@article{2-s2.0-85201389758,

title = {Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana},

author = { B. Wójcikowska and K. Chwiałkowska and K. Nowak and S. Citerne and J. Morończyk and A.M. Wójcik and A. Kiwior-Wesołowska and J. Francikowski and M. Kwaśniewski and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85201389758&doi=10.1186%2fs12864-024-10623-5&partnerID=40&md5=610b94d9150b69d42cedfa57e0bee734},

doi = {10.1186/s12864-024-10623-5},

year  = {2024},

date = {2024-01-01},

journal = {BMC Genomics},

volume = {25},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. Results: To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2;4-dichlorophenoxyacetic acid; 2;4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. Conclusion: The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants. © The Author(s) 2024.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85203646112,

title = {miR156-SPL and miR169-NF-YA Modules Regulate the Induction of Somatic Embryogenesis in Arabidopsis via LEC- and Auxin-Related Pathways},

author = { K. Nowak and A.M. Wójcik and K. Konopka and A. Jarosz and K. Dombert and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85203646112&doi=10.3390%2fijms25179217&partnerID=40&md5=795e29b568cf2506ff073245689df897},

doi = {10.3390/ijms25179217},

year  = {2024},

date = {2024-01-01},

journal = {International Journal of Molecular Sciences},

volume = {25},

number = {17},

publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},

abstract = {The embryogenic transition of plant somatic cells to produce somatic embryos requires extensive reprogramming of the cell transcriptome. The prominent role of transcription factors (TFs) and miRNAs in controlling somatic embryogenesis (SE) induction in plants was documented. The profiling of MIRNA expression in the embryogenic culture of Arabidopsis implied the contribution of the miR156 and miR169 to the embryogenic induction. In the present study, the function of miR156 and miR169 and the candidate targets, SPL and NF-YA genes, were investigated in Arabidopsis SE. The results showed that misexpression of MIRNA156 and candidate SPL target genes (SPL2; 3; 4; 5; 9; 10; 11; 13; 15) negatively affected the embryogenic potential of transgenic explants, suggesting that specific fine-tuning of the miR156 and target genes expression levels seems essential for efficient SE induction. The results revealed that SPL11 under the control of miR156 might contribute to SE induction by regulating the master regulators of SE, the LEC (LEAFY COTYLEDON) genes (LEC1; LEC2; FUS3). Moreover, the role of miR169 and its candidate NF-YA targets in SE induction was demonstrated. The results showed that several miR169 targets, including NF-YA1, 3, 5, 8, and 10, positively regulated SE. We found, that miR169 via NF-YA5 seems to modulate the expression of a master SE regulator LEC1/NF-YA and other auxin-related genes: YUCCA (YUC4; 10) and PIN1 in SE induction. The study provided new insights into miR156-SPL and miR169-NF-YA functions in the auxin-related and LEC-controlled regulatory network of SE. © 2024 by the authors.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85176574335,

title = {The improvement of the in vitro plant regeneration in barley with the epigenetic modifier of histone acetylation, trichostatin A},

author = { K. Nowak and B. Wójcikowska and M. Gajecka and A. Elżbieciak and J. Morończyk and A.M. Wójcik and P. Żemła and S. Citerne and A. Kiwior-Wesołowska and J. Zbieszczyk and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85176574335&doi=10.1007%2fs13353-023-00800-9&partnerID=40&md5=aba91f468acebb6e7ac6030f68dc49f7},

