Genome-wide analysis of day/night DNA methylation differences in Populus nigra.
DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation pat...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2018-01-01
|
| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC5749751?pdf=render |
| _version_ | 1828871211330830336 |
|---|---|
| author | Chang-Jun Ding Li-Xiong Liang Shu Diao Xiao-Hua Su Bing-Yu Zhang |
| author_facet | Chang-Jun Ding Li-Xiong Liang Shu Diao Xiao-Hua Su Bing-Yu Zhang |
| author_sort | Chang-Jun Ding |
| collection | DOAJ |
| description | DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation. |
| first_indexed | 2024-12-13T06:27:56Z |
| format | Article |
| id | doaj.art-49144d34b3fa4982984536a3554f4fab |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-13T06:27:56Z |
| publishDate | 2018-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-49144d34b3fa4982984536a3554f4fab2022-12-21T23:56:41ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01131e019029910.1371/journal.pone.0190299Genome-wide analysis of day/night DNA methylation differences in Populus nigra.Chang-Jun DingLi-Xiong LiangShu DiaoXiao-Hua SuBing-Yu ZhangDNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.http://europepmc.org/articles/PMC5749751?pdf=render |
| spellingShingle | Chang-Jun Ding Li-Xiong Liang Shu Diao Xiao-Hua Su Bing-Yu Zhang Genome-wide analysis of day/night DNA methylation differences in Populus nigra. PLoS ONE |
| title | Genome-wide analysis of day/night DNA methylation differences in Populus nigra. |
| title_full | Genome-wide analysis of day/night DNA methylation differences in Populus nigra. |
| title_fullStr | Genome-wide analysis of day/night DNA methylation differences in Populus nigra. |
| title_full_unstemmed | Genome-wide analysis of day/night DNA methylation differences in Populus nigra. |
| title_short | Genome-wide analysis of day/night DNA methylation differences in Populus nigra. |
| title_sort | genome wide analysis of day night dna methylation differences in populus nigra |
| url | http://europepmc.org/articles/PMC5749751?pdf=render |
| work_keys_str_mv | AT changjunding genomewideanalysisofdaynightdnamethylationdifferencesinpopulusnigra AT lixiongliang genomewideanalysisofdaynightdnamethylationdifferencesinpopulusnigra AT shudiao genomewideanalysisofdaynightdnamethylationdifferencesinpopulusnigra AT xiaohuasu genomewideanalysisofdaynightdnamethylationdifferencesinpopulusnigra AT bingyuzhang genomewideanalysisofdaynightdnamethylationdifferencesinpopulusnigra |