@article{2-s2.0-85189377322,

title = {Immunostaining for Epigenetic Modifications in Fagopyrum Calli},

author = { A. Tomasiak and K. Sala and A.J. Brąszewska-Zalewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85189377322&doi=10.1007%2f978-1-0716-3794-4_2&partnerID=40&md5=ba44f6e08e628a3d22f30061dfd1067a},

doi = {10.1007/978-1-0716-3794-4_2},

year  = {2024},

date = {2024-01-01},

journal = {Methods in Molecular Biology},

volume = {2791},

pages = {15-22},

publisher = {Humana Press Inc.},

abstract = {Immunostaining is a well-established technique for identifying specific proteins in tissue samples with specific antibodies to identify a single target protein. It is commonly used in research and provides information about cellular localization and protein expression levels. This chapter describes a detailed protocol for immunostaining fixed Fagopyrum calli embedded in Steedman’s wax using nine antibodies raised against histone H3 and H4 methylation and acetylation on several lysines and DNA methylation. © The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85189131499,

title = {Quantitative Analysis of Epigenetic Modifications in Fagopyrum Nuclei with Confocal Microscope, ImageJ, and R Studio},

author = { A. Tomasiak and L.S. Berg and K. Sala and A.J. Brąszewska-Zalewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85189131499&doi=10.1007%2f978-1-0716-3794-4_3&partnerID=40&md5=2e906c642e07c360cc42e16730512155},

doi = {10.1007/978-1-0716-3794-4_3},

year  = {2024},

date = {2024-01-01},

journal = {Methods in Molecular Biology},

volume = {2791},

pages = {23-33},

publisher = {Humana Press Inc.},

abstract = {Epigenetic programming plays a vital role in regulating pluripotency genes, which become activated or inactivated during the processes of dedifferentiation and differentiation during an organism’s development. The analysis of epigenetic modifications has become possible through the technique of immunostaining, where specific antibodies allow the identification of a single target protein. This chapter describes a detailed protocol for the analysis of the epigenetic modifications with the use of confocal microscopy, subsequent image, and statistical analysis on the example of Fagopyrum calli with the use of nine antibodies raised against histone H3 and H4 methylation and acetylation on several lysines as well as DNA methylation. © The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85171857887,

title = {Multi-omics insights into the positive role of strigolactone perception in barley drought response},

author = { A. Daszkowska-Golec and D. Mehta and R.G. Uhrig and A.J. Brąszewska-Zalewska and O. Novák and I.M. Fontana and M. Melzer and T. Płociniczak and M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85171857887&doi=10.1186%2fs12870-023-04450-1&partnerID=40&md5=b4cdbd82982d8b64f033dd023c188683},

doi = {10.1186/s12870-023-04450-1},

issn = {14712229},

year  = {2023},

date = {2023-01-01},

journal = {BMC Plant Biology},

volume = {23},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: Drought is a major environmental stress that affects crop productivity worldwide. Although previous research demonstrated links between strigolactones (SLs) and drought, here we used barley (Hordeum vulgare) SL-insensitive mutant hvd14 (dwarf14) to scrutinize the SL-dependent mechanisms associated with water deficit response. Results: We have employed a combination of transcriptomics, proteomics, phytohormonomics analyses, and physiological data to unravel differences between wild-type and hvd14 plants under drought. Our research revealed that drought sensitivity of hvd14 is related to weaker induction of abscisic acid-responsive genes/proteins, lower jasmonic acid content, higher reactive oxygen species content, and lower wax biosynthetic and deposition mechanisms than wild-type plants. In addition, we identified a set of transcription factors (TFs) that are exclusively drought-induced in the wild-type barley. Conclusions: Critically, we resolved a comprehensive series of interactions between the drought-induced barley transcriptome and proteome responses, allowing us to understand the profound effects of SLs in alleviating water-limiting conditions. Several new avenues have opened for developing barley more resilient to drought through the information provided. Moreover, our study contributes to a better understanding of the complex interplay between genes, proteins, and hormones in response to drought, and underscores the importance of a multidisciplinary approach to studying plant stress response mechanisms. © 2023, BioMed Central Ltd., part of Springer Nature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85170843148,

title = {Global epigenetic analysis revealed dynamic fluctuations in levels of DNA methylation and histone modifications in the calli of Fagopyrum with different capacity for morphogenesis},

author = { A. Tomasiak and K. Sala-Cholewa and L.S. Berg and A.J. Brąszewska-Zalewska and A. Betekhtin},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85170843148&doi=10.1007%2fs11240-023-02595-3&partnerID=40&md5=8648c9098bbba39042e86d738aaaf7a0},

