Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip.
@article{Cortijo2014GenomewideAO,
title={Genome-wide analysis of DNA methylation in Arabidopsis using MeDIP-chip.},
author={Sandra Cortijo and Ren{\'e} Wardenaar and Maria Colom{\'e}-Tatch{\'e} and Frank Johannes and Vincent Colot},
journal={Methods in molecular biology},
year={2014},
volume={1112},
pages={
125-49
}
}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 of purposes, it is best known for its role in stable transcriptional silencing of transposable elements and epigenetic regulation of some genes. In addition, it is increasingly recognized that alterations in DNA methylation patterns can sometimes be inherited across multiple generations and thus are a source of…
Figures and Tables from this paper
20 Citations
TET-mediated epimutagenesis of the Arabidopsis thaliana methylome
- Biology
- 2017
Application of TET-mediated epimutagenesis to agriculturally significant plants may result in differential expression of alleles normally silenced by DNA methylation, uncovering previously hidden phenotypic variations.
TET-mediated epimutagenesis of the Arabidopsis thaliana methylome
- BiologyNature Communications
- 2018
It is shown that expression of a human ten–eleven translocation enzyme can generate heritable hypomethylation alleles in Arabidopsis, providing a novel method to manipulate DNA methylation for breeding and research purposes.
MeDIP-HMM: genome-wide identification of distinct DNA methylation states from high-density tiling arrays
- BiologyBioinform.
- 2012
It is found that MeDIP-HMM is a fast and precise method for the analysis of methylome data, enabling the identification of distinct DNA methylation levels.
Extensive Natural Epigenetic Variation at a De Novo Originated Gene
- BiologyPLoS genetics
- 2013
It is reported that the gene Qua-Quine Starch of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature, and this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5′end of the gene.
Locus-Specific DNA Methylation Analysis and Applications to Plants
- Biology
- 2017
This chapter describes an exhaustive list of methods devoted to the locus-specific analysis of DNA methylation which have proven to be applicable to plant genomes and their potential use in high throughput screening of plant population.
Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation
- BiologyProceedings of the National Academy of Sciences
- 2012
It is demonstrated that the suppression of COs within pericentromeric regions of chromosomes persists in this experimental setting, and suppression is reinforced within 3-Mb regions flanking pericentrumeric boundaries, and this effect appears to be compensated by increased recombination activity in chromosome arms.
Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis.
- BiologyMethods in molecular biology
- 2013
MeDIP-chip performs reasonably well in detecting DNA methylation at probe-level resolution, yielding a genome-wide combined false-positive and false-negative rate of about 0.21, and is a reasonable alternative to WGBS-seq in emerging Arabidopsis population epigenetic studies.
TEACHING TOOLS IN PLANT BIOLOGYTM: LECTURE NOTES Introduction to Epigenetic Gene Regulation
- Biology
- 2013
Genetic studies have identified the molecular pathways for DNA and chromatin modification that underlie these processes, and genome profiling tools have revealed that they are pervasive and have a role in regulating most of the genome.
Prediction of Plant Height in Arabidopsis thaliana Using DNA Methylation Data
- BiologyGenetics
- 2015
This work used methylation information for predicting plant height (PH) in Arabidopsis thaliana nonparametrically, using reproducing kernel Hilbert spaces (RKHS) regression and created a kernel that mimics the genomic relationship matrix in genomic best linear unbiased prediction (G-BLUP).
References
SHOWING 1-10 OF 12 REFERENCES
Principles and challenges of genome-wide DNA methylation analysis
- BiologyNature Reviews Genetics
- 2010
There is such a diversity of DNA methylation profiling techniques that it can be challenging to select one, and this Review discusses the different approaches and their relative merits and introduces considerations for data analysis.
Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning
- BiologyNature
- 2008
A map at single-base-pair resolution of methylated cytosines for Arabidopsis is generated by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology.
Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits
- BiologyPLoS genetics
- 2009
The demonstration that numerous epialleles across the genome can be stable over many generations in the absence of selection or extensive DNA sequence variation highlights the need to integrate epigenetic information into population genetics studies.
Features of the Arabidopsis recombination landscape resulting from the combined loss of sequence variation and DNA methylation
- BiologyProceedings of the National Academy of Sciences
- 2012
It is demonstrated that the suppression of COs within pericentromeric regions of chromosomes persists in this experimental setting, and suppression is reinforced within 3-Mb regions flanking pericentrumeric boundaries, and this effect appears to be compensated by increased recombination activity in chromosome arms.
Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes.
- BiologyGenes & development
- 2009
Although analysis after eight generations of inbreeding, supported by genome-wide DNA methylation profiling, identified recombined parental chromosomal segments, these were interspersed with unexpectedly high frequencies of nonparental methylation polymorphism, which complicate linkage-based epigenomic mapping.
Comparing genome-wide chromatin profiles using ChIP-chip or ChIP-seq
- Computer ScienceBioinform.
- 2010
A parametric classification approach is introduced for the simultaneous analysis of two (or more) ChIP samples and is recommended as a first-pass algorithm to identify candidate regions in the epigenome, possibly followed by some type of second- pass algorithm to fine-tune detected peaks in accordance with biological or technological criteria.
Epigenome dynamics: a quantitative genetics perspective
- BiologyNature Reviews Genetics
- 2008
It is argued that it is timely to consider novel experimental strategies and analysis models to capture the potentially dynamic interplay between chromatin and DNA sequence factors in complex traits.
Finite Mixture Models
- Computer ScienceWiley Series in Probability and Statistics
- 2000
The important role of finite mixture models in the statistical analysis of data is underscored by the ever-increasing rate at which articles on mixture applications appear in the statistical and ge...
A Tutorial on Hidden Markov Models and Selected Applications
- Geology
- 1989
The fabric comprises a novel type of netting which will have particular utility in screening out mosquitoes and like insects and pests. The fabric is defined of voids having depth as well as width…














