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  - Mladenov, Velimir
AU  - Fotopoulos, Vasileios
AU  - Kaiserli, Eirini
AU  - Karalija, Erna
AU  - Maury, Stephane
AU  - Baranek, Miroslav
AU  - Segal, Na’ama
AU  - Testillano, Pilar S.
AU  - Vassileva, Valya
AU  - Pinto, Glória
AU  - Nagel, Manuela
AU  - Hoenicka, Hans
AU  - Miladinović, Dragana
AU  - Gallusci, Philippe
AU  - Vergata, Chiara
AU  - Kapazoglou, Aliki
AU  - Abraham, Eleni
AU  - Tani, Eleni
AU  - Gerakari, Maria
AU  - Sarri, Efi
AU  - Avramidou, Evangelia
AU  - Gašparović, Mateo
AU  - Martinelli, Federico
PY  - 2021
UR  - http://fiver.ifvcns.rs/handle/123456789/4049
AB  - Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.
PB  - Basel : MDPI
T2  - International Journal of Molecular Sciences
T1  - Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops
IS  - 13
SP  - 7118
VL  - 22
DO  - 10.3390/ijms22137118
ER  - 

@article{
author = "Mladenov, Velimir and Fotopoulos, Vasileios and Kaiserli, Eirini and Karalija, Erna and Maury, Stephane and Baranek, Miroslav and Segal, Na’ama and Testillano, Pilar S. and Vassileva, Valya and Pinto, Glória and Nagel, Manuela and Hoenicka, Hans and Miladinović, Dragana and Gallusci, Philippe and Vergata, Chiara and Kapazoglou, Aliki and Abraham, Eleni and Tani, Eleni and Gerakari, Maria and Sarri, Efi and Avramidou, Evangelia and Gašparović, Mateo and Martinelli, Federico",
year = "2021",
abstract = "Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.",
publisher = "Basel : MDPI",
journal = "International Journal of Molecular Sciences",
title = "Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops",
number = "13",
pages = "7118",
volume = "22",
doi = "10.3390/ijms22137118"
}

Mladenov, V., Fotopoulos, V., Kaiserli, E., Karalija, E., Maury, S., Baranek, M., Segal, N., Testillano, P. S., Vassileva, V., Pinto, G., Nagel, M., Hoenicka, H., Miladinović, D., Gallusci, P., Vergata, C., Kapazoglou, A., Abraham, E., Tani, E., Gerakari, M., Sarri, E., Avramidou, E., Gašparović, M.,& Martinelli, F.. (2021). Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops. in International Journal of Molecular Sciences
Basel : MDPI., 22(13), 7118.
https://doi.org/10.3390/ijms22137118

Mladenov V, Fotopoulos V, Kaiserli E, Karalija E, Maury S, Baranek M, Segal N, Testillano PS, Vassileva V, Pinto G, Nagel M, Hoenicka H, Miladinović D, Gallusci P, Vergata C, Kapazoglou A, Abraham E, Tani E, Gerakari M, Sarri E, Avramidou E, Gašparović M, Martinelli F. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops. in International Journal of Molecular Sciences. 2021;22(13):7118.
doi:10.3390/ijms22137118 .

Mladenov, Velimir, Fotopoulos, Vasileios, Kaiserli, Eirini, Karalija, Erna, Maury, Stephane, Baranek, Miroslav, Segal, Na’ama, Testillano, Pilar S., Vassileva, Valya, Pinto, Glória, Nagel, Manuela, Hoenicka, Hans, Miladinović, Dragana, Gallusci, Philippe, Vergata, Chiara, Kapazoglou, Aliki, Abraham, Eleni, Tani, Eleni, Gerakari, Maria, Sarri, Efi, Avramidou, Evangelia, Gašparović, Mateo, Martinelli, Federico, "Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops" in International Journal of Molecular Sciences, 22, no. 13 (2021):7118,
https://doi.org/10.3390/ijms22137118 . .