doi = {10.1007/s11240-023-02595-3},

issn = {01676857},

year  = {2023},

date = {2023-01-01},

journal = {Plant Cell, Tissue and Organ Culture},

volume = {155},

number = {3},

pages = {743-757},

publisher = {Springer Science and Business Media B.V.},

abstract = {Buckwheat characterises with high susceptibility to in vitro tissue culture conditions, which have been researched extensively to study a plethora of processes. F. tataricum morphogenic callus (MC) is characterised by its capacity for morphogenesis for up to ten years of culture, displaying an extraordinary level of genome stability, and comprises of proembryogenic cell complexes (PECC),which are the structures resembling somatic embryos arrested on the pre-globular stage. The non-morphogenic callus (NC) that appears on the surface of MC after approximately two years of culture due to endoreduplication cycles, is characterised by aneuploidy, rapid growth rate and high level of oxidative stress. F. esculentum embryogenic callus (EC) has different morphological and histological features, remains stable for up to three years of culture, has a dense, globular structure, and is capable of forming embryoids from the masses of embryogenic cells, but does not produce a non-embryogenic clone. In this work, immunocytochemical analyses revealed dynamic epigenetic changes in Fagopyrum calli. We demonstrated that; decreased level of H3K4me2 seems to be associated with pluripotency acquisition in F. esculentum EC and F. tataricum MC; DNA hypomethylation appears to be connected with the acquisition of the embryogenic potential and PECC reinitiation in F. tataricum MC. Moreover, we observed that H4K16ac and H4K5ac exhibited the highest variability during the course of passage in NC. Elevated levels of these modifications on day zero and day six for H4K16ac and H4K5ac, respectively, seem to be connected with endoreplication peaks, the processes which are characteristic of this callus. © 2023, The Author(s).},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85140431417,

title = {Airborne Bacteria in Gliwice—The Industrialized City in Poland},

author = { M.A. Kowalski and J.S. Pastuszka and A.J. Brąszewska-Zalewska and J. Cyrys and E. Bra̧goszewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85140431417&doi=10.3390%2fatmos13101721&partnerID=40&md5=2264e218f5915f5f466bf871132c05db},

doi = {10.3390/atmos13101721},

issn = {20734433},

year  = {2022},

date = {2022-01-01},

journal = {Atmosphere},

volume = {13},

number = {10},

publisher = {MDPI},

abstract = {The results of the study on the characteristics of the viable (culturable) and total bacterial particles in the ambient air in Gliwice, Poland, are presented. The concentration of viable bacteria in the air ranged from 57 CFU m−3 (Colony Forming Units per cubic meter) during winter to 305 CFU m−3 in spring, while the concentration of all bacteria (live and dead) in the air, measured in selected days, ranged from 298 cells m−3 in winter to over 25 thousand per m3 in autumn. A field study was also carried out to find out the level of the sterilization rate (k) for airborne bacteria. The obtained value of k for viable bacteria exposed to UV solar radiation in Gliwice was approximately 10 cm2 W−1s−1. The patterns of the size distributions of viable bacteria found in three seasons, spring, summer, and autumn, were similar, showing a peak in the range of 3.3–4.7 µm. In the winter season, the main peak was shifted into the smaller particles with an aerodynamic diameter ranging from 2.1 to 4.7 µm. The dominant group of culturable bacteria within the studied period was Gram-positive rods-forming endospores (34–55%), while the least frequent were Gram-negative rods (2%). This research can be used to assess the health effects of exposure to bacterial aerosols in people living in this area. © 2022 by the authors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85126018562,

title = {Insights into the Histone Acetylation-Mediated Regulation of the Transcription Factor Genes That Control the Embryogenic Transition in the Somatic Cells of Arabidopsis},

author = { J. Morończyk and A.J. Brąszewska-Zalewska and B. Wójcikowska and K. Chwiałkowska and K. Nowak and A.M. Wójcik and M. Kwaśniewski and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85126018562&doi=10.3390%2fcells11050863&partnerID=40&md5=b2d79e5ee5e0aad3ef0629dc7393c322},

doi = {10.3390/cells11050863},

issn = {20734409},

year  = {2022},

date = {2022-01-01},

journal = {Cells},

volume = {11},

number = {5},

publisher = {MDPI},

abstract = {Somatic embryogenesis (SE), which is a process that involves the in vitro-induced embryo-genic reprogramming of plant somatic cells, requires dynamic changes in the cell transcriptome. These changes are fine-tuned by many genetic and epigenetic factors, including posttranslational histone modifications such as histone acetylation. Antagonistically acting enzymes, histone acetyltransferases (HATs) and deacetylases (HDACs), which control histone acetylation in many developmental pro-cesses, are believed to control SE. However, the function of specific HAT/HDACs and the genes that are subjected to histone acetylation-mediated regulation during SE have yet to be revealed. Here, we present the global and gene-specific changes in histone acetylation in Arabidopsis explants that are undergoing SE. In the TSA (trichostatin A)-induced SE, we demonstrate that H3 and H4 acetylation might control the expression of the critical transcription factor (TF) genes of a vital role in SE, including LEC1, LEC2 (LEAFY COTYLEDON 1; 2), FUS3 (FUSCA 3) and MYB118 (MYB DOMAIN PROTEIN 118). Within the HATs and HDACs, which mainly positively regulate SE, we identified HDA19 as negatively affecting SE by regulating LEC1, LEC2 and BBM. Finally, we provide some evidence on the role of HDA19 in the histone acetylation-mediated regulation of LEC2 during SE. Our results reveal an essential function of histone acetylation in the epigenetic mechanisms that control the TF genes that play critical roles in the embryogenic reprogramming of plant somatic cells. The results implicate the complexity of Hac-related gene regulation in embryogenic induction and point to differences in the regulatory mechanisms that are involved in auxin-and TSA-induced SE. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85109312579,

title = {Dna methylation—an epigenetic mark in mutagen-treated brachypodium distachyon cells},

