Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription

By Daniel Zilberman, Mary Gehring, R. Tran, Tracy J. Ballinger, Steven Henikoff. Nature Genetics, 2007

1,389 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/35c2ee9497e8051bdf4c8d2a827f3162ca208581

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Citations in the corpus

Widespread dynamic DNA methylation in response to biotic stress (2012, background): “In Arabidopsis, DNA methylation is deposited at CG, CHG, and CHH sequences (where H is A, C, or T) through three genetically separable pathways to regulate transposon silencing (6), genomic imprinting (7–9), and stable gene silencing (3, 4, 10, 11).”
A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci (2008, background): “While it will ultimately be important to know in detail the methylation status of whole genomes, this currently represents a technical challenge that has been addressed only for the small-genomed plant Arabidopsis [33,34].”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, neutral): “thaliana plants grown in one environment (Zhang et al., 2006; Zilberman et al., 2007; Cokus et al., 2008; Lister et al., 2008).”
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. (2008, neutral): “In higher eukaryotes, DNA methylation is involved in myriad essential processes, including embryogenesis, genomic imprinting, and tumorigenesis in mammals, and in transposon silencing and gene regulation in plants (Bestor, 2000; Li et al., 1992; Lippman et al., 2004; Rhee et al., 2002; Zhang et al.,”
Survival of the sparsest: robust gene networks are parsimonious (2008, background): “In another study (Zilberman et al, 2007), experiments showed that highly methylated genes become upregulated when methylation is lost, whereas unmethylated regions often contain highly expressed genes that are regulated by specific transcription factors.”
Cancer epigenomics: DNA methylomes and histone-modification maps (2007, background): “thaliana have recently been published, paving the way for other epigenome”
Epigenetic correlates of plant phenotypic plasticity: DNA methylation differs between prickly and nonprickly leaves in heterophyllous Ilex aquifolium (Aquifoliaceae) trees (2013, background): “First, DNA methylation in plants controls gene expression levels and is also involved in gene regulation during development (Zilberman et al., 2007; Gibney & Nolan, 2010; Zhang et al., 2011).”
Epigenomic diversity in a global collection of Arabidopsis thaliana accessions (2016, neutral): “gbM is associated with constitutive gene expression (Tran et al., 2005; Zhang et al., 2006; Zilberman et al., 2007), and the expression levels of gbM genes were indeed higher than those of unmethylated (UM) and TE-like methylated (teM; mCHG or mCHH and/or mCG) genes across all tested accessions (Fig”
Epigenetic regulation of stress responses in plants. (2009, methodology): “The precipitated DNA is then analyzed by PCR or wholegenome tiling microarrays [53,54].”
Principles and challenges of genome-wide DNA methylation analysis (2010, background): “However, CpG DNA methylation is increased in the gene bodies of actively transcribed genes in plant”
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). (2008, background): “MeDIP combined with microarrays is a powerful approach for DNA methylation profiling (Weber et al. 2005, 2007; Keshet et al. 2006; Zhang et al. 2006; Zilberman et al. 2006).”
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis (2008, methodology): “MeDIP/mDIP, combined with microarrays (MeDIP-chip), was used to delineate the first high-resolution whole-genome DNA methylation profile of any genome ( Arabidopsis”
Genome-wide mapping of alternative splicing in Arabidopsis thaliana. (2010, methodology): “We compared the chromosomal profiles of transcript-derived RNA-seq coverage with the cytosine methyla- tion distribution (Zilberman et al. 2007; data set GEO GSE5974).”