-based Transcriptional Regulation: Technologies, Applications, and Future Directions.DNA · 2025Article
- Interrogating the Regulatory Function of HAQERs during Human Cortical Development.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
34 authors.
David Yao *Department of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-2232-524X
Josh Tycko *Department of Genetics, Stanford University, Stanford, CA, USA. joshtycko@hms.harvard.edu.ORCID http://orcid.org/0000-0002-4108-0575
Jin Woo Oh *Departments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0002-3545-5481
Lexi R Bounds *Department of Biomedical Engineering, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0002-4734-3743
Sager J Gosai *Broad Institute of Harvard & MIT, Cambridge, MA, USA.
Lazaros Lataniotis *Department of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-6507-5191
Ava Mackay-SmithUniversity Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA.ORCID http://orcid.org/0000-0003-0404-0563
Benjamin R DoughtyDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-0447-4468
Idan GabdankDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-5025-5886
Henri SchmidtDepartment of Computer Science, Princeton University, Princeton, NJ, USA.
Tania Guerrero-AltamiranoUniversity Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, USA.
Keith SiklenkaCenter for Advanced Genomic Technologies, Duke University, Durham, NC, USA.
Katherine GuoDepartment of Genetics, Stanford University, Stanford, CA, USA.
Alexander D WhiteDepartment of Electrical Engineering, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-5387-310X
Ingrid YoungworthDepartment of Genetics, Stanford University, Stanford, CA, USA.
Kalina AndreevaDepartment of Genetics, Stanford University, Stanford, CA, USA.
Xingjie RenDepartment of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0002-2348-4162
Alejandro BarreraCenter for Advanced Genomic Technologies, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0001-9244-9822
Yunhai LuoDepartment of Genetics, Stanford University, Stanford, CA, USA.
Galip Gürkan YardımcıKnight Cancer Center, Oregon Health and Science University, Portland, OR, USA.
Ryan TewheyThe Jackson Laboratory, Bar Harbor, ME, USA.ORCID http://orcid.org/0000-0002-4607-8001
Anshul KundajeDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-3084-2287
William J GreenleafDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0003-1409-3095
Pardis C SabetiBroad Institute of Harvard & MIT, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-9843-1890
Christina LeslieComputational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.ORCID http://orcid.org/0000-0002-4571-5910
Yuri PritykinDepartment of Computer Science, Princeton University, Princeton, NJ, USA.ORCID http://orcid.org/0000-0001-6589-981X
Jill E MooreProgram in Bioinformatics and Integrative Biology, RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA, USA.
Michael A BeerDepartments of Biomedical Engineering and Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-9955-3809
Charles A GersbachDepartment of Biomedical Engineering, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0003-1478-4013
Timothy E ReddyCenter for Advanced Genomic Technologies, Duke University, Durham, NC, USA.ORCID http://orcid.org/0000-0002-7629-061X
Yin ShenDepartment of Neurology, Institute for Human Genetics, University of California, San Franscisco, San Francisco, CA, USA.ORCID http://orcid.org/0000-0001-9901-5613
Jesse M EngreitzDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0002-5754-1719
Michael C BassikDepartment of Genetics, Stanford University, Stanford, CA, USA.ORCID http://orcid.org/0000-0001-5185-8427
Steven K ReillyDepartment of Genetics, Yale University, New Haven, CT, USA. steven.k.reilly@yale.edu.ORCID http://orcid.org/0000-0003-3140-1483
Funding
X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4MA Data Coordinating Center for ENCODEU24HG009397 · NHGRI · STANFORD UNIVERSITY · PI CHERRY, J. MICHAEL · 2017 to 2023
