Cargando…

Demethylation alters transcriptome profiling of buds and leaves in ‘Kyoho’ grape

BACKGROUND: Grape buds and leaves are directly associated with the physiology and metabolic activities of the plant, which is monitored by epigenetic modifications induced by environment and endogenous factors. Methylation is one of the epigenetic regulators that could be involved in DNA levels and...

Descripción completa

Detalles Bibliográficos
Autores principales: Jia, Haoran, Zhang, Zibo, Sadeghnezhad, Ehsan, Pang, Qianqian, Li, Shangyun, Pervaiz, Tariq, Su, Ziwen, Dong, Tianyu, Fang, Jinggui, Jia, Haifeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7716455/
https://www.ncbi.nlm.nih.gov/pubmed/33276735
http://dx.doi.org/10.1186/s12870-020-02754-0
_version_ 1783619164037971968
author Jia, Haoran
Zhang, Zibo
Sadeghnezhad, Ehsan
Pang, Qianqian
Li, Shangyun
Pervaiz, Tariq
Su, Ziwen
Dong, Tianyu
Fang, Jinggui
Jia, Haifeng
author_facet Jia, Haoran
Zhang, Zibo
Sadeghnezhad, Ehsan
Pang, Qianqian
Li, Shangyun
Pervaiz, Tariq
Su, Ziwen
Dong, Tianyu
Fang, Jinggui
Jia, Haifeng
author_sort Jia, Haoran
collection PubMed
description BACKGROUND: Grape buds and leaves are directly associated with the physiology and metabolic activities of the plant, which is monitored by epigenetic modifications induced by environment and endogenous factors. Methylation is one of the epigenetic regulators that could be involved in DNA levels and affect gene expression in response to stimuli. Therefore, changes of gene expression profile in leaves and bud through inhibitors of DNA methylation provide a deep understanding of epigenetic effects in regulatory networks. RESULTS: In this study, we carried out a transcriptome analysis of ‘Kyoho’ buds and leaves under 5-azacytidine (5-azaC) exposure and screened a large number of differentially expressed genes (DEGs). GO and KEGG annotations showed that they are mainly involved in photosynthesis, flavonoid synthesis, glutathione metabolism, and other metabolic processes. Functional enrichment analysis also provided a holistic perspective on the transcriptome profile when 5-azaC bound to methyltransferase and induced demethylation. Enrichment analysis of transcription factors (TFs) also showed that the MYB, C2H2, and bHLH families are involved in the regulation of responsive genes under epigenetic changes. Furthermore, hormone-related genes have also undergone significant changes, especially gibberellin (GA) and abscisic acid (ABA)-related genes that responded to bud germination. We also used protein-protein interaction network to determine hub proteins in response to demethylation. CONCLUSIONS: These findings provide new insights into the establishment of molecular regulatory networks according to how methylation as an epigenetic modification alters transcriptome patterns in bud and leaves of grape.
format Online
Article
Text
id pubmed-7716455
institution National Center for Biotechnology Information
language English
publishDate 2020
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-77164552020-12-04 Demethylation alters transcriptome profiling of buds and leaves in ‘Kyoho’ grape Jia, Haoran Zhang, Zibo Sadeghnezhad, Ehsan Pang, Qianqian Li, Shangyun Pervaiz, Tariq Su, Ziwen Dong, Tianyu Fang, Jinggui Jia, Haifeng BMC Plant Biol Research Article BACKGROUND: Grape buds and leaves are directly associated with the physiology and metabolic activities of the plant, which is monitored by epigenetic modifications induced by environment and endogenous factors. Methylation is one of the epigenetic regulators that could be involved in DNA levels and affect gene expression in response to stimuli. Therefore, changes of gene expression profile in leaves and bud through inhibitors of DNA methylation provide a deep understanding of epigenetic effects in regulatory networks. RESULTS: In this study, we carried out a transcriptome analysis of ‘Kyoho’ buds and leaves under 5-azacytidine (5-azaC) exposure and screened a large number of differentially expressed genes (DEGs). GO and KEGG annotations showed that they are mainly involved in photosynthesis, flavonoid synthesis, glutathione metabolism, and other metabolic processes. Functional enrichment analysis also provided a holistic perspective on the transcriptome profile when 5-azaC bound to methyltransferase and induced demethylation. Enrichment analysis of transcription factors (TFs) also showed that the MYB, C2H2, and bHLH families are involved in the regulation of responsive genes under epigenetic changes. Furthermore, hormone-related genes have also undergone significant changes, especially gibberellin (GA) and abscisic acid (ABA)-related genes that responded to bud germination. We also used protein-protein interaction network to determine hub proteins in response to demethylation. CONCLUSIONS: These findings provide new insights into the establishment of molecular regulatory networks according to how methylation as an epigenetic modification alters transcriptome patterns in bud and leaves of grape. BioMed Central 2020-12-04 /pmc/articles/PMC7716455/ /pubmed/33276735 http://dx.doi.org/10.1186/s12870-020-02754-0 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research Article
Jia, Haoran
Zhang, Zibo
Sadeghnezhad, Ehsan
Pang, Qianqian
Li, Shangyun
Pervaiz, Tariq
Su, Ziwen
Dong, Tianyu
Fang, Jinggui
Jia, Haifeng
Demethylation alters transcriptome profiling of buds and leaves in ‘Kyoho’ grape
title Demethylation alters transcriptome profiling of buds and leaves in ‘Kyoho’ grape
title_full Demethylation alters transcriptome profiling of buds and leaves in ‘Kyoho’ grape
title_fullStr Demethylation alters transcriptome profiling of buds and leaves in ‘Kyoho’ grape
title_full_unstemmed Demethylation alters transcriptome profiling of buds and leaves in ‘Kyoho’ grape
title_short Demethylation alters transcriptome profiling of buds and leaves in ‘Kyoho’ grape
title_sort demethylation alters transcriptome profiling of buds and leaves in ‘kyoho’ grape
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7716455/
https://www.ncbi.nlm.nih.gov/pubmed/33276735
http://dx.doi.org/10.1186/s12870-020-02754-0
work_keys_str_mv AT jiahaoran demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT zhangzibo demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT sadeghnezhadehsan demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT pangqianqian demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT lishangyun demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT pervaiztariq demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT suziwen demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT dongtianyu demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT fangjinggui demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape
AT jiahaifeng demethylationalterstranscriptomeprofilingofbudsandleavesinkyohogrape