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Epigenomes 2019, 3(1), 4; https://doi.org/10.3390/epigenomes3010004

Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance

1
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, Portugal
2
Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
3
IBET, Apartado 12, 2781-901 Oeiras, Portugal
*
Author to whom correspondence should be addressed.
Current address: Memorial Sloan Kettering Cancer Center, 1275 York Avenue, NY 10065, USA
Received: 5 November 2018 / Revised: 7 December 2018 / Accepted: 15 January 2019 / Published: 18 January 2019
(This article belongs to the Special Issue Plant Epigenetics)
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Abstract

Chromatin structure, DNA methylation, and histone modifications act in a concerted manner to influence gene expression and therefore plant phenotypes. Environmental stresses are often associated with extensive chromatin rearrangements and modifications of epigenetic levels and patterns. Stress-tolerant plants can be a good tool to unveil potential connections between specific epigenetic modifications and stress tolerance capacity. We analyzed genome wide DNA methylation of a salt-tolerant rice variety under salinity and identified a set of differentially methylated regions (DMRs) between control and stress samples using high-throughput sequencing of DNA immunoprecipitated with the 5-methylcytosine antibody (MeDIP-Seq). The examination of DNA methylation pattern at DMRs regions revealed a general tendency for demethylation events in stress samples as compared to control. In addition, DMRs appear to influence the expression of genes located in their vicinity. We hypothesize that short regions as DMRs can shape the chromatin landscape of specific genomic regions and, therefore, may modulate the function of several genes. In this sense, the identification of DMRs represents one step towards to uncover new players in the regulation of stress-responsive genes and new target genes with potential application in enhancement of plant salinity-tolerance. View Full-Text
Keywords: differentially methylated regions (DMRs); MeDIP-Seq; rice; salt stress tolerance differentially methylated regions (DMRs); MeDIP-Seq; rice; salt stress tolerance
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Ferreira, L.J.; Donoghue, M.T.A.; Barros, P.; Saibo, N.J.; Santos, A.P.; Oliveira, M.M. Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance. Epigenomes 2019, 3, 4.

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