Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance
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-toler...
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| Format: | Article |
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MDPI AG
2019-01-01
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| Series: | Epigenomes |
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| Online Access: | http://www.mdpi.com/2075-4655/3/1/4 |
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| author | Liliana J. Ferreira Mark T. A. Donoghue Pedro Barros Nelson J. Saibo Ana Paula Santos M. Margarida Oliveira |
| author_facet | Liliana J. Ferreira Mark T. A. Donoghue Pedro Barros Nelson J. Saibo Ana Paula Santos M. Margarida Oliveira |
| author_sort | Liliana J. Ferreira |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T19:18:39Z |
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| id | doaj.art-7ca15784f7bd417fae3c06094b291454 |
| institution | Directory Open Access Journal |
| issn | 2075-4655 |
| language | English |
| last_indexed | 2024-03-12T19:18:39Z |
| publishDate | 2019-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Epigenomes |
| spelling | doaj.art-7ca15784f7bd417fae3c06094b2914542023-08-02T05:22:01ZengMDPI AGEpigenomes2075-46552019-01-0131410.3390/epigenomes3010004epigenomes3010004Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt ToleranceLiliana J. Ferreira0Mark T. A. Donoghue1Pedro Barros2Nelson J. Saibo3Ana Paula Santos4M. Margarida Oliveira5Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, PortugalCold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USAInstituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, PortugalInstituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, PortugalInstituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, PortugalInstituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress. Av. da República, 2780-157 Oeiras, PortugalChromatin 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.http://www.mdpi.com/2075-4655/3/1/4differentially methylated regions (DMRs)MeDIP-Seqricesalt stress tolerance |
| spellingShingle | Liliana J. Ferreira Mark T. A. Donoghue Pedro Barros Nelson J. Saibo Ana Paula Santos M. Margarida Oliveira Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance Epigenomes differentially methylated regions (DMRs) MeDIP-Seq rice salt stress tolerance |
| title | Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance |
| title_full | Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance |
| title_fullStr | Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance |
| title_full_unstemmed | Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance |
| title_short | Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance |
| title_sort | uncovering differentially methylated regions dmrs in a salt tolerant rice variety under stress one step towards new regulatory regions for enhanced salt tolerance |
| topic | differentially methylated regions (DMRs) MeDIP-Seq rice salt stress tolerance |
| url | http://www.mdpi.com/2075-4655/3/1/4 |
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