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Related Concept Videos

CRISPR and crRNAs02:53

CRISPR and crRNAs

Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
The CRISPR-Cas system stores a copy of foreign DNA in the host genome and uses it to identify the foreign DNA upon reinfection. CRISPR-Cas has three different...
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
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Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Related Experiment Video

Updated: May 10, 2026

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
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Multicenter integrated analysis of noncoding CRISPRi screens.

David Yao1, Josh Tycko2,3, Jin Woo Oh4

  • 1Department of Genetics, Stanford University, Stanford, CA, USA.

Nature Methods
|March 20, 2024
PubMed
Summary
This summary is machine-generated.

ENCODE4 functional characterization centers used pooled CRISPR screens to systematically investigate cis-regulatory elements (CREs). Guidelines and a data resource were developed to accelerate functional genomics of the noncoding genome.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Functional Genomics

Background:

  • The ENCODE Consortium annotates noncoding cis-regulatory elements (CREs) to understand gene regulation.
  • Pooled, noncoding CRISPR screens provide a systematic method to study cis-regulatory mechanisms.

Purpose of the Study:

  • To establish guidelines for screening endogenous noncoding elements using CRISPR interference (CRISPRi).
  • To provide an accessible data resource and tools for the functional characterization of the noncoding genome.

Main Methods:

  • Conducted 108 pooled, noncoding CRISPR screens in human cell lines (>540,000 perturbations).
  • Utilized 332 functionally confirmed CRE-gene links in K562 cells for guideline development.
  • Benchmarked five CRISPR screen analysis tools, identifying CASA as robust and conservative.

Main Results:

  • Established guidelines for CRISPRi screening of endogenous noncoding elements, including detection of low-effect CREs.
  • Identified a DNA strand bias for CRISPRi in transcribed regions, impacting screen design.
  • Developed a data resource with predesigned single guide RNAs for 3,275,697 ENCODE SCREEN candidate CREs.

Conclusions:

  • The study provides practical guidelines and a valuable data resource to advance functional genomics of the noncoding genome.
  • These resources will accelerate the systematic functional characterization of cis-regulatory elements using CRISPRi screens.