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Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa

BACKGROUND: Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the patte...

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Autores principales: Vining, Kelly, Pomraning, Kyle R, Wilhelm, Larry J, Ma, Cathleen, Pellegrini, Matteo, Di, Yanming, Mockler, Todd C, Freitag, Michael, Strauss, Steven H
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728041/
https://www.ncbi.nlm.nih.gov/pubmed/23799904
http://dx.doi.org/10.1186/1471-2229-13-92
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author Vining, Kelly
Pomraning, Kyle R
Wilhelm, Larry J
Ma, Cathleen
Pellegrini, Matteo
Di, Yanming
Mockler, Todd C
Freitag, Michael
Strauss, Steven H
author_facet Vining, Kelly
Pomraning, Kyle R
Wilhelm, Larry J
Ma, Cathleen
Pellegrini, Matteo
Di, Yanming
Mockler, Todd C
Freitag, Michael
Strauss, Steven H
author_sort Vining, Kelly
collection PubMed
description BACKGROUND: Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation. RESULTS: We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes. CONCLUSIONS: DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements.
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spelling pubmed-37280412013-07-31 Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa Vining, Kelly Pomraning, Kyle R Wilhelm, Larry J Ma, Cathleen Pellegrini, Matteo Di, Yanming Mockler, Todd C Freitag, Michael Strauss, Steven H BMC Plant Biol Research Article BACKGROUND: Cytosine DNA methylation (5mC) is an epigenetic modification that is important to genome stability and regulation of gene expression. Perturbations of 5mC have been implicated as a cause of phenotypic variation among plants regenerated through in vitro culture systems. However, the pattern of change in 5mC and its functional role with respect to gene expression, are poorly understood at the genome scale. A fuller understanding of how 5mC changes during in vitro manipulation may aid the development of methods for reducing or amplifying the mutagenic and epigenetic effects of in vitro culture and plant transformation. RESULTS: We investigated the in vitro methylome of the model tree species Populus trichocarpa in a system that mimics routine methods for regeneration and plant transformation in the genus Populus (poplar). Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we compared the methylomes of internode stem segments from micropropagated explants, dedifferentiated calli, and internodes from regenerated plants. We found that more than half (56%) of the methylated portion of the genome appeared to be differentially methylated among the three tissue types. Surprisingly, gene promoter methylation varied little among tissues, however, the percentage of body-methylated genes increased from 9% to 14% between explants and callus tissue, then decreased to 8% in regenerated internodes. Forty-five percent of differentially-methylated genes underwent transient methylation, becoming methylated in calli, and demethylated in regenerants. These genes were more frequent in chromosomal regions with higher gene density. Comparisons with an expression microarray dataset showed that genes methylated at both promoters and gene bodies had lower expression than genes that were unmethylated or only promoter-methylated in all three tissues. Four types of abundant transposable elements showed their highest levels of 5mC in regenerated internodes. CONCLUSIONS: DNA methylation varies in a highly gene- and chromosome-differential manner during in vitro differentiation and regeneration. 5mC in redifferentiated tissues was not reset to that in original explants during the study period. Hypermethylation of gene bodies in dedifferentiated cells did not interfere with transcription, and may serve a protective role against activation of abundant transposable elements. BioMed Central 2013-06-25 /pmc/articles/PMC3728041/ /pubmed/23799904 http://dx.doi.org/10.1186/1471-2229-13-92 Text en Copyright © 2013 Vining et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Vining, Kelly
Pomraning, Kyle R
Wilhelm, Larry J
Ma, Cathleen
Pellegrini, Matteo
Di, Yanming
Mockler, Todd C
Freitag, Michael
Strauss, Steven H
Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
title Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
title_full Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
title_fullStr Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
title_full_unstemmed Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
title_short Methylome reorganization during in vitro dedifferentiation and regeneration of Populus trichocarpa
title_sort methylome reorganization during in vitro dedifferentiation and regeneration of populus trichocarpa
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728041/
https://www.ncbi.nlm.nih.gov/pubmed/23799904
http://dx.doi.org/10.1186/1471-2229-13-92
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