Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

17.7K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.7K
Epigenetic Regulation01:46

Epigenetic Regulation

31.0K
Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
31.0K
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

23.3K
Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the...
23.3K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.8K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.8K
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

13.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
13.3K
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

14.9K
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,...
14.9K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Thoracoabdominal Asynchrony in Healthy Children.

Journal of sleep research·2026
Same author

Altered neurodevelopmental trajectories of brain structure in Tourette syndrome and Chronic Tic Disorders.

medRxiv : the preprint server for health sciences·2026
Same author

Genome-wide meta-analysis identifies genetic drivers of bile acid metabolism in intrahepatic cholestasis of pregnancy.

Nature communications·2026
Same author

Proteomic Profiling Using a Proximity Extension Assay Panel on Serum Samples Stored at -25°C Over Several Decades.

Proteomics·2026
Same author

Psychological distress and tumor cell β2-adrenergic receptor levels in patients with surgically resected non-small cell lung cancer.

Acta oncologica (Stockholm, Sweden)·2026
Same author

Distinct metabolic signatures of Alzheimer's and Parkinson's disease revealed through genetic overlap.

EBioMedicine·2026
Same journal

Lineage tracing from cellular heritage to disease destiny.

Nature genetics·2026
Same journal

Multiomics analysis of primary metabolism reveals the genetic basis of nitrogen partitioning modulated by ZmAVT1A-1 in maize.

Nature genetics·2026
Same journal

No evidence of immunosurveillance in mutation-hotspot-driven clonal hematopoiesis.

Nature genetics·2026
Same journal

Near-perfect genome sequencing in medical genetics.

Nature genetics·2026
Same journal

Three decades of cancer genetics.

Nature genetics·2026
Same journal

Advances and challenges of splicing prediction with AI.

Nature genetics·2026
See all related articles

Related Experiment Video

Updated: Jun 19, 2025

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.1K

The correlation between CpG methylation and gene expression is driven by sequence variants.

Olafur Andri Stefansson1, Brynja Dogg Sigurpalsdottir2,3, Solvi Rognvaldsson2

  • 1deCODE genetics/Amgen Inc., Reykjavik, Iceland. olafurs@decode.is.

Nature Genetics
|July 24, 2024
PubMed
Summary
This summary is machine-generated.

DNA methylation patterns in CpG sites regulate gene expression. Allele-specific methylation quantitative trait loci (ASM-QTLs) driven by DNA sequence variation explain most of the link between gene expression and CpG methylation.

More Related Videos

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
13:11

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

18.8K
Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
09:42

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Published on: September 7, 2017

9.7K

Related Experiment Videos

Last Updated: Jun 19, 2025

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

37.1K
Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain
13:11

Optimized Analysis of DNA Methylation and Gene Expression from Small, Anatomically-defined Areas of the Brain

Published on: July 12, 2012

18.8K
Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
09:42

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Published on: September 7, 2017

9.7K

Area of Science:

  • Genomics
  • Epigenetics
  • Molecular Biology

Background:

  • Gene promoter and enhancer sequences are typically unmethylated at CpG sites, correlating with gene expression.
  • DNA methylation is understood to play a regulatory role in gene expression.

Purpose of the Study:

  • To investigate haplotype-specific methylation rates across millions of CpG units in whole-blood genomes.
  • To identify methylation-depleted sequences and their association with genetic variants.
  • To determine the role of DNA sequence variation in allele-specific methylation and gene expression.

Main Methods:

  • Utilized nanopore sequencing to determine methylation rates for 15.3 million CpG units across 7,179 whole-blood genomes.
  • Identified 189,178 methylation-depleted sequences (three or more proximal CpGs unmethylated on at least one haplotype).
  • Performed RNA sequencing on 896 samples to correlate methylation patterns with gene expression.

Main Results:

  • Discovered 77,789 methylation-depleted sequences associated with 80,503 cis-acting sequence variants, termed allele-specific methylation quantitative trait loci (ASM-QTLs).
  • Demonstrated that ASM-QTLs (DNA sequence variability) drive the correlation between gene expression and CpG methylation.
  • Found ASM-QTLs to be significantly enriched among variants associated with hematological traits (40.2-fold enrichment).

Conclusions:

  • ASM-QTLs are crucial functional elements in the noncoding genome, linking DNA sequence variation to epigenetic regulation.
  • DNA sequence variability, as captured by ASM-QTLs, is a primary driver of allele-specific gene expression influenced by DNA methylation.
  • These findings highlight the importance of ASM-QTLs in understanding the genetic and epigenetic basis of complex traits, particularly hematological ones.