Journal ArticleDOI
Spontaneous epigenetic variation in the Arabidopsis thaliana methylome
Claude Becker,Jörg Hagmann,Jonas Müller,Daniel Koenig,Oliver Stegle,Karsten M. Borgwardt,Detlef Weigel +6 more
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TLDR
Compared genome-wide DNA methylation among 10 A. thaliana lines, differentially methylated sites were farther from transposable elements and showed less association with short interfering RNA expression than invariant positions, which has important implications for the potential contribution of sequence-independent epialleles to plant evolution.Abstract:
Heritable epigenetic polymorphisms, such as differential cytosine methylation, can underlie phenotypic variation. Moreover, wild strains of the plant Arabidopsis thaliana differ in many epialleles, and these can influence the expression of nearby genes. However, to understand their role in evolution, it is imperative to ascertain the emergence rate and stability of epialleles, including those that are not due to structural variation. We have compared genome-wide DNA methylation among 10 A. thaliana lines, derived 30 generations ago from a common ancestor. Epimutations at individual positions were easily detected, and close to 30,000 cytosines in each strain were differentially methylated. In contrast, larger regions of contiguous methylation were much more stable, and the frequency of changes was in the same low range as that of DNA mutations. Like individual positions, the same regions were often affected by differential methylation in independent lines, with evidence for recurrent cycles of forward and reverse mutations. Transposable elements and short interfering RNAs have been causally linked to DNA methylation. In agreement, differentially methylated sites were farther from transposable elements and showed less association with short interfering RNA expression than invariant positions. The biased distribution and frequent reversion of epimutations have important implications for the potential contribution of sequence-independent epialleles to plant evolution.read more
Citations
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Journal ArticleDOI
Transgenerational Epigenetic Inheritance: myths and mechanisms
TL;DR: Although the inheritance of epigenetic characters can certainly occur-particularly in plants-how much is due to the environment and the extent to which it happens in humans remain unclear.
Journal ArticleDOI
Charting a dynamic DNA methylation landscape of the human genome
Michael J. Ziller,Hongcang Gu,Fabian Müller,Julie Donaghey,Julie Donaghey,Linus T.-Y. Tsai,Oliver Kohlbacher,Philip L. De Jager,Philip L. De Jager,Evan D. Rosen,Evan D. Rosen,David A. Bennett,Bradley E. Bernstein,Bradley E. Bernstein,Andreas Gnirke,Alexander Meissner,Alexander Meissner +16 more
TL;DR: Although in theory every CpG can change its methylation state, the results suggest that only a fraction does so as part of coordinated regulatory programs, which highlights the general inefficiency of whole-genome bisulphite sequencing.
Journal ArticleDOI
RNA-directed DNA methylation: an epigenetic pathway of increasing complexity
Marjori Matzke,Rebecca A. Mosher +1 more
TL;DR: RNA-directed DNA methylation, the major small RNA-mediated epigenetic pathway in plants, is implicated in pathogen defence, stress responses and reproduction, as well as in interallelic and intercellular communication.
Journal ArticleDOI
Widespread dynamic DNA methylation in response to biotic stress
Robert H. Dowen,Mattia Pelizzola,Robert J. Schmitz,Ryan Lister,Jill M. Dowen,Joseph R. Nery,Jack E. Dixon,Joseph R. Ecker +7 more
TL;DR: An unexpected role for DNA methylation is reported in regulation of the Arabidopsis thaliana immune system and changes within repetitive sequences or transposons can regulate neighboring genes in response to SA stress.
Journal ArticleDOI
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions
TL;DR: BSmooth is presented, an alignment, quality control and analysis pipeline that provides accurate and precise results even with low coverage data, appropriately handling biological replicates.
References
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Journal ArticleDOI
Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
Book
ggplot2: Elegant Graphics for Data Analysis
TL;DR: This book describes ggplot2, a new data visualization package for R that uses the insights from Leland Wilkisons Grammar of Graphics to create a powerful and flexible system for creating data graphics.
Journal ArticleDOI
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
TL;DR: EdgeR as mentioned in this paper is a Bioconductor software package for examining differential expression of replicated count data, which uses an overdispersed Poisson model to account for both biological and technical variability and empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference.
Journal ArticleDOI
The control of the false discovery rate in multiple testing under dependency
Yoav Benjamini,Daniel Yekutieli +1 more
TL;DR: In this paper, it was shown that a simple FDR controlling procedure for independent test statistics can also control the false discovery rate when test statistics have positive regression dependency on each of the test statistics corresponding to the true null hypotheses.
Journal ArticleDOI
Statistical significance for genomewide studies
John D. Storey,Robert Tibshirani +1 more
TL;DR: This work proposes an approach to measuring statistical significance in genomewide studies based on the concept of the false discovery rate, which offers a sensible balance between the number of true and false positives that is automatically calibrated and easily interpreted.
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