Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species

I Huh, X Wu, T Park, SV Yi - Briefings in bioinformatics, 2019 - academic.oup.com
DNA methylation is one of the most extensively studied epigenetic modifications of genomic
DNA. In recent years, sequencing of bisulfite-converted DNA, particularly via next …

Characterization of epigenetic biomarkers using new molecular approaches

MV Gentil, S Maury - Genomics-Assisted Crop Improvement: Vol. 1 …, 2007 - Springer
Plants exhibit a polymorphism of DNA methylation status in their genomes in relation to
various breeding traits and phenotypes. Evidence for relationships between DNA …

DNA Methylation analysis in barley and other species with large genomes

K Chwialkowska, U Korotko, M Kwasniewski - Barley: Methods and …, 2019 - Springer
Detailed DNA methylation analyses in plant species with large and highly repetitive
genomes can be challenging as well as costly. Here, we describe a complete protocol for a …

Bisulfite sequencing using small DNA amounts

S Edelmann, S Scholten - Plant chromatin dynamics: methods and …, 2018 - Springer
Bisulfite sequencing (BS-seq) enables the detection of DNA methylation at cytosine residues
(5mC) at single-nucleotide resolution. For many applications, a limiting factor of …

Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population

KS Araki, T Kubo, H Kudoh - PLoS One, 2017 - journals.plos.org
In sessile organisms such as plants, spatial genetic structures of populations show long-
lasting patterns. These structures have been analyzed across diverse taxa to understand the …

Plant epigenomics—deciphering the mechanisms of epigenetic inheritance and plasticity in plants

C Köhler, N Springer - Genome Biology, 2017 - Springer
It is an exciting time to study plant epigenetics. Technological advances are providing
unprecedented opportunities to monitor chromatin modifications, gene expression, and …

Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage

VN Ibañez, M van Antro, C Peña-Ponton… - Journal of …, 2023 - academic.oup.com
DNA methylation in plant genomes occurs in different sequences and genomic contexts that
have very different properties. DNA methylation that occurs in CG (mCG) sequence context …

Genome-Wide Analysis of DNA Methylation in Arabidopsis Using MeDIP-Chip

S Cortijo, R Wardenaar, M Colomé-Tatché… - Plant Epigenetics and …, 2014 - Springer
DNA methylation is an epigenetic mark that is essential for preserving genome integrity and
normal development in plants and mammals. Although this modification may serve a variety …

Ecological epigenetics: beyond MS-AFLP

AW Schrey, M Alvarez, CM Foust… - Integrative and …, 2013 - academic.oup.com
Ecological Epigenetics studies the relationship between epigenetic variation and
ecologically relevant phenotypic variation. As molecular epigenetic mechanisms often …

Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions

HT Lee - Plant Bioinformatics: Methods and Protocols, 2022 - Springer
The mechanism of the addition of a methyl group to cytosine has been identified as one of
several heritable epigenetic mechanisms. In plants, DNA methylation is involved in …