title: Epigenetic differences between shoots and roots in Arabidopsis reveals tissue-specific regulation.
abstract: DNA methylation and nucleosome densities play a critical role in the regulation of gene expression. While much is known about the mechanisms of transcriptional control that are mediated by these, less is known about the degree to which they are tissue-specific. By comparing DNA methylation, nucleosome densities and transcriptional levels in different tissue types we can gain a clearer understanding of the extent to which these mechanisms influence gene expression in a tissue specific manner. We compared DNA methylation in Arabidopsis shoots and roots and found extensive differences across the genome. We computed DNA methylation differences between roots and shoots at single cytosines and found that one in every 173 cytosines was differentially methylated. In addition we compared DNA methylation with tissue specific gene expression and nucleosome density measurements to identify associations between these. We also identified a group of genes that are strongly correlated with these epigenetic marks and are significantly differentially methylated between roots and shoots. These root-specific genes are part of the extensin family, and are preferentially methylated and have at least 10-fold higher expression and lower nucleosome density in roots relative to shoots.
authors.affiliation: Department of Molecular, Cell and Developmental Biology; University of California, Los Angeles; Los Angeles, CA USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Widman
authors.affiliation: Department of Molecular, Cell and Developmental Biology; University of California, Los Angeles; Los Angeles, CA USA.
authors.forename: Suhua
authors.initials: S
authors.lastname: Feng
authors.affiliation: Department of Molecular, Cell and Developmental Biology; University of California, Los Angeles; Los Angeles, CA USA.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Jacobsen
authors.affiliation: Department of Molecular, Cell and Developmental Biology; University of California, Los Angeles; Los Angeles, CA USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D004251:DNA Transposable Elements; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D006023:Glycoproteins / Q000235:genetics / Q000378:metabolism; D009707:Nucleosomes / Q000378:metabolism; D009928:Organ Specificity; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics* / Q000378:metabolism; D018520:Plant Shoots / Q000235:genetics* / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D006023:Glycoproteins; D009707:Nucleosomes; D010940:Plant Proteins; C005488:extensin protein, plant
keywords: DNA methylation; arabidopsis; epigenetics; gene expression; nucleosome positioning; roots; shoots; tissue differentiation