TY  - JOUR
AU  - Agius, Dolores Rita
AU  - Kapazoglou, Aliki
AU  - Avramidou, Evangelia
AU  - Baranek, Miroslav
AU  - Carneros, Elena
AU  - Caro, Elena
AU  - Castiglione, Stefano
AU  - Cicatelli, Angela
AU  - Radanović, Aleksandra
AU  - Ebejer, Jean-Paul
AU  - Gackowski, Daniel
AU  - Guarino, Francesco
AU  - Gulya, Andrea
AU  - Hidvegi, Norbert
AU  - Hoenicka, Hans
AU  - Inacio, Vera
AU  - Johannes, Frank
AU  - Karalija, Erna
AU  - Lieberman-Lazarovich, Michal
AU  - Martinelli, Federico
AU  - Maury, Stephane
AU  - Mladenov, Velimir
AU  - Morais-Cecılio, Leonor
AU  - Pecinka, Ales
AU  - Tani, Eleni
AU  - Testillano, Pilar S.
AU  - Todorov, Dimitar
AU  - Valledor, Luis
AU  - Vassileva, Valya
PY  - 2023
UR  - http://fiver.ifvcns.rs/handle/123456789/3777
AB  - 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.
PB  - Frontiers Media S.A.
T2  - Frontiers in Plant Science
T1  - Exploring the crop epigenome: a comparison of DNA methylation profiling techniques
SP  - 1181039
VL  - 14
DO  - 10.3389/fpls.2023.1181039
ER  - 

@article{
author = "Agius, Dolores Rita and Kapazoglou, Aliki and Avramidou, Evangelia and Baranek, Miroslav and Carneros, Elena and Caro, Elena and Castiglione, Stefano and Cicatelli, Angela and Radanović, Aleksandra and Ebejer, Jean-Paul and Gackowski, Daniel and Guarino, Francesco and Gulya, Andrea and Hidvegi, Norbert and Hoenicka, Hans and Inacio, Vera and Johannes, Frank and Karalija, Erna and Lieberman-Lazarovich, Michal and Martinelli, Federico and Maury, Stephane and Mladenov, Velimir and Morais-Cecılio, Leonor and Pecinka, Ales and Tani, Eleni and Testillano, Pilar S. and Todorov, Dimitar and Valledor, Luis and Vassileva, Valya",
year = "2023",
abstract = "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.",
publisher = "Frontiers Media S.A.",
journal = "Frontiers in Plant Science",
title = "Exploring the crop epigenome: a comparison of DNA methylation profiling techniques",
pages = "1181039",
volume = "14",
doi = "10.3389/fpls.2023.1181039"
}

Agius, D. R., Kapazoglou, A., Avramidou, E., Baranek, M., Carneros, E., Caro, E., Castiglione, S., Cicatelli, A., Radanović, A., Ebejer, J., Gackowski, D., Guarino, F., Gulya, A., Hidvegi, N., Hoenicka, H., Inacio, V., Johannes, F., Karalija, E., Lieberman-Lazarovich, M., Martinelli, F., Maury, S., Mladenov, V., Morais-Cecılio, L., Pecinka, A., Tani, E., Testillano, P. S., Todorov, D., Valledor, L.,& Vassileva, V.. (2023). Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. in Frontiers in Plant Science
Frontiers Media S.A.., 14, 1181039.
https://doi.org/10.3389/fpls.2023.1181039

Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanović A, Ebejer J, Gackowski D, Guarino F, Gulya A, Hidvegi N, Hoenicka H, Inacio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecılio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. in Frontiers in Plant Science. 2023;14:1181039.
doi:10.3389/fpls.2023.1181039 .

Agius, Dolores Rita, Kapazoglou, Aliki, Avramidou, Evangelia, Baranek, Miroslav, Carneros, Elena, Caro, Elena, Castiglione, Stefano, Cicatelli, Angela, Radanović, Aleksandra, Ebejer, Jean-Paul, Gackowski, Daniel, Guarino, Francesco, Gulya, Andrea, Hidvegi, Norbert, Hoenicka, Hans, Inacio, Vera, Johannes, Frank, Karalija, Erna, Lieberman-Lazarovich, Michal, Martinelli, Federico, Maury, Stephane, Mladenov, Velimir, Morais-Cecılio, 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" in Frontiers in Plant Science, 14 (2023):1181039,
https://doi.org/10.3389/fpls.2023.1181039 . .