author = { A.W. Bara and A.J. Brąszewska-Zalewska and J. Kwaśniewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85109312579&doi=10.3390%2fplants10071408&partnerID=40&md5=b16ce0dc3093d3f07d410ec9fd6c6159},

doi = {10.3390/plants10071408},

issn = {22237747},

year  = {2021},

date = {2021-01-01},

journal = {Plants},

volume = {10},

number = {7},

publisher = {MDPI AG},

abstract = {The chromatin structure is significantly influenced by some epigenetic modifications including DNA methylation. The nuclear organization plays an essential role in the cell response to external stresses including mutagens. We present an analysis of the correlation between epigenetic modifications and the instability of the Brachypodium distachyon genome, which are observed as mi-cronuclei, following maleic hydrazide (MH) and nitroso-N-methylurea (MNU) treatments. We compared the level of DNA methylation in the control (untreated) and mutagen-treated B. distachyon nuclei. An immunostaining method using specific antibodies against modified DNA anti-5-methyl-cytosine was used for the evaluation of DNA methylation in a single nucleus and micronucleus. Interestingly, we showed an alteration of DNA methylation in cells after mutagenic treatments. The results indicate that DNA methylation might be involved in the response of the B. distachyon genome to mutagenic treatments. This demonstrates that analyses of the epigenetic modifications should be integrated into current plant genetic toxicology in order to explain the mechanisms of DNA damage and repair in plants. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85100110960,

title = {Defining the cell wall, cell cycle and chromatin landmarks in the responses of brachypodium distachyon to salinity},

author = { E.A. Wolny and A. Skalska and A.J. Brąszewska-Zalewska and L.A.J. Mur and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85100110960&doi=10.3390%2fijms22020949&partnerID=40&md5=aacee36bf01649a69d0bc62ec3e40d65},

doi = {10.3390/ijms22020949},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {2},

pages = {1-23},

publisher = {MDPI AG},

abstract = {Excess salinity is a major stress that limits crop yields. Here, we used the model grass Brachypodium distachyon (Brachypodium) reference line Bd21 in order to define the key molecular events in the responses to salt during germination. Salt was applied either throughout the germination period (“salt stress”) or only after root emergence (“salt shock”). Germination was affected at ≥100 mM and root elongation at ≥75 mM NaCl. The expression of arabinogalactan proteins (AGPs), FLA1, FLA10, FLA11, AGP20 and AGP26, which regulate cell wall expansion (especially FLA11), were mostly induced by the “salt stress” but to a lesser extent by “salt shock”. Cytological assessment using two AGP epitopes, JIM8 and JIM13 indicated that “salt stress” increases the fluorescence signals in rhizodermal and exodermal cell wall. Cell division was suppressed at >75 mM NaCl. The cell cycle genes (CDKB1; CDKB2; CYCA3; CYCB1; WEE1) were induced by “salt stress” in a concentration-dependent manner but not CDKA, CYCA and CYCLIN-D4-1-RELATED. Under “salt shock”, the cell cycle genes were optimally expressed at 100 mM NaCl. These changes were consistent with the cell cycle arrest, possibly at the G1 phase. The salt-induced genomic damage was linked with the oxidative events via an increased glutathione accumulation. Histone acetylation and methylation and DNA methylation were visualized by immunofluorescence. Histone H4 acetylation at lysine 5 increased strongly whereas DNA methylation decreased with the application of salt. Taken together, we suggest that salt-induced oxidative stress causes genomic damage but that it also has epigenetic effects, which might modulate the cell cycle and AGP expression gene. Based on these landmarks, we aim to encourage functional genomics studies on the responses of Brachypodium to salt. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85096048767,

title = {Diverse roles of max1 homologues in rice},

author = { M. Marzec and A. Situmorang and P.B. Brewer and A.J. Brąszewska-Zalewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096048767&doi=10.3390%2fgenes11111348&partnerID=40&md5=3076172ff4c3df945998075a69bb0bf9},

doi = {10.3390/genes11111348},

issn = {20734425},

year  = {2020},

date = {2020-01-01},

journal = {Genes},

volume = {11},

number = {11},

pages = {1-33},

publisher = {MDPI AG},

abstract = {Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85078293343,

title = {Prime Editing: A New Way for Genome Editing},

author = { M. Marzec and A.J. Brąszewska-Zalewska and G. Hensel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078293343&doi=10.1016%2fj.tcb.2020.01.004&partnerID=40&md5=d0dadda1407e926632f5e2d681e92a0b},

doi = {10.1016/j.tcb.2020.01.004},

issn = {09628924},

year  = {2020},

date = {2020-01-01},

journal = {Trends in Cell Biology},

volume = {30},

number = {4},

pages = {257-259},

publisher = {Elsevier Ltd},

abstract = {Precise and efficient use of genome editing tools are hampered by the introduction of DNA double-strand breaks, donor DNA templates, or homology-directed repair. A recent study expands the genome editing toolbox with the introduction of prime editing, which overcomes previous challenges and introduces insertions, deletions, and all putative 12 types of base-to-base conversions in human cells. © 2020 Elsevier Ltd},

note = {24},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85068470318,

title = {BABA-induced DNA methylome adjustment to intergenerational defense priming in potato to Phytophthora infestans},

