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Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detecti...

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Autores principales: Agius, Dolores Rita, Kapazoglou, Aliki, Avramidou, Evangelia, Baranek, Miroslav, Carneros, Elena, Caro, Elena, Castiglione, Stefano, Cicatelli, Angela, Radanovic, Aleksandra, Ebejer, Jean-Paul, Gackowski, Daniel, Guarino, Francesco, Gulyás, Andrea, Hidvégi, Norbert, Hoenicka, Hans, Inácio, Vera, Johannes, Frank, Karalija, Erna, Lieberman-Lazarovich, Michal, Martinelli, Federico, Maury, Stéphane, Mladenov, Velimir, Morais-Cecílio, Leonor, Pecinka, Ales, Tani, Eleni, Testillano, Pilar S., Todorov, Dimitar, Valledor, Luis, Vassileva, Valya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10306282/
https://www.ncbi.nlm.nih.gov/pubmed/37389288
http://dx.doi.org/10.3389/fpls.2023.1181039
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author Agius, Dolores Rita
Kapazoglou, Aliki
Avramidou, Evangelia
Baranek, Miroslav
Carneros, Elena
Caro, Elena
Castiglione, Stefano
Cicatelli, Angela
Radanovic, Aleksandra
Ebejer, Jean-Paul
Gackowski, Daniel
Guarino, Francesco
Gulyás, Andrea
Hidvégi, Norbert
Hoenicka, Hans
Inácio, Vera
Johannes, Frank
Karalija, Erna
Lieberman-Lazarovich, Michal
Martinelli, Federico
Maury, Stéphane
Mladenov, Velimir
Morais-Cecílio, Leonor
Pecinka, Ales
Tani, Eleni
Testillano, Pilar S.
Todorov, Dimitar
Valledor, Luis
Vassileva, Valya
author_facet Agius, Dolores Rita
Kapazoglou, Aliki
Avramidou, Evangelia
Baranek, Miroslav
Carneros, Elena
Caro, Elena
Castiglione, Stefano
Cicatelli, Angela
Radanovic, Aleksandra
Ebejer, Jean-Paul
Gackowski, Daniel
Guarino, Francesco
Gulyás, Andrea
Hidvégi, Norbert
Hoenicka, Hans
Inácio, Vera
Johannes, Frank
Karalija, Erna
Lieberman-Lazarovich, Michal
Martinelli, Federico
Maury, Stéphane
Mladenov, Velimir
Morais-Cecílio, Leonor
Pecinka, Ales
Tani, Eleni
Testillano, Pilar S.
Todorov, Dimitar
Valledor, Luis
Vassileva, Valya
author_sort Agius, Dolores Rita
collection PubMed
description Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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spelling pubmed-103062822023-06-29 Exploring the crop epigenome: a comparison of DNA methylation profiling techniques Agius, Dolores Rita Kapazoglou, Aliki Avramidou, Evangelia Baranek, Miroslav Carneros, Elena Caro, Elena Castiglione, Stefano Cicatelli, Angela Radanovic, Aleksandra Ebejer, Jean-Paul Gackowski, Daniel Guarino, Francesco Gulyás, Andrea Hidvégi, Norbert Hoenicka, Hans Inácio, Vera Johannes, Frank Karalija, Erna Lieberman-Lazarovich, Michal Martinelli, Federico Maury, Stéphane Mladenov, Velimir Morais-Cecílio, Leonor Pecinka, Ales Tani, Eleni Testillano, Pilar S. Todorov, Dimitar Valledor, Luis Vassileva, Valya Front Plant Sci Plant Science Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method. Frontiers Media S.A. 2023-05-30 /pmc/articles/PMC10306282/ /pubmed/37389288 http://dx.doi.org/10.3389/fpls.2023.1181039 Text en Copyright © 2023 Agius, Kapazoglou, Avramidou, Baranek, Carneros, Caro, Castiglione, Cicatelli, Radanovic, Ebejer, Gackowski, Guarino, Gulyás, Hidvégi, Hoenicka, Inácio, Johannes, Karalija, Lieberman-Lazarovich, Martinelli, Maury, Mladenov, Morais-Cecílio, Pecinka, Tani, Testillano, Todorov, Valledor and Vassileva https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Agius, Dolores Rita
Kapazoglou, Aliki
Avramidou, Evangelia
Baranek, Miroslav
Carneros, Elena
Caro, Elena
Castiglione, Stefano
Cicatelli, Angela
Radanovic, Aleksandra
Ebejer, Jean-Paul
Gackowski, Daniel
Guarino, Francesco
Gulyás, Andrea
Hidvégi, Norbert
Hoenicka, Hans
Inácio, Vera
Johannes, Frank
Karalija, Erna
Lieberman-Lazarovich, Michal
Martinelli, Federico
Maury, Stéphane
Mladenov, Velimir
Morais-Cecílio, Leonor
Pecinka, Ales
Tani, Eleni
Testillano, Pilar S.
Todorov, Dimitar
Valledor, Luis
Vassileva, Valya
Exploring the crop epigenome: a comparison of DNA methylation profiling techniques
title Exploring the crop epigenome: a comparison of DNA methylation profiling techniques
title_full Exploring the crop epigenome: a comparison of DNA methylation profiling techniques
title_fullStr Exploring the crop epigenome: a comparison of DNA methylation profiling techniques
title_full_unstemmed Exploring the crop epigenome: a comparison of DNA methylation profiling techniques
title_short Exploring the crop epigenome: a comparison of DNA methylation profiling techniques
title_sort exploring the crop epigenome: a comparison of dna methylation profiling techniques
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10306282/
https://www.ncbi.nlm.nih.gov/pubmed/37389288
http://dx.doi.org/10.3389/fpls.2023.1181039
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