title: Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs.
abstract: Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. As root hairs are single-cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single-cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single-cell root hairs as compared with multicellular stripped roots, as well as in response to heat stress. Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated than were stripped roots. However, in response to heat stress, both root hairs and stripped roots showed hypomethylation in each context, especially in the CHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons. Taken together, the data indicate that changes in DNA methylation are directly or indirectly associated with expression of genes and transposons within the context of either specific tissues/cells or stress (heat).
authors.affiliation: Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Md Shakhawat
authors.initials: MS
authors.lastname: Hossain
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.|Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 30508602, Japan.
authors.forename: Taiji
authors.identifier: http://orcid.org/0000-0002-6871-9199
authors.initials: T
authors.lastname: Kawakatsu
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602-6810, USA.
authors.forename: Kyung Do
authors.initials: KD
authors.lastname: Kim
authors.affiliation: Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA.
authors.forename: Ning
authors.initials: N
authors.lastname: Zhang
authors.affiliation: Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Cuong T
authors.initials: CT
authors.lastname: Nguyen
authors.affiliation: Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA.
authors.forename: Saad M
authors.initials: SM
authors.lastname: Khan
authors.affiliation: Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Josef M
authors.initials: JM
authors.lastname: Batek
authors.affiliation: Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA.|Department of Molecular Microbiology and Immunology and Office of Research, School of Medicine, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.affiliation: HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, AL, 35806, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: HudsonAlpha Genome Sequencing Center, 601 Genome Way, Huntsville, AL, 35806, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: Department of Genetics, The University of Georgia, 120 East Green Street, Athens, GA, 30602, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
authors.affiliation: Department of Computer Science, Informatics Institute and Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA.
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602-6810, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA, 92037, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
authors.affiliation: Divisions of Plant Science and Biochemistry, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Stacey
mesh_terms: D003596:Cytosine / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018869:Heat-Shock Response / Q000235:genetics; D018517:Plant Roots / Q000166:cytology* / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013025:Glycine max / Q000166:cytology* / Q000235:genetics*; D013312:Stress, Physiological / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D003596:Cytosine
keywords: DNA methylation; bisulfite sequencing; differentially methylated regions (DMRs); epigenetics; heat stress; root hairs; single cell; stripped roots