author = { D. Kuźnicki and B. Meller and M. Arasimowicz-Jelonek and A.J. Brąszewska-Zalewska and A. Drozda and J. Floryszak-Wieczorek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85068470318&doi=10.3389%2ffpls.2019.00650&partnerID=40&md5=2957c650835652de73890865e141e86b},

doi = {10.3389/fpls.2019.00650},

issn = {1664462X},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Plant Science},

volume = {10},

publisher = {Frontiers Media S.A.},

abstract = {We provide evidence that alterations in DNA methylation patterns contribute to the regulation of stress-responsive gene expression for an intergenerational resistance of β-aminobutyric acid (BABA)-primed potato to Phytophthora infestans. Plants exposed to BABA rapidly modified their methylation capacity toward genome-wide DNA hypermethylation. De novo induced DNA methylation (5-mC) correlated with the up-regulation of Chromomethylase 3 (CMT3), Domains rearranged methyltransferase 2 (DRM2), and Repressor of silencing 1 (ROS1) genes in potato. BABA transiently activated DNA hypermethylation in the promoter region of the R3a resistance gene triggering its downregulation in the absence of the oomycete pathogen. However, in the successive stages of priming, an excessive DNA methylation state changed into demethylation with the active involvement of potato DNA glycosylases. Interestingly, the 5-mC–mediated changes were transmitted into the next generation in the form of intergenerational stress memory. Descendants of the primed potato, which derived from tubers or seeds carrying the less methylated R3a promoter, showed a higher transcription of R3a that associated with an augmented intergenerational resistance to virulent P. infestans when compared to the inoculated progeny of unprimed plants. Furthermore, our study revealed that enhanced transcription of some SA-dependent genes (NPR1; StWRKY1; and PR1) was not directly linked with DNA methylation changes in the promoter region of these genes, but was a consequence of methylation-dependent alterations in the transcriptional network. © 2019 Kuźnicki, Meller, Arasimowicz-Jelonek, Braszewska-Zalewska, Drozda and Floryszak-Wieczorek.},

note = {25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054137635,

title = {Germination and the early stages of seedling development in brachypodium distachyon},

author = { E.A. Wolny and A. Betekhtin and M. Rojek-Jelonek and A.J. Brąszewska-Zalewska and J. Lusinska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054137635&doi=10.3390%2fijms19102916&partnerID=40&md5=6bc3a0bce97cc709e1970b6a859568af},

doi = {10.3390/ijms19102916},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {10},

publisher = {MDPI AG},

abstract = {Successful germination and seedling development are crucial steps in the growth of a new plant. In this study, we investigated the course of the cell cycle during germination in relation to grain hydration in the model grass Brachypodium distachyon (Brachypodium) for the first time. Flow cytometry was performed to monitor the cell cycle progression during germination and to estimate DNA content in embryo tissues. The analyses of whole zygotic embryos revealed that the relative DNA content was 2C, 4C, 8C, and 16C. Endoreplicated nuclei were detected in the scutellum and coleorhiza cells, whereas the rest of the embryo tissues only had nuclei with a 2C and 4C DNA content. This study was accompanied by a spatiotemporal profile analysis of the DNA synthetic activity in the organs of Brachypodium embryos during germination using EdU labelling. Upon imbibition, nuclear DNA replication was initiated in the radicle within 11 h and subsequently spread towards the plumule. The first EdU-labelled prophases were observed after 14 h of imbibition. Analysis of selected genes that are involved in the regulation of the cell cycle, such as those encoding cyclin-dependent kinases and cyclins, demonstrated an increase in their expression profiles. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85013775595,

title = {Histone H3 and H4 acetylation patterns are more dynamic than those of DNA methylation in Brachypodium distachyon embryos during seed maturation and germination},

author = { E.A. Wolny and A.J. Brąszewska-Zalewska and D. Kroczek and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85013775595&doi=10.1007%2fs00709-017-1088-x&partnerID=40&md5=8beaeb9cef0bb0cad966271c94b002e0},

doi = {10.1007/s00709-017-1088-x},

issn = {0033183X},

year  = {2017},

date = {2017-01-01},

journal = {Protoplasma},

volume = {254},

number = {5},

pages = {2045-2052},

publisher = {Springer-Verlag Wien},

abstract = {The transition of seeds from a dry to a metabolically active state requires significant changes in both the spatial and temporal patterns of gene expression, and this transcriptional reprogramming involves various modifications of the chromatin structure. There are several factors that can greatly influence the structure of chromatin, one of which is the chemical modifications of histone proteins and DNA itself. In this study, we analysed the distribution of three epigenetic markers, i.e. acetylation of histone H4 (H4K16ac) and histone H3 (H3K18ac) as well as DNA methylation (5mC) in Brachypodium distachyon embryos during the four stages of seed development—maturation, desiccation (quiescence), imbibition and germination. Our results indicate that both H4K16ac and H3K18ac are at a very high level in embryos during seed imbibition, but that the patterns of DNA methylation are considerably more stable in embryos during seed development. © 2017, The Author(s).},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85021211772,

title = {Epigenomic diversification within the genus Lupinus},

author = { K. Susek and A.J. Brąszewska-Zalewska and A.J. Bewick and R. Hasterok and R.J. Schmitz and B. Naganowska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021211772&doi=10.1371%2fjournal.pone.0179821&partnerID=40&md5=d1e72da8b641004db9c57e2d2f85606f},