$26.0MThe Duke FUNCTION Center: Pioneering the comprehensive identification of combinatorial noncoding causes of diseaseRM1HG011123 · NHGRI · DUKE UNIVERSITY · PI GREGORY E CRAWFORD, Raluca Gordan · 2020 to 2026
$21.9MHigh-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular PhenotypesUM1HG012053 · NHGRI · DUKE UNIVERSITY · PI GREGORY E CRAWFORD, Charles A. Gersbach · 2021 to 2026
$10.7MEDAC: ENCODE Data Analysis CenterU24HG009446 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GERSTEIN, MARK BENDER, WENG, ZHIPING · 2017 to 2022
$10.4MHigh throughput CRISPR-mediated functional validation of regulatory elementsUM1HG009402 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI REN, BING, SHEN, YIN · 2017 to 2021
$8.4MBeyond GWAS: High Throughput Functional Genomics & Epigenome Editing to Elucidate the Effects of Genetic Associations for SchizophreniaR01MH125236 · NIMH · DUKE UNIVERSITY · PI CRAWFORD, GREGORY E, GERSBACH, CHARLES A. · 2021 to 2025
$8.1MDeciphering the Genomics of Gene Network Regulation of T Cell and Fibroblast States in Autoimmune InflammationU01HG012103 · NHGRI · SLOAN-KETTERING INST CAN RESEARCH · PI Christina S Leslie, Alexander Y Rudensky · 2021 to 2026
$7.5MThe function and regulation of the novel pregnancy-specific hexokinase HKDC1R01DK104927 · NIDDK · UNIVERSITY OF ILLINOIS AT CHICAGO · PI LAYDEN, BRIAN THOMAS, REDDY, TIMOTHY E · 2015 to 2024
$7.2MComprehensive functional characterization and dissection of noncoding regulatory elements and human genetic variationUM1HG009435 · NHGRI · BROAD INSTITUTE, INC. · PI SABETI, PARDIS CHRISTINE · 2017 to 2021
$6.6MHigh-throughput systematic characterization of regulatory element functionUM1HG009436 · NHGRI · STANFORD UNIVERSITY · PI BASSIK, MICHAEL C, GREENLEAF, WILLIAM JAMES · 2017 to 2021
$5.4MRegulatory Mechanisms of CD4+ T Cell DifferentiationUM1HG009428 · NHGRI · DUKE UNIVERSITY · PI CIOFANI, MARIA, CRAWFORD, GREGORY E · 2017 to 2021
$4.6MNCI NIH HHS P30 CA008748NHGRI NIH HHS R00 HG009917NHGRI NIH HHS R00 HG010669NHGRI NIH HHS R01 HG010741NHGRI NIH HHS R01 HG012367NHGRI NIH HHS R01 HG012872NHGRI NIH HHS R35 HG011329NHGRI NIH HHS RM1 HG011123NHGRI NIH HHS U01 HG009380NHGRI NIH HHS U01 HG009395NHGRI NIH HHS U01 HG009431NHGRI NIH HHS U01 HG012103NHGRI NIH HHS U24 HG009397NHGRI NIH HHS U24 HG009446NHGRI NIH HHS UM1 HG009402NHGRI NIH HHS UM1 HG009428NHGRI NIH HHS UM1 HG009435NHGRI NIH HHS UM1 HG009436NHGRI NIH HHS UM1 HG012053NIDDK NIH HHS K00 DK126120NIDDK NIH HHS R01 DK104927NIGMS NIH HHS T32 GM144291NIMH NIH HHS R01 MH125236NINDS NIH HHS R01 NS128028
Abstract
The ENCODE Consortium's efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to investigate cis-regulatory mechanisms. The ENCODE4 Functional Characterization Centers conducted 108 screens in human cell lines, comprising >540,000 perturbations across 24.85 megabases of the genome. Using 332 functionally confirmed CRE-gene links in K562 cells, we established guidelines for screening endogenous noncoding elements with CRISPR interference (CRISPRi), including accurate detection of CREs that exhibit variable, often low, transcriptional effects. Benchmarking five screen analysis tools, we find that CASA produces the most conservative CRE calls and is robust to artifacts of low-specificity single guide RNAs. We uncover a subtle DNA strand bias for CRISPRi in transcribed regions with implications for screen design and analysis. Together, we provide an accessible data resource, predesigned single guide RNAs for targeting 3,275,697 ENCODE SCREEN candidate CREs with CRISPRi and screening guidelines to accelerate functional characterization of the noncoding genome.
Indexed as
Clustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Cas SystemsGenomeHumansK562 CellsRNA, Guide, CRISPR-Cas SystemsRNA, Guide, CRISPR-Cas Systems
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