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Related Concept Videos

Mutations01:39

Mutations

Overview
Mutations01:39

Mutations

Overview
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
Base Excision Repair01:54

Base Excision Repair

One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
RNA Editing02:23

RNA Editing

RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...

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DNA Methylation: Bisulphite Modification and Analysis
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Detecting Methylation Changes Induced by Prime Editing.

Ronin Joshua S Cosiquien1, Isaiah J Whalen1, Phillip Wong1

  • 1Department of Medicine, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA.

Genes
|July 29, 2025
PubMed
Summary
This summary is machine-generated.

Prime editing, a precise gene editing tool, may cause localized DNA methylation changes, particularly in CpG islands and coding regions. These epigenetic alterations could impact gene expression and cellular pathways, requiring further safety assessments for therapeutic use.

Keywords:
CRISPR/Cas9CpGgene editingmethylationoff-targetprime editing

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Area of Science:

  • Molecular Biology
  • Epigenetics
  • Genomics

Background:

  • Prime editing offers enhanced precision over CRISPR-Cas9 gene editing.
  • Potential off-target effects, including epigenetic modifications like DNA methylation, require investigation for prime editing.
  • Understanding DNA methylation changes is crucial for safe genome editing applications.

Purpose of the Study:

  • To investigate whether prime editing induces aberrant CpG methylation patterns in human cells.
  • To compare the epigenetic effects of prime editing (PE2) with CRISPR-Cas9.
  • To identify specific genomic regions susceptible to prime editing-induced methylation changes.

Main Methods:

  • Whole-genome bisulfite sequencing (WGBS) to analyze DNA methylation patterns.
  • Comparison of methylation profiles between control, Cas9-edited, and PE2-edited cells.
  • Bioinformatic analyses including differential methylation region (DMR) identification and functional enrichment (Gene Ontology, KEGG pathways).

Main Results:

  • Overall methylation similarity was observed between Cas9 and PE2 edited cells.
  • Localized, aberrant CpG methylation changes were detected in PE2-edited cells, particularly in CpG islands and exon regions.
  • PE2 editing showed a higher proportion of DMRs in coding sequences and increased CpG island methylation compared to Cas9 editing.

Conclusions:

  • Prime editing can induce localized DNA methylation changes in human cells, affecting regulatory and coding regions.
  • CpG islands and coding sequences are susceptible to epigenetic alterations by prime editing.
  • These subtle epigenetic changes may influence gene expression and cellular pathways, necessitating careful consideration for therapeutic genome editing development.