Conservation and divergence of methylation patterning in plants and animals

By Suhua Feng, Shawn Cokus, Xiaoyu Zhang, Pao-Yang Chen, M. Bostick, M. Goll, Jonathan Hetzel, J. Jain, Steven H. Strauss, M. Halpern and 5 more. Proceedings of the National Academy of Sciences of the United States of America, 2010

1,199 citations recorded by the source corpus.

Subfields: Plant Science

View Paper: https://www.semanticscholar.org/paper/bea058741245bc0a0054d09daa59c039dd74a17b

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In Plant Science

1. M. Lelu-Walter
2. A. Bird
3. Sébastien Duplessis
4. Brandon S. Gaut
5. Bruno Fady

Citations in the corpus

• The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates (2011, background): “For example, site effects in nuclear genes have been characterized in only a couple of cases, and even known contributors to site variation, such as DNA methylation, have been described in only a small number of lineages (Feng et al. 2010, Zemach et al. 2010).”
• DNA methylation: superior or subordinate in the epigenetic hierarchy? (2011, background): “However, the finding that intragenic methylation contributes to gene silencing(51) is seemingly contradictory to others’ conclusions that gene body methylation correlates with increased transcription.(2,89,95,96,100) The discrepancy may arise from the different methods of measuring DNA methylation a”
• Epigenomic Analysis of Multi-lineage Differentiation of Human Embryonic Stem Cells (2013, neutral): “elegans) or varies considerably in its pattern relative to gene activity in invertebrates (Feng et al., 2010; Zemach et al., 2010).”
• Linking epigenetics and biological conservation: Towards a conservation epigenetics perspective (2019, neutral): “In vertebrates, organisms generally display high levels of methylation distributed in a continuous fashion over the genome except in some specific regions called CpG islands often corresponding to promoters and regulatory sequences of active genes (Feng, Cokus, et al., 2010).”
• Epigenetic regulation of gene responsiveness in Arabidopsis (2014, background): “Consistently, DNA methylation is nearly absent around TSSs of genes in many organisms especially when the genes are active whereas TSS DNA methylation does not show remarkable decrease for the genes with low expression (Lister et al., 2008; Feng et al., 2010; Zemach et al., 2010).”
• Tet1 and Tet2 regulate 5-hydroxymethylcytosine production and cell lineage specification in mouse embryonic stem cells (2011, background): “Recent whole-genome analyses have provided insights into the complexity of methylation patterns in plant and animal species (Farthing et al., 2008; Feng et al., 2010a; Lister et al., 2009; Meissner et al., 2008; Zemach et al., 2010).”
• Forest tree genomics: 10 achievements from the past 10 years and future prospects (2016, background): “Indeed, determination of the poplar methylome revealed features particular to this tree, such as a higher CHG methylation level than reported for other plants (Feng et al. 2010) and low”
• CpG islands and the regulation of transcription. (2011, background): “Extensive DNA methylome analysis has documented nonmethylated regions at both extremities of plant transcription units (Feng et al. 2010; Zemach et al. 2010).”