TY  - JOUR
AU  - Guarino, Francesco
AU  - Cicatelli, Angela
AU  - Castiglione, Stefano
AU  - Agius, Dolores
AU  - Orhun, Gul Ebru
AU  - Fragkostefanakis, Sotirios
AU  - Leclercq, Julie
AU  - Dobránszki, Judit
AU  - Kaiserli, Eirini
AU  - Lieberman-Lazarovich, Michal
AU  - Sõmera, Merike
AU  - Sarmiento, Cecilia
AU  - Vettori, Cristina
AU  - Paffetti, Donatella
AU  - Poma, Anna
AU  - Moschou, Panagiotis
AU  - Gašparović, Mateo
AU  - Yousefi, Sanaz
AU  - Vergata, Chiara
AU  - Berger, Margot
AU  - Gallusci, Philippe
AU  - Miladinović, Dragana
AU  - Martinelli, Federico
PY  - 2022
UR  - http://fiver.ifvcns.rs/handle/123456789/2666
AB  - Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
PB  - Lausanne : Frontiers Media S.A.
T2  - Frontiers in Genetics
T1  - An epigenetic alphabet of crop adaptation to climate change
SP  - 818727
VL  - 13
DO  - 10.3389/fgene.2022.818727
ER  - 

@article{
author = "Guarino, Francesco and Cicatelli, Angela and Castiglione, Stefano and Agius, Dolores and Orhun, Gul Ebru and Fragkostefanakis, Sotirios and Leclercq, Julie and Dobránszki, Judit and Kaiserli, Eirini and Lieberman-Lazarovich, Michal and Sõmera, Merike and Sarmiento, Cecilia and Vettori, Cristina and Paffetti, Donatella and Poma, Anna and Moschou, Panagiotis and Gašparović, Mateo and Yousefi, Sanaz and Vergata, Chiara and Berger, Margot and Gallusci, Philippe and Miladinović, Dragana and Martinelli, Federico",
year = "2022",
abstract = "Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.",
publisher = "Lausanne : Frontiers Media S.A.",
journal = "Frontiers in Genetics",
title = "An epigenetic alphabet of crop adaptation to climate change",
pages = "818727",
volume = "13",
doi = "10.3389/fgene.2022.818727"
}

Guarino, F., Cicatelli, A., Castiglione, S., Agius, D., Orhun, G. E., Fragkostefanakis, S., Leclercq, J., Dobránszki, J., Kaiserli, E., Lieberman-Lazarovich, M., Sõmera, M., Sarmiento, C., Vettori, C., Paffetti, D., Poma, A., Moschou, P., Gašparović, M., Yousefi, S., Vergata, C., Berger, M., Gallusci, P., Miladinović, D.,& Martinelli, F.. (2022). An epigenetic alphabet of crop adaptation to climate change. in Frontiers in Genetics
Lausanne : Frontiers Media S.A.., 13, 818727.
https://doi.org/10.3389/fgene.2022.818727

Guarino F, Cicatelli A, Castiglione S, Agius D, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma A, Moschou P, Gašparović M, Yousefi S, Vergata C, Berger M, Gallusci P, Miladinović D, Martinelli F. An epigenetic alphabet of crop adaptation to climate change. in Frontiers in Genetics. 2022;13:818727.
doi:10.3389/fgene.2022.818727 .

Guarino, Francesco, Cicatelli, Angela, Castiglione, Stefano, Agius, Dolores, Orhun, Gul Ebru, Fragkostefanakis, Sotirios, Leclercq, Julie, Dobránszki, Judit, Kaiserli, Eirini, Lieberman-Lazarovich, Michal, Sõmera, Merike, Sarmiento, Cecilia, Vettori, Cristina, Paffetti, Donatella, Poma, Anna, Moschou, Panagiotis, Gašparović, Mateo, Yousefi, Sanaz, Vergata, Chiara, Berger, Margot, Gallusci, Philippe, Miladinović, Dragana, Martinelli, Federico, "An epigenetic alphabet of crop adaptation to climate change" in Frontiers in Genetics, 13 (2022):818727,
https://doi.org/10.3389/fgene.2022.818727 . .