doi = {10.1371/journal.pone.0179821},

issn = {19326203},

year  = {2017},

date = {2017-01-01},

journal = {PLoS ONE},

volume = {12},

number = {6},

publisher = {Public Library of Science},

abstract = {Deciphering the various chemical modifications of both DNA and the histone compound of chromatin not only leads to a better understanding of the genome-wide organisation of epigenetic landmarks and their impact on gene expression but may also provide some insights into the evolutionary processes. Although both histone modifications and DNA methylation have been widely investigated in various plant genomes, here we present the first study for the genus Lupinus. Lupins, which are members of grain legumes (pulses), are beneficial for food security, nutrition, health and the environment. In order to gain a better understanding of the epigenetic organisation of genomes in lupins we applied the immunostaining of methylated histone H3 and DNA methylation as well as whole-genome bisulfite sequencing. We revealed variations in the patterns of chromatin modifications at the chromosomal level among three crop lupins, i.e. L. angustifolius (2n = 40), L. albus (2n = 50) and L. luteus (2n = 52), and the legume model plant Medicago truncatula (2n = 16). Different chromosomal patterns were found depending on the specific modification, e.g. H3K4me2 was localised in the terminal parts of L. angustifolius and M. truncatula chromosomes, which is in agreement with the results that have been obtained for other species. Interestingly, in L. albus and L. luteus this modification was limited to one arm in the case of all of the chromosomes in the complement. Additionally, H3K9me2 was detected in all of the analysed species except L. luteus. DNA methylation sequencing (CG; CHG and CHH contexts) of aforementioned crop but also wild lupins such as L. cosentinii (2n = 32), L. digitatus (2n = 36), L. micranthus (2n = 52) and L. pilosus (2n = 42) supported the range of interspecific diversity. The examples of epigenetic modifications illustrate the diversity of lupin genomes and could be helpful for elucidating further epigenetic changes in the evolution of the lupin genome. © 2017 Susek et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85018650559,

title = {Ovaries of the white worm (Enchytraeus albidus, Annelida, Clitellata) are composed of 16-celled meroistic germ-line cysts},

author = { A.Z. Urbisz and Ł. Chajec and A.J. Brąszewska-Zalewska and J. Kubrakiewicz and P. Świątek},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85018650559&doi=10.1016%2fj.ydbio.2017.04.009&partnerID=40&md5=335b711be43689e8276747bd0ec658e1},

doi = {10.1016/j.ydbio.2017.04.009},

issn = {00121606},

year  = {2017},

date = {2017-01-01},

journal = {Developmental Biology},

volume = {426},

number = {1},

pages = {28-42},

publisher = {Academic Press Inc.},

abstract = {The paired ovaries of E. albidus are like a bunch of grapes and are composed of clearly separated units, syncytial germ cysts (clusters), which are surrounded by a thin layer of somatic cells. Each cyst maintains the connection with the ovary by an extended stalk that is composed of somatic cells. The spatial architecture of the germ-line cysts found in E. albidus is the same as in other clitellate annelids that have been studied to date. As a rule, germ cells are located at the cyst periphery and each has only one ring canal that connects it to the common and centrally located cytoplasmic mass, the cytophore. Here we present data about the F-actin and microtubular cytoskeleton and some molecular components of the germ-line cysts. We show that the ring canals have an inner rim that is enriched with microfilaments and proteins that contain phosphotyrosine. The microtubules form a loose network in the cytoplasm of the oocyte and nurse cells; moreover, some of them pass through the ring canals to the cytophore. Numerous microtubules are also located in the somatic cells. The germ-line cysts in E. albidus ovaries consist of 16 cells, which is the lowest known number of interconnected germ cells within clitellate annelids. During oogenesis, the fate of interconnected germ cells differentiates and only one cell develops as the future egg, while the other 15 become nurse cells. This differentiation means ovary meroism. The nurse cells gather cell organelles and storage material that then pass through the ring canals and cytophore moving towards the growing oocyte. At the end of oogenesis, the vitellogenic oocyte surrounds the siblings’ cells together with the cytophore and engulfs their remnants into the ooplasm. No morphological or molecular markers of the apoptosis of the nurse cells were found. Moreover, the nurse cells did not undergo polyploidisation. The measured DNA level was 4 C, which indicates that these cells are not highly-specialised. © 2017 Elsevier Inc.},

note = {19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84998631680,

title = {DNA replication after mutagenic treatment in Hordeum vulgare},

author = { J. Kwaśniewska and A. Kus and M. Swoboda and A.J. Brąszewska-Zalewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84998631680&doi=10.1016%2fj.mrgentox.2016.10.006&partnerID=40&md5=fb1288a84b96b55dfee37c8008069a19},

doi = {10.1016/j.mrgentox.2016.10.006},

issn = {13835718},

year  = {2016},

date = {2016-01-01},

journal = {Mutation Research - Genetic Toxicology and Environmental Mutagenesis},

