Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.)
Abstract Background Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulat...
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Format: | Article |
Language: | English |
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BMC
2018-11-01
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Series: | BMC Plant Biology |
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Online Access: | http://link.springer.com/article/10.1186/s12870-018-1553-5 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hongyu Zhang Asif Ali Feixue Hou Tingkai Wu Daiming Guo Xiufeng Zeng Fangfang Wang Huixia Zhao Xiaoqiong Chen Peizhou Xu Xianjun Wu |
spellingShingle |
Hongyu Zhang Asif Ali Feixue Hou Tingkai Wu Daiming Guo Xiufeng Zeng Fangfang Wang Huixia Zhao Xiaoqiong Chen Peizhou Xu Xianjun Wu Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.) BMC Plant Biology WGD DNA methylation mRNA expression Digital gene expression MeDIP sequencing Sodium bisulfite sequencing |
author_facet |
Hongyu Zhang Asif Ali Feixue Hou Tingkai Wu Daiming Guo Xiufeng Zeng Fangfang Wang Huixia Zhao Xiaoqiong Chen Peizhou Xu Xianjun Wu |
author_sort |
Hongyu Zhang |
title |
Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.) |
title_short |
Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.) |
title_full |
Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.) |
title_fullStr |
Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.) |
title_full_unstemmed |
Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.) |
title_sort |
effects of ploidy variation on promoter dna methylation and gene expression in rice (oryza sativa l.) |
publisher |
BMC |
series |
BMC Plant Biology |
issn |
1471-2229 |
publishDate |
2018-11-01 |
description |
Abstract Background Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants. Results In our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing). Conclusions We found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice. |
topic |
WGD DNA methylation mRNA expression Digital gene expression MeDIP sequencing Sodium bisulfite sequencing |
url |
http://link.springer.com/article/10.1186/s12870-018-1553-5 |
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doaj-57394971c8f744c58456e1f9f63730a22020-11-25T01:59:02ZengBMCBMC Plant Biology1471-22292018-11-0118111210.1186/s12870-018-1553-5Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.)Hongyu Zhang0Asif Ali1Feixue Hou2Tingkai Wu3Daiming Guo4Xiufeng Zeng5Fangfang Wang6Huixia Zhao7Xiaoqiong Chen8Peizhou Xu9Xianjun Wu10211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural University211-Key Laboratory of Crop Genetic Resources and Genetic Improvement, Ministry of Education, Institute of Rice Research, Sichuan Agricultural UniversityAbstract Background Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants. Results In our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing). Conclusions We found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice.http://link.springer.com/article/10.1186/s12870-018-1553-5WGDDNA methylationmRNA expressionDigital gene expressionMeDIP sequencingSodium bisulfite sequencing |