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Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs (MethylC-seq)

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. Since 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 to multi-cellular 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 as compared to stripped roots. However, in response to heat stress, both root hairs and stripped roots showed more hypomethylation in each context, especially in the mCHH 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 of dynamic DNA methylation directly or indirectly is associated with expression of genes and transposons either within the context of specific tissues/cells or stress (heat).

ORGANISM(S): Glycine max

PROVIDER: GSE90142 | GEO | 2017/08/01

SECONDARY ACCESSION(S): PRJNA354570

REPOSITORIES: GEO

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Project description:Azospirillum is a plant growth promoting rhizobacteria (PGPR) with ability to produce several phytohormones such as auxins, mainly indole-3-acetic acid (IAA). The positive interaction of Azospirillum with plants has been simplified and explained through the bacterial capacity to produce IAA. Typical changes on root architecture by promoting the number of lateral roots and hair formation, and reducing the primary root length were established in inoculated plants. These changes increase the root surface improving the water and nutrients acquisition, and thus the growth of the whole plant. The mechanisms by which Azospirillum induces such changes fails to be explained only by the bacterial capacity to produce IAA. In this work, we have evaluated the root architecture and gene expression changes occurred in Arabidopsis thaliana inoculated with A. brasilense Az39 and the IAA-deficient mutant (Az39 ipdC-), or treated with exogenous IAA solution to confirm both, the IAA-dependent and IAA-independent Azospirillum´s pathways to promote the root growth. Our results demonstrate the ability of Az39 to modify the primary root development through IAA biosynthesis, while other IAA-independent mechanisms were related to an increase in the lateral roots development and the root hairs number. Jasmonates, ethylene and salicylic acid were increased in the IAA-deficient bacterial treatments, as the ipdC mutant significantly up-regulated transcription of genes enriched of these phytohormones signaling after 7 days. Further, the physical presence of the inactive bacteria (Az39φ) seems to mediate the development of root hairs, a mechanism common to other non-PGPR as E. coli DH5α. Our results suggest that Az39 inoculation induces morphological changes in root architecture through both IAA-dependent and independent mechanism. The IAA biosynthesis by Az39 reduces the primary root length; while the cells contact with the roots increases the root hairs production. Both the synthesis of active IAA and the presence of metabolically active Az39 cells increase the growth and development of lateral roots.

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Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs (MethylC-seq)

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