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Related Concept Videos

CRISPR and crRNAs02:53

CRISPR and crRNAs

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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.
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

Updated: Oct 11, 2025

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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Single-cell characterization of CRISPR-modified transcript isoforms with nanopore sequencing.

Heon Seok Kim1, Susan M Grimes1, Anna C Hooker1

  • 1Division of Oncology, Department of Medicine, Stanford University School of Medicine, CCSR 1115, 269 Campus Drive, Stanford, CA-94305, USA.

Genome Biology
|December 7, 2021
PubMed
Summary
This summary is machine-generated.

We developed a novel single-cell method to detect CRISPR-edited mRNA structures, revealing how genetic variants and splicing factors influence alternative mRNA isoforms and transcriptome profiles.

Keywords:
Alternative splicingSingle-cell CRISPR screenSingle-cell long-read CRISPR screenSingle-cell long-read sequencingSingle-cell sequencingTranscript isoform

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Alternative mRNA splicing generates diverse transcript isoforms, crucial for cellular function.
  • Understanding the regulation of alternative splicing is key to deciphering gene expression complexity.
  • CRISPR-Cas9 technology offers precise genome editing but its impact on transcript structure at single-cell resolution requires advanced detection methods.

Purpose of the Study:

  • To develop a single-cell method for detecting CRISPR-modified mRNA transcript structures.
  • To assess the contribution of genetic variants and splicing factors to alternative mRNA isoforms.
  • To investigate the regulation of alternative splicing by CRISPR-Cas9 editing and its transcriptome-wide consequences.

Main Methods:

  • A novel single-cell approach combining long-read sequencing for transcript structure characterization.
  • Short-read sequencing to correlate single-cell gene expression profiles with guide RNA sequences.
  • CRISPR-Cas9 gene editing to target specific exon-intron segments or splicing factors.

Main Results:

  • The method enables detection of targeted genomic edits and transcript isoform structures at single-cell resolution.
  • It allows assessment of how genetic variants at splicing sites influence alternative mRNA isoforms.
  • The study elucidates the regulatory mechanisms of alternative splicing influenced by CRISPR-Cas9 editing.

Conclusions:

  • This single-cell approach provides unprecedented resolution for studying CRISPR-induced transcriptomic changes.
  • It offers a powerful tool for dissecting the complex interplay between genome editing, splicing, and transcriptome diversity.
  • The findings advance our understanding of gene regulation and facilitate the study of genetic variants impacting splicing.