doi = {10.1007/s13353-023-00800-9},

year  = {2024},

date = {2024-01-01},

journal = {Journal of Applied Genetics},

volume = {65},

number = {1},

pages = {13-30},

publisher = {Springer Science and Business Media Deutschland GmbH},

abstract = {Genotype-limited plant regeneration is one of the main obstacles to the broader use of genetic transformation in barley breeding. Thus, developing new approaches that might improve responses of in vitro recalcitrant genotypes remains at the center of barley biotechnology. Here, we analyzed different barley genotypes, including “Golden Promise,” a genotype commonly used in the genetic transformation, and four malting barley cultivars of poor regenerative potential. The expression of hormone-related transcription factor (TF) genes with documented roles in plant regeneration was analyzed in genotypes with various plant-regenerating capacities. The results indicated differential expression of auxin-related TF genes between the barley genotypes in both the explants and the derived cultures. In support of the role of auxin in barley regeneration, distinct differences in the accumulation of free and oxidized auxin were observed in explants and explant-derived callus cultures of barley genotypes. Following the assumption that modifying gene expression might improve plant regeneration in barley, we treated the barley explants with trichostatin A (TSA), which affects histone acetylation. The effects of TSA were genotype-dependent as TSA treatment improved plant regeneration in two barley cultivars. TSA-induced changes in plant regeneration were associated with the increased expression of auxin biosynthesis-involved TFs. The study demonstrated that explant treatment with chromatin modifiers such as TSA might provide a new and effective epigenetic approach to improving plant regeneration in recalcitrant barley genotypes. © 2023, The Author(s).},

note = {4},

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-s2.0-85140796333,

title = {Polish Contribution to Global Research on Somatic Embryogenesis},

author = { A. Mikuła and M.D. Gaj and M. Grzyb and T. Hazubska-Przybył and E. Kȩpczyńska and J. Kȩpczyński and J.J. Rybczyński and K. Tomiczak and A.M. Wójcik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85140796333&doi=10.5586%2fasbp.9115&partnerID=40&md5=7ea17dc93b91bd67a0f5aef943cfa327},

doi = {10.5586/asbp.9115},

issn = {00016977},

year  = {2022},

date = {2022-01-01},

journal = {Acta Societatis Botanicorum Poloniae},

volume = {91},

publisher = {Polish Botanical Society},

abstract = {Somatic embryogenesis (SE) is a complex process that begins with regaining totipotency in some somatic cells, proceeds through embryo development and maturation, and ends with the formation of a whole plant. Since the first publications on SE in 1958, this regeneration process has been applied to the in vitro propagation of many plant species and has led to the development of some specific model systems. SE has been used to expand our understanding of the cytomorphological, physiological, biochemical, and genetic processes that govern the earliest developmental events in the life of plants. This paper summarizes the achievements of Polish research groups working on SE systems established for several plants (gentians; the tree fern Cyathea delgadii Sternb.; and conifers) and three model species (Arabidopsis thaliana; Medicago sativa; and M. truncatula). SE systems have used a broad spectrum of experimental approaches involving genomic tools (transcriptomics; proteomics; and chromatin analyses), physiological methods which focus on phytohormones, and cytological techniques. Studies on the experimental models of A. thaliana and Medicago spp. have resulted in the identification of new genetic and epigenetic elements of the complex regulatory network controlling embryogenic induction in plant somatic cells. The protocol developed for ferns has provided a unique and simple system for cytological analysis of early SE events that occur in a single cell of initial explants. Gentian embryogenic suspension cultures have successfully been used in broad biotechnological applications, including plant transformation, protoplast isolation, culture, and fusion. Systems described for coniferous species effectively produced many vigorous somatic seedlings and cost-efficient storage of genotypes during clonal field-testing. The research undertaken by Polish scientists has resulted in developing experimental systems that have enabled significant advances in SE knowledge. © The Author(s) 2022.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85087908202,

title = {Research tools for the functional genomics of plant mirnas during zygotic and somatic embryogenesis},

author = { A.M. Wójcik},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85087908202&doi=10.3390%2fijms21144969&partnerID=40&md5=bdaae13a12c39a288a74b900b5ebf947},

doi = {10.3390/ijms21144969},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {14},

pages = {1-25},

publisher = {MDPI AG},

abstract = {During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented. © 2020 by the author. Licensee MDPI, Basel, Switzerland.},

