CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes

CRISPR knockout screens outperform shRNA and CRISPR-interference screens in a side-by-side comparison. High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based on clustered regularly interspaced shor...

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Published in:Nature biotechnology Vol. 34; no. 6; pp. 631 - 633
Main Authors: Evers, Bastiaan, Jastrzebski, Katarzyna, Heijmans, Jeroen P M, Grernrum, Wipawadee, Beijersbergen, Roderick L, Bernards, Rene
Format: Journal Article
Language:English
Published: New York Nature Publishing Group US 01.06.2016
Nature Publishing Group
Subjects:
49/47
631/1647/1511
631/1647/2163
631/208/191
Agriculture
Bioinformatics
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
brief-communication
Clustered Regularly Interspaced Short Palindromic Repeats - genetics
Comparative analysis
Gene Expression Profiling - methods
Gene Knockout Techniques - methods
Genetic Markers - genetics
Genetic screening
Genetic testing
Genetic Testing - methods
High-throughput screening (Biochemical assaying)
Life Sciences
Oncology
R&D
Reagents
Research & development
Ribonucleic acid
RNA
RNA, Small Interfering - genetics
ISSN:1087-0156, 1546-1696, 1546-1696
Online Access:Get full text
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Abstract CRISPR knockout screens outperform shRNA and CRISPR-interference screens in a side-by-side comparison. High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based on clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) or its transcriptionally repressive variant, CRISPR-interference (CRISPRi), with a traditional short hairpin RNA (shRNA)-based system for performing lethality screens. We find that the CRISPR technology performed best, with low noise, minimal off-target effects and consistent activity across reagents.
AbstractList High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based on clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) or its transcriptionally repressive variant, CRISPR-interference (CRISPRi), with a traditional short hairpin RNA (shRNA)-based system for performing lethality screens. We find that the CRISPR technology performed best, with low noise, minimal off-target effects and consistent activity across reagents.
CRISPR knockout screens outperform shRNA and CRISPR-interference screens in a side-by-side comparison. High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based on clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) or its transcriptionally repressive variant, CRISPR-interference (CRISPRi), with a traditional short hairpin RNA (shRNA)-based system for performing lethality screens. We find that the CRISPR technology performed best, with low noise, minimal off-target effects and consistent activity across reagents.
High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based on clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) or its transcriptionally repressive variant, CRISPR-interference (CRISPRi), with a traditional short hairpin RNA (shRNA)-based system for performing lethality screens. We find that the CRISPR technology performed best, with low noise, minimal off-target effects and consistent activity across reagents.High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based on clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) or its transcriptionally repressive variant, CRISPR-interference (CRISPRi), with a traditional short hairpin RNA (shRNA)-based system for performing lethality screens. We find that the CRISPR technology performed best, with low noise, minimal off-target effects and consistent activity across reagents.
Audience Academic
Author Jastrzebski, Katarzyna
Grernrum, Wipawadee
Heijmans, Jeroen P M
Bernards, Rene
Evers, Bastiaan
Beijersbergen, Roderick L
Author_xml – sequence: 1
  givenname: Bastiaan
  surname: Evers
  fullname: Evers, Bastiaan
  organization: Division of Molecular Carcinogenesis, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute
– sequence: 2
  givenname: Katarzyna
  surname: Jastrzebski
  fullname: Jastrzebski, Katarzyna
  organization: Division of Molecular Carcinogenesis, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute
– sequence: 3
  givenname: Jeroen P M
  surname: Heijmans
  fullname: Heijmans, Jeroen P M
  organization: Division of Molecular Carcinogenesis, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute
– sequence: 4
  givenname: Wipawadee
  surname: Grernrum
  fullname: Grernrum, Wipawadee
  organization: Division of Molecular Carcinogenesis, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute
– sequence: 5
  givenname: Roderick L
  surname: Beijersbergen
  fullname: Beijersbergen, Roderick L
  organization: Division of Molecular Carcinogenesis, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute
– sequence: 6
  givenname: Rene
  orcidid: 0000-0001-8677-3423
  surname: Bernards
  fullname: Bernards, Rene
  email: r.bernards@nki.nl
  organization: Division of Molecular Carcinogenesis, Cancer Systems Biology Centre and Cancer Genomics Centre Netherlands, The Netherlands Cancer Institute
BackLink https://www.ncbi.nlm.nih.gov/pubmed/27111720$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright Springer Nature America, Inc. 2016
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Snippet CRISPR knockout screens outperform shRNA and CRISPR-interference screens in a side-by-side comparison. High-throughput genetic screens have become essential...
High-throughput genetic screens have become essential tools for studying a wide variety of biological processes. Here we experimentally compare systems based...
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SubjectTerms 49/47
631/1647/1511
631/1647/2163
631/208/191
Agriculture
Bioinformatics
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
brief-communication
Clustered Regularly Interspaced Short Palindromic Repeats - genetics
Comparative analysis
Gene Expression Profiling - methods
Gene Knockout Techniques - methods
Genetic Markers - genetics
Genetic screening
Genetic testing
Genetic Testing - methods
High-throughput screening (Biochemical assaying)
Life Sciences
Oncology
R&D
Reagents
Research & development
Ribonucleic acid
RNA
RNA, Small Interfering - genetics
Title CRISPR knockout screening outperforms shRNA and CRISPRi in identifying essential genes
URI https://link.springer.com/article/10.1038/nbt.3536
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