Papers by Václav Brázda
International Journal of Molecular Sciences, Jul 30, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Briefings in Bioinformatics, Mar 1, 2022
Republic. His research interests include molecular virology, noncanonical forms of nucleic acids,... more Republic. His research interests include molecular virology, noncanonical forms of nucleic acids, protein interactions and bioinformatics.
Molecular Biology, 2019
Cruciform structures are preferential targets for many architectural and regulatory proteins, as ... more Cruciform structures are preferential targets for many architectural and regulatory proteins, as well as a number of DNA binding proteins with weak sequence specificity. Some of these proteins are also capable of inducing the formation of cruciform structures upon DNA binding. In this paper we analyzed the amino acid composition of eighteen cruciform binding proteins of Homo sapiens. Comparison with general amino acid frequencies in all human proteins revealed unique differences, with notable enrichment for lysine and serine and/or depletion for alanine, glycine, glutamine, arginine, tyrosine and tryptophan residues. Based on bootstrap resampling and fuzzy cluster analysis, multiple molecular mechanisms of interaction with cruciform DNA structures could be suggested, including those involved in DNA repair, transcription and chromatin regulation. The proteins DEK, HMGB1 and TOP1 in particular formed a very distinctive group. Nonetheless, a strong interaction network connecting nearly all the cruciform binding proteins studied was demonstrated. Data reported here will be very useful for future prediction of new cruciform binding proteins or even construction of predictive tool/web-based application.
Life, Jan 10, 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
International Journal of Molecular Sciences, May 31, 2022
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Microbiology Spectrum
Our manuscript reports for the first time a complete analysis of inverted repeats in all fully se... more Our manuscript reports for the first time a complete analysis of inverted repeats in all fully sequenced bacterial genomes. Thanks to the availability of unique computational resources, we were able to statistically evaluate the presence and localization of these important regulatory sequences in bacterial genomes. This work revealed a strong abundance of these sequences in regulatory regions and provides researchers with a valuable tool for their manipulation.
Non-canonical secondary structures in DNA are increasingly being revealed as critical players in ... more Non-canonical secondary structures in DNA are increasingly being revealed as critical players in DNA metabolism, including modulating the accessibility and activity of promoters. These structures comprise the so-called G-quadruplexes (G4s) that are formed from sequences rich in guanine bases. Using a well-defined transcriptional reporter system, we sought to systematically investigate the impact of the presence of G4 structures on transcription in yeastS. cerevisiae. To this aim, different G4 prone sequences were modeled to vary the chance of intramolecular G4 formation, analyzedin vitroby Thioflavin T binding test and circular dichroism and then placed at the yeastADE2locus on chromosome XV, downstream and adjacent to a P53 response element (RE) and upstream from a minimalCYC1promoter and Luciferase 1 (LUC1) reporter gene in isogenic strains. While the minimalCYC1promoter provides for basal reporter activity, the P53 RE enablesLUC1transactivation under the control of the human P53 ...
Genes
P53, P63, and P73 proteins belong to the P53 family of transcription factors, sharing a common ge... more P53, P63, and P73 proteins belong to the P53 family of transcription factors, sharing a common gene organization that, from the P1 and P2 promoters, produces two groups of mRNAs encoding proteins with different N-terminal regions; moreover, alternative splicing events at C-terminus further contribute to the generation of multiple isoforms. P53 family proteins can influence a plethora of cellular pathways mainly through the direct binding to specific DNA sequences known as response elements (REs), and the transactivation of the corresponding target genes. However, the transcriptional activation by P53 family members can be regulated at multiple levels, including the DNA topology at responsive promoters. Here, by using a yeast-based functional assay, we evaluated the influence that a G-quadruplex (G4) prone sequence adjacent to the p53 RE derived from the apoptotic PUMA target gene can exert on the transactivation potential of full-length and N-terminal truncated P53 family α isoforms...
Briefings in Bioinformatics
In a recently published paper, we have found that SARS-CoV-2 hot-spot mutations are significantly... more In a recently published paper, we have found that SARS-CoV-2 hot-spot mutations are significantly associated with inverted repeat loci and CG dinucleotides. However, fast-spreading strains with new mutations (so-called mink farm mutations, England mutations and Japan mutations) have been recently described. We used the new datasets to check the positioning of mutation sites in genomes of the new SARS-CoV-2 strains. Using an open-access Palindrome analyzer tool, we found mutations in these new strains to be significantly enriched in inverted repeat loci.
