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

RNA-seq03:21

RNA-seq

11.7K
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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.7K
Next-generation Sequencing03:00

Next-generation Sequencing

97.7K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
97.7K
Sanger Sequencing01:57

Sanger Sequencing

773.1K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
773.1K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

12.6K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
12.6K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.8K

You might also read

Related Articles

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

Sort by
Same author

Circulating Beta3-Adrenoreceptor as Novel Independent Biomarker for Risk Assessment in Neuroblastoma Patients.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology·2026
Same author

Long-term mavacamten exposure reduces force and sarcomere density in a hiPSC model of hypertrophic cardiomyopathy.

Cardiovascular research·2026
Same author

Targeting Synaptic Vesicle Endocytosis in Nociceptors Provides Sustained Pain Relief.

bioRxiv : the preprint server for biology·2026
Same author

β3-adrenergic blockade targets fatty acid oxidation to induce ferroptotic vulnerability in pediatric T-ALL.

Biology direct·2026
Same author

Preclinical models of female pelvic pain disorders.

Pain·2026
Same author

Menstrual distress in medical students: symptomatic burden, attitudes, and perceived unmet educational needs.

The journal of sexual medicine·2026

Related Experiment Video

Updated: Jan 14, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

14.6K

PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing.

Gianluca Mattei1, Marta Baragli1, Barbara Gega2

  • 1Department of Information Engineering, University of Florence, 50139 Florence, Italy; albertomagi@gmail.com gianluca.mattei@unifi.it marta.baragli@unifi.it.

Genome Research
|October 20, 2025
PubMed
Summary

PoreMeth2, a new R library, analyzes epiallelic diversity using Nanopore sequencing to identify differentially methylated regions (DMRs). This method enhances epigenetic analysis across the entire human methylome, offering insights into gene regulation.

More Related Videos

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

26.2K
Methyl-binding DNA capture Sequencing for Patient Tissues
08:40

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

9.0K

Related Experiment Videos

Last Updated: Jan 14, 2026

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
11:26

Sequencing of mRNA from Whole Blood using Nanopore Sequencing

Published on: June 3, 2019

14.6K
Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
13:47

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

26.2K
Methyl-binding DNA capture Sequencing for Patient Tissues
08:40

Methyl-binding DNA capture Sequencing for Patient Tissues

Published on: October 31, 2016

9.0K

Area of Science:

  • Epigenetics and Genomics
  • Computational Biology
  • Bioinformatics

Background:

  • Differential methylation analysis traditionally identifies consecutive CpG sites with altered average methylation.
  • Epiallelic patterns and their frequencies offer deeper insights into genomic region formation.
  • Existing methods using short-read sequencing limit epiallele analysis to high CpG density regions, covering only half the human methylome.

Purpose of the Study:

  • To introduce PoreMeth2, a novel R library for analyzing epiallelic diversity and methylation frequency from Nanopore data.
  • To enable comprehensive differential methylation region (DMR) identification across diverse genomic contexts.
  • To provide insights into the formation mechanisms of DMRs and their regulatory roles.

Main Methods:

  • Development of PoreMeth2, an R package integrating epiallelic diversity and methylation frequency.
  • Utilizing long-read Nanopore sequencing data for epiallele frequency analysis.
  • Application of PoreMeth2 to cancer and glial cell datasets for DMR identification and annotation.

Main Results:

  • PoreMeth2 successfully identifies DMRs by integrating epiallelic diversity and methylation frequency.
  • The method enables analysis across both high and low CpG density regions, expanding coverage of the human methylome.
  • PoreMeth2 demonstrates superior performance compared to state-of-the-art methods in distinguishing epigenomic alterations impacting gene expression.

Conclusions:

  • PoreMeth2 advances differential methylation analysis by incorporating epiallelic information from long-read sequencing.
  • The library provides a powerful tool for understanding DMR formation mechanisms and their regulatory functions.
  • PoreMeth2 enhances the ability to identify epigenomic alterations with significant effects on gene expression.