note = {2},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85082731253,

title = {Epigenetic regulation of auxin-induced somatic embryogenesis in plants},

author = { B. Wójcikowska and A.M. Wójcik and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85082731253&doi=10.3390%2fijms21072307&partnerID=40&md5=ab1fc9ddb6bd291d0c7e177c7d8313d0},

doi = {10.3390/ijms21072307},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {7},

publisher = {MDPI AG},

abstract = {Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted. © 2020, MDPI AG. All rights reserved.},

note = {30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85079636159,

title = {Current perspectives on the auxin-mediated genetic network that controls the induction of somatic embryogenesis in plants},

author = { A.M. Wójcik and B. Wójcikowska and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079636159&doi=10.3390%2fijms21041333&partnerID=40&md5=280c4b8858da9a30c603d1009ec24500},

doi = {10.3390/ijms21041333},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {4},

publisher = {MDPI AG},

abstract = {Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo-and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2;4-dichlorophenoxyacetic acid; which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down-and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {52},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85090863996,

title = {AGL15 controls the embryogenic reprogramming of somatic cells in arabidopsis through the histone acetylation-mediated repression of the mirna biogenesis genes},

author = { K. Nowak and J. Morończyk and A.M. Wójcik and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85090863996&doi=10.3390%2fijms21186733&partnerID=40&md5=63d2df1c0f8e6e068cb818919a3e59ae},

doi = {10.3390/ijms21186733},

issn = {16616596},

year  = {2020},

date = {2020-01-01},

journal = {International Journal of Molecular Sciences},

volume = {21},

number = {18},

pages = {1-20},

publisher = {MDPI AG},

abstract = {The embryogenic transition of somatic cells requires an extensive reprogramming of the cell transcriptome. Relevantly, the extensive modulation of the genes that have a regulatory function, in particular the genes encoding the transcription factors (TFs) and miRNAs, have been indicated as controlling somatic embryogenesis (SE) that is induced in vitro in the somatic cells of plants. Identifying the regulatory relationships between the TFs and miRNAs during SE induction is of central importance for understanding the complex regulatory interplay that fine-tunes a cell transcriptome during the embryogenic transition. Hence, here, we analysed the regulatory relationships between AGL15 (AGAMOUS-LIKE 15) TF and miR156 in an embryogenic culture of Arabidopsis. Both AGL15 and miR156 control SE induction and AGL15 has been reported to target the MIR156 genes in planta. The results showed that AGL15 contributes to the regulation of miR156 in an embryogenic culture at two levels that involve the activation of the MIR156 transcription and the containment of the abundance of mature miR156 by repressing the miRNA biogenesis genes DCL1 (DICER-LIKE1), SERRATE and HEN1 (HUA-ENHANCER1). To repress the miRNA biogenesis genes AGL15 seems to co-operate with the TOPLESS co-repressors (TPL and TPR1-4), which are components of the SIN3/HDAC silencing complex. The impact of TSA (trichostatin A), an inhibitor of the HDAC histone deacetylases, on the expression of the miRNA biogenesis genes together with the ChIP results implies that histone deacetylation is involved in the AGL15-mediated repression of miRNA processing. The results indicate that HDAC6 and HDAC19 histone deacetylases might co-operate with AGL15 in silencing the complex that controls the abundance of miR156 during embryogenic induction. This study provides new evidence about the histone acetylation-mediated control of the miRNA pathways during the embryogenic reprogramming of plant somatic cells and the essential role of AGL15 in this regulatory mechanism. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054500845,

title = {Trichostatin a triggers an embryogenic transition in arabidopsis explants via an auxin-related pathway},

author = { B. Wójcikowska and M. Botor and J. Morończyk and A.M. Wójcik and T. Nodzyński and J. Karcz and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054500845&doi=10.3389%2ffpls.2018.01353&partnerID=40&md5=cbe7e1e0677493466506c918a06e7cf0},