Many experimental studies have documented a correlation of pro-inflammatory cytokine elevations w... more Many experimental studies have documented a correlation of pro-inflammatory cytokine elevations with induction and maintenance of neuropathic pain. In our experiments, Wistar rats operated on unilateral chronic constriction injury of the sciatic nerve and sham-operated rats were allowed to survive for 1, 3, 7 and 14 days. Withdrawal thresholds for mechanical allodynia and thermal hyperalgesia were measured in the ipsi- and contralateral hind and fore paws. Expression of TNFa and IL-6 mRNAs was investigated by in situ hybridization and quantified by means of qRT-PCR in L4-L5 (homonymous) and C7-C8 (heteronymous) dorsal root ganglia (DRG). Bilateral up-regulation of TNFa and IL-6 mRNAs was found in the neurons and satellite glial cells of DRG from all investigated segments. TNFa mRNA was peaked in L4-L5 DRG at one day while IL-6 mRNA three days from CCI. Elevation of TNFa and IL-6 mRNAs in C7-C8 DRG was of lower magnitude when compared with L4-L5 DRG. An increased level of cytokine mR...
Wallerian degeneration following mechanical injury of the peripheral nerve is essential stimulus ... more Wallerian degeneration following mechanical injury of the peripheral nerve is essential stimulus for cellular and molecular changes inducing neuropathic pain. Unilateral chronic constriction injury (CCI) of the sciatic nerve was performed aseptically in sixty fore rats. Neuropathic pain induction was tested by withdrawal threshold of mechanoallodynia and thermal hyperalgesia. Expression of TNFa and IL-6 protein as well as mRNA was investigated bilaterally by immunohistochemistry, Western blot, ELISA and in situ hybridization in both lumbar (L4-5) and cervical (C7-8) DRG following CCI for 1, 3, 7 and 14 days. In addition, FluoroRuby (dextran-TRITC) was injected intrathecally in the level of L4-L5 or C7-C8 spinal segments. Although mechanoallodynia and thermal hyperalgesia were detected predominantly in the ipsilateral hind paws from 1 to 14 days, levels of cytokine proteins and mRNA were enhanced bilaterally in both cervical and lumbar DRG. FluoroRuby penetrated from intrathecal spac...
Following mechanical injury to a peripheral nerve, Wallerian degeneration is an essential stimulu... more Following mechanical injury to a peripheral nerve, Wallerian degeneration is an essential stimulus for inducing the cellular and molecular changes that underlie neuropathic pain. Compelling data suggest that hyperalgesia, allodynia and ongoing pain due to peripheral nerve injury are associated with neuroinflammation in the dorsal root ganglia (DRG), which is characterized by an upregulation of pro- and anti-inflammatory cytokines. Unilateral chronic constriction injury (CCI) of the sciatic nerve was performed aseptically in sixty-four rats. Neuropathic pain was measured as the withdrawal thresholds of mechanoallodynia and thermal hyperalgesia. On post-CCI days 1, 3, 7 and 14, expression of TNFa and IL-6 was measured bilaterally in the lumbar (L4-L5) and cervical (C7-C8) DRG using immunohistochemistry, western blot analysis, ELISA and in situ hybridization. In addition, the tracers FluoroRuby and FluoroEmerald were injected intrathecally at the level of lumbar or cervical spinal segm...
International Journal of Molecular Sciences, 2021
R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed... more R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA–DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as important in human diseases. Therefore, its prevalence and distribution in genomes are studied intensively. However, in silico tools for R-loop prediction are limited, and therefore, we have developed the R-loop tracker tool, which was implemented as a part of the DNA Analyser web server. This new tool is focused upon (1) prediction of R-loops in genomic DNA without length and sequence limitations; (2) integration of R-loop tracker results with other tools for nucleic acids analyses, including Genome Browser; (3) internal cross-evaluation of in silico results with experimental data, where available; (4) easy export and correlation analyses with other ge...
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Papers by Václav Brázda