Related Experiment Video
Updated: Feb 14, 2026

A Rat Methyl-Seq Platform to Identify Epigenetic Changes Associated with Stress Exposure
Published on: October 24, 2018
Defiant: (DMRs: easy, fast, identification and ANnoTation) identifies differentially Methylated regions from
David E Condon1, Phu V Tran2, Yu-Chin Lien3
1Department of Genetics, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
Background:
Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion.
Results:
We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data.
Conclusions:
Defiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays.
Related Concept Videos
Oppositional Defiant Disorder
Diagnostic Criteria and...
Genome Annotation and Assembly
The Eukaryotic Promoter Region
Role of Hippocampus in Memory
IR Frequency Region: Fingerprint Region
Gene Evolution - Fast or Slow?
In contrast, regions which code...