doi = {10.3389/fpls.2018.01353},

issn = {1664462X},

year  = {2018},

date = {2018-01-01},

journal = {Frontiers in Plant Science},

volume = {9},

publisher = {Frontiers Media S.A.},

abstract = {Auxin is an important regulator of plant ontogenies including embryo development and the exogenous application of this phytohormone has been found to be necessary for the induction of the embryogenic response in plant explants that have been cultured in vitro. However, in the present study, we show that treatment of Arabidopsis explants with trichostatin A (TSA), which is a chemical inhibitor of histone deacetylases, induces somatic embryogenesis (SE) without the exogenous application of auxin. We found that the TSA-treated explants generated somatic embryos that developed efficiently on the adaxial side of the cotyledons, which are the parts of an explant that are involved in auxin-induced SE. A substantial reduction in the activity of histone deacetylase (HDAC) was observed in the TSA-treated explants, thus confirming a histone acetylation-related mechanism of the TSA-promoted embryogenic response. Unexpectedly, the embryogenic effect of TSA was lower on the auxin-supplemented media and this finding further suggests an auxin-related mechanism of TSA-induced SE. Congruently, we found a significantly increased content of indolic compounds, which is indicative of IAA and an enhanced DR5::GUS signal in the TSA-treated explants. In line with these results, two of the YUCCA genes (YUC1 and YUC10), which are involved in auxin biosynthesis, were found to be distinctly up-regulated during TSA-induced SE and their expression was colocalised with the explant sites that are involved in SE. Beside auxin, ROS were extensively accumulated in response to TSA, thereby indicating that a stress-response is involved in TSA-triggered SE. Relevantly, we showed that the genes encoding the transcription factors (TFs) that have a regulatory function in auxin biosynthesis including LEC1, LEC2, BBM, and stress responses (MYB118) were highly up-regulated in the TSA-treated explants. Collectively, the results provide several pieces of evidence about the similarities between the molecular pathways of SE induction that are triggered by TSA and 2,4-D that involve the activation of the auxin-responsive TF genes that have a regulatory function in auxin biosynthesis and stress responses. The study suggests the involvement of histone acetylation in the auxin-mediated release of the embryogenic program of development in the somatic cells of Arabidopsis. © 2018 Wójcikowska, Botor, Morończyk, Wójcik, Nodzyński, Karcz and Gaj.},

note = {36},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85054553781,

title = {Whole mount in situ localization of mirnas and mrnas during somatic embryogenesis in arabidopsis},

author = { A.M. Wójcik and M. Mosiolek and J. Karcz and M.D. Nodine and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054553781&doi=10.3389%2ffpls.2018.01277&partnerID=40&md5=45983ecce8697f5aad654572bc8a0228},

doi = {10.3389/fpls.2018.01277},

issn = {1664462X},

year  = {2018},

date = {2018-01-01},

journal = {Frontiers in Plant Science},

volume = {9},

publisher = {Frontiers Media S.A.},

abstract = {Somatic embryogenesis (SE) results from the transition of differentiated plant somatic cells into embryogenic cells that requires the extensive reprogramming of the somatic cell transcriptome. Commonly, the SE-involved genes are identified by analyzing the heterogeneous population of explant cells and thus, it is necessary to validate the expression of the candidate genes in the cells that are competent for embryogenic transition. Here, we optimized and implemented the whole mount in situ hybridization (WISH) method (Bleckmann and Dresselhaus; 2016; Dastidar et al.; 2016) in order to analyze the spatiotemporal localization of miRNAs (miR156; miR166; miR390; miR167) and mRNAs such as WOX5 and PHABULOSA-target of miR165/166 during the SE that is induced in Arabidopsis explants. This study presents a detailed step-by-step description of the WISH procedure in which DIG-labeled LNA and RNA probes were used to detect miRNAs and mRNAs, respectively. The usefulness of the WISH in the functional analysis of the SE-involved regulatory pathways is demonstrated and the advantages of this method are highlighted: (i) the ability to analyze intact non-sectioned plant tissue; (ii) the specificity of transcript detection; (iii) the detection of miRNA; and (iv) a semi-quantitative assessment of the RNA abundance. © 2018 Wójcik, Mosiolek, Karcz, Nodine and Gaj.},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85038354165,