volume = {812},

pages = {20-28},

publisher = {Elsevier B.V.},

abstract = {The temporal and spatial properties of DNA replication in plants related to DNA damage and mutagenesis is poorly understood. Experiments were carried out to explore the relationships between DNA replication, chromatin structure and DNA damage in nuclei from barley root tips. We quantitavely analysed the topological organisation of replication foci using pulse EdU labelling during the S phase and its relationship with the DNA damage induced by mutagenic treatment with maleic hydrazide (MH), nitroso-N-methyl-urea (MNU) and gamma ray. Treatment with mutagens did not change the characteristic S-phase patterns in the nuclei; however, the frequencies of the S-phase-labelled cells after treatment differed from those observed in the control cells. The analyses of DNA replication in barley nuclei were extended to the micronuclei induced by mutagens. Replication in the chromatin of the micronuclei was rare. The results of simultanous TUNEL reaction to identify cells with DNA strand breaks and the labelling of the S-phase cells with EdU revealed the possibility of DNA replication occurring in damaged nuclei. For the first time, the intensity of EdU fluorescence to study the rate of DNA replication was analysed. © 2016 Elsevier B.V.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84982170413,

title = {Functional analysis of the new barley gene HvKu80 indicates that it plays a key role in double-strand DNA break repair and telomere length regulation},

author = { M. Stolarek and D. Gruszka and A.J. Brąszewska-Zalewska and M. Maluszynski},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84982170413&doi=10.1093%2fmutage%2fgev033&partnerID=40&md5=62c7781e376e0346a571d5b2399c2368},

doi = {10.1093/mutage/gev033},

issn = {02678357},

year  = {2015},

date = {2015-01-01},

journal = {Mutagenesis},

volume = {30},

number = {6},

pages = {785-797},

publisher = {Oxford University Press},

abstract = {Genotoxic stress causes a reduced stability of the plant genome and has a detrimental effect on plant growth and productivity. Double-strand breaks (DSBs) are the most harmful of all DNA lesions because they cause the loss of genetic information on both strands of the DNA helix. In the presented study the coding and genomic sequences of the HvKu80 gene were determined. A mutational analysis of two fragments of HvKu80 using TILLING (Targeting Induced Local Lesions IN Genomes) allowed 12 mutations to be detected, which resulted in identification of 11 alleles. Multidirectional analyses demonstrated that the HvKu80 gene is involved in the elimination of DSBs in Hordeum vulgare. The barley mutants carrying the identified ku80.c and ku80.j alleles accumulated bleomycin-induced DSBs to a much greater extent than the parent cultivar 'Sebastian'. The altered reaction of the mutants to DSB-inducing agent and the kinetics of DNA repair in these genotypes are associated with a lower expression level of the mutated gene. The study also demonstrated the significant role of the HvKu80 gene in the regulation of telomere length in barley. © The Author 2015. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society. All rights reserved.},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84939940248,

title = {Alleles of newly identified barley gene HvPARP3 exhibit changes in efficiency of DNA repair},

author = { M. Stolarek and D. Gruszka and A.J. Brąszewska-Zalewska and M. Maluszynski},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84939940248&doi=10.1016%2fj.dnarep.2015.02.018&partnerID=40&md5=c463b719252b1fff6815ff799bf586b4},

doi = {10.1016/j.dnarep.2015.02.018},

issn = {15687864},

year  = {2015},

date = {2015-01-01},

journal = {DNA Repair},

volume = {28},

pages = {116-130},

publisher = {Elsevier B.V.},

abstract = {Genome integrity is constantly challenged by endo- and exogenous DNA-damaging factors. The influence of genotoxic agents causes an accumulation of DNA lesions, which if not repaired, become mutations that can cause various abnormalities in a cell metabolism. The main pathway of DSB repair, which is based on non-homologous recombination, is canonical non-homologous end joining (C-NHEJ). It has been shown that this mechanism is highly conserved in both Pro- and Eukaryotes. The mechanisms that underlie DSB repair through C-NHEJ have mainly been investigated in mammalian systems, and therefore our knowledge about this process is much more limited as far as plants, and crop plants in particular, are concerned. Recent studies have demonstrated that PARP3 is an important response factor to the presence of DSB in a genome. The aims of this study were to identify the sequence of the barley PARP3 gene, to perform a mutational analysis of the sequence that was identified using the TILLING (Targeting Induced Local Lesions IN Genomes) method and to phenotype the mutants that were identified through their exposure to mutagenic treatment with the DSB-inducing chemical - bleomycin. A functional analysis led to the identification of a series of parp3 alleles. The mutants were characterized using several different approaches, including quantifying the DSB and γH2AX foci, which validated the function of the HvPARP3 gene in DSB repair in barley. The potential involvement of the HvPARP3 gene in the regulation of telomere length in barley was also analyzed. © 2015 Elsevier B.V.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84944031628,

title = {In situ analysis of epigenetic modifications in the chromatin of Brachypodium distachyon embryos},

author = { E.A. Wolny and A.J. Brąszewska-Zalewska and D. Kroczek and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84944031628&doi=10.1080%2f15592324.2015.1011948&partnerID=40&md5=3b979188a97b567a2cf78e22419d2247},

