Publications

@article{Misova20211914,

title = {Repression of a large number of genes requires interplay between homologous recombination and HIRA},

author = {I Misova and A Pitelova and J Budis and J Gazdarica and T Sedlackova and A Jordakova and Z Benko and M Smondrkova and N Mayerova and K Pichlerova and L Strieskova and M Prevorovsky and J Gregan and L Cipak and T Szemes and S B Polakova},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85102408904&doi=10.1093%2fnar%2fgkab027&partnerID=40&md5=77d6eafd60e9cb1a1c3c8237566b8cc1},

doi = {10.1093/nar/gkab027},

issn = {03051048},

year  = {2021},

date = {2021-01-01},

urldate = {2021-01-01},

journal = {Nucleic Acids Research},

volume = {49},

number = {4},

pages = {1914-1934},

publisher = {Oxford University Press},

abstract = {During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δtranscriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δare closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway. © 2021 The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.},

keywords = {Epigenetics, Transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Šubr2020,

title = {Comparative transcriptome analysis of two cucumber cultivars with different sensitivity to cucumber mosaic virus infection},

author = {Z Šubr and L Predajňa and K Šoltys and B Bokor and J Budiš and M Glasa},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85079843504&doi=10.3390%2fpathogens9020145&partnerID=40&md5=c92697bfc9481af2a87da1aae35966e1},

doi = {10.3390/pathogens9020145},

issn = {20760817},

year  = {2020},

date = {2020-01-01},

journal = {Pathogens},

volume = {9},

number = {2},

publisher = {MDPI AG},

abstract = {Cucumber mosaic virus (CMV), with extremely broad host range including both monocots and dicots around the world, belongs to most important viral crop threats. Either natural or genetically constructed sources of resistance are being intensively investigated; for this purpose, exhaustive knowledge of molecular virus-host interaction during compatible and incompatible infection is required. New technologies and computer-based “omics” on various levels contribute markedly to this topic. In this work, two cucumber cultivars with different response to CMV challenge were tested, i.e., sensitive cv. Vanda and resistant cv. Heliana. The transcriptomes were prepared from both cultivars at 18 days after CMV or mock inoculation. Subsequently, four independent comparative analyses of obtained data were performed, viz. mock-and CMV-inoculated samples within each cultivar, samples from mock-inoculated cultivars to each other and samples from virus-inoculated cultivars to each other. A detailed picture of CMV-influenced genes, as well as constitutive differences in cultivar-specific gene expression was obtained. The compatible CMV infection of cv. Vanda caused downregulation of genes involved in photosynthesis, and induction of genes connected with protein production and modification, as well as components of signaling pathways. CMV challenge caused practically no change in the transcription profile of the cv. Heliana. The main differences between constitutive transcription activity of the two cultivars relied in the expression of genes responsible for methylation, phosphorylation, cell wall organization and carbohydrate metabolism (prevailing in cv. Heliana), or chromosome condensation and glucan biosynthesis (prevailing in cv. Vanda). Involvement of several genes in the resistant cucumber phenotype was predicted; this can be after biological confirmation potentially applied in breeding programs for virus-resistant crops. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

keywords = {Plants, Transcriptomics, Viruses},

pubstate = {published},

tppubtype = {article}

}

@article{Pangallo2019416,

title = {Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation},

author = {D Pangallo and L Kraková and A Puškárová and K Šoltys and M Bučková and J Koreňová and J Budiš and T Kuchta},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85063597246&doi=10.1016%2fj.fm.2019.03.015&partnerID=40&md5=ebfc8c9f9e3d1955df5b867600b581a5},

doi = {10.1016/j.fm.2019.03.015},

issn = {07400020},

year  = {2019},

date = {2019-01-01},

journal = {Food Microbiology},

volume = {82},

pages = {416-425},

publisher = {Academic Press},

abstract = {The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes’ milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening. © 2019 Elsevier Ltd},

keywords = {Bacteria, Food microbiome, Metagenomics, Transcriptomics},

pubstate = {published},

tppubtype = {article}

}

@article{Strieskova20198,

title = {Ultracentrifugation enrichment protocol followed by total RNA sequencing allows assembly of the complete mitochondrial genome},

author = {L Strieskova and I Gazdaricova and M Kajsik and K Soltys and J Budis and O Pos and M Lickova and B Klempa and T Szemes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85064954323&doi=10.1016%2fj.jbiotec.2019.04.019&partnerID=40&md5=90856f6a0fd40fd7eeaf877edfdbdeb3},

doi = {10.1016/j.jbiotec.2019.04.019},

issn = {01681656},

year  = {2019},

date = {2019-01-01},

journal = {Journal of Biotechnology},

volume = {299},

pages = {8-12},

publisher = {Elsevier B.V.},

abstract = {The mitochondrial genome is an independent genetic system in each eukaryotic cell outside the nuclear genome. Mitochondrial DNA (mtDNA) appears in high copy number within one cell, unlike nuclear DNA, which exists in two copies. But nevertheless, mtDNA represent only small part of total cellular DNA what causes problematic analysis and identification of relevant mutations. While most researchers tend to overlook it because of its small size, the mitochondrial genome contains genes that are essential for cellular energetics and survival. Because of the increased awareness on the importance of metabolism and bioenergetics in a wide variety of human diseases, more and more mtDNA studies were performed. Mitochondrial genome research has established the connection between mtDNA and a wide variety of diseases such as cancer or neurodegenerative disorders. At the present time, several methods are known, that allow sequencing of mtDNA. However, genomic analysis is often complicated due to the low content of mtDNA compared to nuclear DNA. For this reason, we have designed a new approach to obtaining the genomic mitochondrial sequence. We chose RNA based sequencing. Since human mtDNA does not contain introns, the reconstruction of whole mitochondrial genome through RNA sequencing seems to be effective. Our method is based on total RNA sequencing coupled with simple ultracentrifugation protocol and de novo assembly. Following our protocol, we were able to assemble a complete mammalian mitochondrial genome with a length of 16,505 bp and an average coverage of 156. The method is a relatively simple and inexpensive which could help in the further research or diagnostics of mtDNA-based diseases. © 2019 Elsevier B.V.},

keywords = {Assembly, Mitochondria, Single nucleotide variants, Transcriptomics},

pubstate = {published},

tppubtype = {article}

}