title = {MiR160 and miR166/165 contribute to the LEC2-mediated auxin response involved in the somatic embryogenesis induction in arabidopsis},

author = { A.M. Wójcik and M.D. Nodine and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85038354165&doi=10.3389%2ffpls.2017.02024&partnerID=40&md5=02bb61c60417ea8910b696b718c48421},

doi = {10.3389/fpls.2017.02024},

issn = {1664462X},

year  = {2017},

date = {2017-01-01},

journal = {Frontiers in Plant Science},

volume = {8},

publisher = {Frontiers Media S.A.},

abstract = {MicroRNAs are non-coding small RNA molecules that are involved in the post-transcriptional regulation of the genes that control various developmental processes in plants, including zygotic embryogenesis (ZE). miRNAs are also believed to regulate somatic embryogenesis (SE), a counterpart of the ZE that is induced in vitro in plant somatic cells. However, the roles of specific miRNAs in the regulation of the genes involved in SE, in particular those encoding transcription factors (TFs) with an essential function during SE including LEAFY COTYLEDON2 (LEC2), remain mostly unknown. The aim of the study was to reveal the function of miR165/166 and miR160 in the LEC2-controlled pathway of SE that is induced in in vitro cultured Arabidopsis explants.In ZE, miR165/166 controls the PHABULOSA/PHAVOLUTA (PHB/PHV) genes, which are the positive regulators of LEC2, while miR160 targets the AUXIN RESPONSE FACTORS (ARF10, ARF16, ARF17) that control the auxin signaling pathway, which plays key role in LEC2-mediated SE. We found that a deregulated expression/function of miR165/166 and miR160 resulted in a significant accumulation of auxin in the cultured explants and the spontaneous formation of somatic embryos. Our results show that miR165/166 might contribute to SE induction via targeting PHB, a positive regulator of LEC2 that controls embryogenic induction via activation of auxin biosynthesis pathway (Wójcikowska et al., 2013). Similar to miR165/166, miR160 was indicated to control SE induction through auxin-related pathways and the negative impact of miR160 on ARF10/ARF16/ARF17 was shown in an embryogenic culture. Altogether, the results suggest that the miR165/166- and miR160-node contribute to the LEC2-mediated auxin-related pathway of embryogenic transition that is induced in the somatic cells of Arabidopsis. A model summarizing the suggested regulatory interactions between the miR165/166-PHB and miR160-ARF10/ARF16/ARF17 nodes that control SE induction in Arabidopsis was proposed. © 2017 Wójcik, Nodine and Gaj.},

note = {44},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85010888075,

title = {MicroRNAs are intensively regulated during induction of somatic embryogenesis in arabidopsis},

author = { K.P. Szyrajew and D. Bielewicz and J. Dolata and A.M. Wójcik and K. Nowak and A. Szczygieł-Sommer and Z. Szweykowska-Kulinska and A. Jarmolowski and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85010888075&doi=10.3389%2ffpls.2017.00018&partnerID=40&md5=d8db68bd8366253f2074f2b48d23b4ca},