doi = {10.1080/15592324.2015.1011948},

issn = {15592316},

year  = {2015},

date = {2015-01-01},

journal = {Plant Signaling and Behavior},

volume = {10},

number = {5},

pages = {1-2},

publisher = {Taylor and Francis Inc.},

abstract = {Epigenetic modifications of the chromatin structure are crucial for many biological processes and act on genes during the development and germination of seeds. The spatial distribution of 3 epigenetic markers, i.e. H4K5ac, H3K4me2 and H3K4me1 was investigated in ‘matured,’ ‘dry,’ ‘imbibed” and ‘germinating’ embryos of a model grass, Brachypodium. Our results indicate that the patterns of epigenetic modification differ in the various types of tissues of embryos that were analyzed. Such a tissue-specific manner of these modifications may be linked to the switch of the gene expression profiles in various organs of the developing embryo. © 2015 Taylor & Francis Group, LLC.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84927171771,

title = {Epigenetic chromatin modifications in barley after mutagenic treatment},

author = { A.J. Brąszewska-Zalewska and M. Tylikowska and J. Kwaśniewska and J. Szymanowska-Pułka},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84927171771&doi=10.1007%2fs13353-014-0226-9&partnerID=40&md5=daed2705cdd37a3b44710696de5374b9},

doi = {10.1007/s13353-014-0226-9},

issn = {12341983},

year  = {2014},

date = {2014-01-01},

journal = {Journal of Applied Genetics},

volume = {55},

number = {4},

pages = {449-456},

publisher = {Springer Verlag},

abstract = {In addition to their normal developmental processes, plants have evolved complex genetic and epigenetic regulatory mechanisms to cope with various environmental stresses. It has been shown that both DNA methylation and histone modifications are involved in DNA damage response to various types of stresses. In this study, we focused on the involvement of two mutagenic agents, chemical (maleic acid hydrazide; MH) and physical (gamma rays), on the global epigenetic modifications of chromatin in barley. Our results indicate that both mutagens strongly influence the level of histone methylation and acetylation. Moreover, we found that gamma irradiation, in contrast to MH, has a more robust influence on the DNA methylation level. This is the first study that brings together mutagenic treatment along with its impact at the level of epigenetic modifications examined using the immunohistochemical method. © The Author(s) 2014},

note = {7},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84904103572,

title = {Spatial distribution of epigenetic modifications in Brachypodium distachyon embryos during seed maturation and germination},

author = { E.A. Wolny and A.J. Brąszewska-Zalewska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84904103572&doi=10.1371%2fjournal.pone.0101246&partnerID=40&md5=73dbd091faa86c9270cf0ac270eeb31e},

doi = {10.1371/journal.pone.0101246},

issn = {19326203},

year  = {2014},

date = {2014-01-01},

journal = {PLoS ONE},

volume = {9},

number = {7},

publisher = {Public Library of Science},

abstract = {Seed development involves a plethora of spatially and temporally synchronised genetic and epigenetic processes. Although it has been shown that epigenetic mechanisms, such as DNA methylation and chromatin remodelling, act on a large number of genes during seed development and germination, to date the global levels of histone modifications have not been studied in a tissue-specific manner in plant embryos. In this study we analysed the distribution of three epigenetic markers, i.e. H4K5ac, H3K4me2 and H3K4me1 in 'matured', 'dry' and 'germinating' embryos of a model grass, Brachypodium distachyon (Brachypodium). Our results indicate that the abundance of these modifications differs considerably in various organs and tissues of the three types of Brachypodium embryos. Embryos from matured seeds were characterised by the highest level of H4K5ac in RAM and epithelial cells of the scutellum, whereas this modification was not observed in the coleorhiza. In this type of embryos H3K4me2 was most evident in epithelial cells of the scutellum. In 'dry' embryos H4K5ac was highest in the coleorhiza but was not present in the nuclei of the scutellum. H3K4me1 was the most elevated in the coleoptile but absent from the coleorhiza, whereas H3K4me2 was the most prominent in leaf primordia and RAM. In embryos from germinating seeds H4K5ac was the most evident in the scutellum but not present in the coleoptile, similarly H3K4me1 was the highest in the scutellum and very low in the coleoptile, while the highest level of H3K4me2 was observed in the coleoptile and the lowest in the coleorhiza. The distinct patterns of epigenetic modifications that were observed may be involved in the switch of the gene expression profiles in specific organs of the developing embryo and may be linked with the physiological changes that accompany seed desiccation, imbibition and germination. © 2014 Wolny et al.},

note = {18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84881192851,

title = {Tissue-Specific Epigenetic Modifications in Root Apical Meristem Cells of Hordeum vulgare},

author = { A.J. Brąszewska-Zalewska and E.A. Wolny and L. Smialek and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84881192851&doi=10.1371%2fjournal.pone.0069204&partnerID=40&md5=0031f46a741a0280b8b236fbf4964b49},

