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

You might also read

Related Articles

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

Sort by
Same author

Protocol to predict gene expression from transcriptomic data using PREDICT.

STAR protocols·2026
Same author

Computational Workflow for Genome-Wide DNA Methylation Profiling and Differential Methylation Analysis.

Bio-protocol·2025
Same author

Library Preparation for Genome-Wide DNA Methylation Profiling.

Bio-protocol·2025
Same author

Single-cell and spatial omics reveal progressive loss of xylem developmental complexity across seed plants.

The Plant cell·2025
Same author

TISCalling: leveraging machine learning to identify translational initiation sites in plants and viruses.

Plant molecular biology·2025
Same author

The peptide hormone RGF1 modulates PLETHORA2 stability via reactive oxygen species-dependent regulation of a cysteine residue.

Plant physiology·2025
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Aug 12, 2025

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

25.6K

Methylome Imputation by Methylation Patterns.

Ya-Ting Sabrina Chang1, Ming-Ren Yen1, Pao-Yang Chen2

  • 1Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.

Methods in Molecular Biology (Clifton, N.J.)
|February 1, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces a new probabilistic imputation method to accurately estimate DNA methylation heterogeneity from low-coverage sequencing data. The faster, more accurate software improves monitoring of epigenetic changes in cellular populations and disease.

Keywords:
Bisulfite sequencingMethylation heterogeneityMethylation patternsProbabilistic-based imputation

More Related Videos

DNA Methylation: Bisulphite Modification and Analysis
12:34

DNA Methylation: Bisulphite Modification and Analysis

Published on: October 21, 2011

105.1K
Methylated DNA Immunoprecipitation
21:24

Methylated DNA Immunoprecipitation

Published on: January 2, 2009

23.4K

Related Experiment Videos

Last Updated: Aug 12, 2025

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

25.6K
DNA Methylation: Bisulphite Modification and Analysis
12:34

DNA Methylation: Bisulphite Modification and Analysis

Published on: October 21, 2011

105.1K
Methylated DNA Immunoprecipitation
21:24

Methylated DNA Immunoprecipitation

Published on: January 2, 2009

23.4K

Area of Science:

  • Epigenetics
  • Genomics
  • Computational Biology

Background:

  • DNA methylation is crucial for biological processes like transcriptional regulation.
  • Current methods struggle to accurately estimate methylation heterogeneity due to low sequencing coverage.
  • Methylation heterogeneity provides insights into cellular dynamics and disease.

Purpose of the Study:

  • To develop a novel probabilistic imputation method for estimating DNA methylation heterogeneity.
  • To address the limitations of low-coverage sequencing data in methylome analysis.
  • To enable more accurate monitoring of epigenetic variations in cellular populations.

Main Methods:

  • Developed a probabilistic-based imputation method using methylation information from neighboring cytosine sites.
  • Utilized information from successive cytosines on the same sequencing reads.
  • Implemented the method into user-friendly software for methylome analysis.

Main Results:

  • The proposed imputation method accurately recovers partially observed methylation patterns.
  • The software demonstrates superior speed and accuracy compared to existing methods.
  • Successfully overcomes challenges posed by low sequencing depth.

Conclusions:

  • The novel imputation method enhances the accuracy of DNA methylation heterogeneity estimation.
  • The software facilitates streamlined monitoring of epigenetic changes.
  • Provides a valuable tool for studying the role of epigenetics in cellular processes and disease.