doi = {10.3389/fpls.2017.00018},

issn = {1664462X},

year  = {2017},

date = {2017-01-01},

journal = {Frontiers in Plant Science},

volume = {8},

publisher = {Frontiers Media S.A.},

abstract = {Several genes encoding transcription factors (TFs) were indicated to have a key role in the induction of somatic embryogenesis (SE), which is triggered in the somatic cells of plants. In order to further explore the genetic regulatory network that is involved in the embryogenic transition induced in plant somatic cells, micro-RNA (miRNAs) molecules, the products of MIRNA (MIR) genes and the common regulators of TF transcripts, were analyzed in an embryogenic culture of Arabidopsis thaliana. In total, the expression of 190 genes of the 114 MIRNA families was monitored during SE induction and the levels of the primary (pri-miRNAs) transcripts vs. the mature miRNAs were investigated. The results revealed that the majority (98%) of the MIR genes were active and that most of them (64%) were differentially expressed during SE. A distinct attribute of the MIR expression in SE was the strong repression of MIR transcripts at the early stage of SE followed by their significant up-regulation in the advanced stage of SE. Comparison of the mature miRNAs vs. pri-miRNAs suggested that the extensive post-transcriptional regulation of miRNA is associated with SE induction. Candidate miRNA molecules of the assumed function in the embryogenic response were identified among the mature miRNAs that had a differential expression in SE, including miR156, miR157, miR159, miR160, miR164, miR166, miR169, miR319, miR390, miR393, miR396, and miR398. Consistent with the central role of phytohormones and stress factors in SE induction, the functions of the candidate miRNAs were annotated to phytohormone and stress responses. To confirm the functions of the candidate miRNAs in SE, the expression patterns of the mature miRNAs and their presumed targets were compared and regulatory relation during SE was indicated for most of the analyzed miRNA-target pairs. The results of the study contribute to the refinement of the miRNA-controlled regulatory pathways that operate during embryogenic induction in plants and provide a valuable platform for the identification of the genes that are targeted by the candidate miRNAs in SE induction. © 2017 Szyrajew, Bielewicz, Dolata, Wójcik, Nowak, Szczygieł-Sommer, Szweykowska-Kulinska, Jarmolowski and Gaj.},

note = {42},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84962159759,

title = {miR393 contributes to the embryogenic transition induced in vitro in Arabidopsis via the modification of the tissue sensitivity to auxin treatment},

author = { A.M. Wójcik and M.D. Gaj},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84962159759&doi=10.1007%2fs00425-016-2505-7&partnerID=40&md5=4feaadd4e14ac53a53e2c2835f7c1a3e},

doi = {10.1007/s00425-016-2505-7},

issn = {00320935},

year  = {2016},

date = {2016-01-01},

journal = {Planta},

volume = {244},

number = {1},

pages = {231-243},

publisher = {Springer Verlag},

abstract = {Main conclusion: miR393 was found to control embryogenic transition in somatic cells in Arabidopsis via control of theTIR1andAFB2auxin receptors genes of the F-box family. miR393 molecules are believed to regulate the expression of the auxin receptors of the TAAR clade. Considering the central role of auxin in the induction of somatic embryogenesis (SE) in plant explants cultured in vitro, the involvement of miR393 in the embryogenic transition of somatic cells has been hypothesised. To verify this assumption, the reporter, overexpressor and mutant lines in genes encoded MIR393 and TIR1/AFB proteins of the F-box family were analysed during SE in Arabidopsis. Expression profiling of MIR393a and MIR393b, mature miR393 and the target genes (TIR1; AFB1; AFB2; AFB3) were investigated in explants undergoing SE. In addition, the embryogenic potential of various genotypes with a modified activity of the MIR393 and TIR1/AFB targets was evaluated. The distinct increase in the accumulation of miR393 that was coupled with a notable down-regulation of TIR1 and AFB2 targets was observed at the early phase of SE induction. Relevant to this observation, the GUS/GFP monitored expression of MIR393, TIR1 and AFB2 transcripts was localised in explant tissue undergoing SE induction. The results suggest the miR393-mediated regulation of TIR1 and AFB2 during embryogenic transition induced in Arabidopsis and a modification of the explant sensitivity to auxin treatment is proposed as underlying this regulatory pathway. © 2016, The Author(s).},

note = {49},

keywords = {},

pubstate = {published},

tppubtype = {article}

}