TY - JOUR
T1 - Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress
T2 - One Step towards New Regulatory Regions for Enhanced Salt Tolerance
AU - Ferreira, Liliana J.
AU - Donoghue, Mark T. A.
AU - Barros, Pedro
AU - Saibo, Nelson J.
AU - Santos, Ana Paula
AU - Oliveira, M. Margarida
PY - 2019
Y1 - 2019
N2 - 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.
AB - 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.
KW - differentially methylated regions (DMRs)
KW - MeDIP-Seq
KW - rice
KW - salt stress tolerance
U2 - 10.3390/epigenomes3010004
DO - 10.3390/epigenomes3010004
M3 - Article
SN - 2075-4655
VL - 3
JO - Epigenomes
JF - Epigenomes
IS - 1
M1 - 4
ER -