doi = {10.1371/journal.pone.0069204},

issn = {19326203},

year  = {2013},

date = {2013-01-01},

journal = {PLoS ONE},

volume = {8},

number = {7},

abstract = {Epigenetic modifications of chromatin structure are essential for many biological processes, including growth and reproduction. Patterns of DNA and histone modifications have recently been widely studied in many plant species, although there is virtually no data on the spatial and temporal distribution of epigenetic markers during plant development. Accordingly, we have used immunostaining techniques to investigate epigenetic modifications in the root apical meristem of Hordeum vulgare. Histone H4 acetylation (H4K5ac), histone H3 dimethylation (H3K4me2; H3K9me2) and DNA methylation (5mC) patterns were established for various root meristem tissues. Distinct levels of those modifications were visualised in the root cap, epidermis, cortex and vascular tissues. The lateral root cap cells seem to display the highest level of H3K9me2 and 5mC. In the epidermis, the highest level of 5mC and H3K9me2 was detected in the nuclei from the boundary of the proximal meristem and the elongation zone, while the vascular tissues were characterized by the highest level of H4K5ac. Some of the modified histones were also detectable in the cytoplasm in a highly tissue-specific manner. Immunolocalisation of epigenetic modifications of chromatin carried out in this way, on longitudinal or transverse sections, provides a unique topographic context within the organ, and will provide some answers to the significant biological question of tissue differentiation processes during root development in a monocotyledon plant species. © 2013 Braszewska-Zalewska et al.},

note = {25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84900340838,

title = {Epigenetic modifications of nuclei differ between root meristematic tissues of Hordeum vulgare},

author = { A.J. Brąszewska-Zalewska and R. Hasterok},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84900340838&doi=10.4161%2fpsb.26711&partnerID=40&md5=f129ce337771fa55a6f7c49a8c6972a9},

doi = {10.4161/psb.26711},

issn = {15592316},

year  = {2013},

date = {2013-01-01},

journal = {Plant Signaling and Behavior},

volume = {8},

number = {10},

publisher = {Landes Bioscience},

abstract = {Recent studies on the role of epigenetic modifications during plant development emphasize the fact that both positional information and tissue specificity are essential factors that establish epigenetic marks and thus determine cell fate and differentiation processes. The root apical meristem (RAM), which contains stem cells and generates radial patterns of tissues, is an ideal model for studying the correlation between cell position and cell-type differentiation, with particular emphasis on the patterns, global levels, and landscapes of epigenetic modifications. To date, there has been no clear evidence for differential levels of histone and DNA modification across root meristematic tissues. Our study clearly indicates that levels of modifications with potential epigenetic effects vary between RAM tissues. Of particular interest is that histone H4 acetylation in the epidermis is not simply replication-dependent and probably plays a role in epidermal cell differentiation. © Landes Bioscience.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84856061156,

title = {Histone H3 methylation patterns in Brassica nigra, Brassica juncea, and Brassica carinata species},

author = { A.J. Brąszewska-Zalewska and A. Dziurlikowska and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856061156&doi=10.1139%2fg11-076&partnerID=40&md5=149b29dccb6319dd6b02a475e75a11e5},

doi = {10.1139/g11-076},

issn = {08312796},

year  = {2012},

date = {2012-01-01},

journal = {Genome},

volume = {55},

number = {1},

pages = {68-74},

abstract = {Core histones are subjected to various post-translational modifications, and one of them, most intensively studied in plants, is the methylation of histone H3. In the majority of analyzed plant species, dimethylation of H3 at lysine 9 (H3K9me2) is detected in heterochromatin domains, whereas methylation of H3 at lysine 4 (H3K4me2) is detected in euchromatin domains. The distribution of H3K9me2 in the interphase nucleus seems to be correlated with genome size, chromatin organization, but also with tissue specificity. In this paper, we present the analysis of the pattern and level of histone H3 methylation for two allotetraploid and one diploid Brassica species. We have found that the pattern of H3K9me2 in interphase nuclei from root meristematic tissue is comparable within the analyzed species and includes both heterochromatin and euchromatin, but the level of modification differs not only among species but even among nuclei in the same phase of the cell cycle within one species. Moreover, the differences in the level of H3K9me2 are not directly coupled with DNA content in the nuclei and are probably tissue specific. © 2012 Published by NRC Research Press.},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-77649277105,

title = {Epigenetic chromatin modifications in Brassica genomes},

author = { A.J. Brąszewska-Zalewska and T. Bernaś and J. Małuszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77649277105&doi=10.1139%2fG09-088&partnerID=40&md5=f7aa6fef2d4feab0d21111c2465ebf75},

doi = {10.1139/G09-088},

issn = {08312796},

year  = {2010},

date = {2010-01-01},

journal = {Genome},

volume = {53},

number = {3},

pages = {203-210},

abstract = {Epigenetic modifications such as histone and DNA methylation are highly conserved among eukaryotes, although the nuclear patterns of these modifications vary between different species. Brassica species represent a very attractive model for analysis of epigenetic changes because of their differences in genome size, ploidy level, and the organization of heterochromatin blocks. Brassica rapa and B. oleracea are diploid species, and B. napus is an allotetraploid species that arose from the hybridization of these two diploids. We found that patterns of DNA and histone H3 methyla-tion differ between Brassica species. The most prominent differences concern the two diploids. DNA methylation was present exclusively in the heterochromatin only in B. rapa. In B. oleracea and B. napus this modification was detected in both euchromatin and heterochromatin. A similar pattern was observed for dimethylation of lysine 9. Dimethylation of lysine 4 is a typical marker of euchromatin in Brassica species, like it is in other plant species. We conclude that the diploid species differ in patterns of analyzed epigenetic modifications and the allotetraploid B. napus has combined patterns from both diploids. Differences in patterns of DNA and histone H3 methylation between Brassica species can be attributed mainly to the genome structure and heterochromatin localization rather than ploidy level.},

note = {25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}