The p53 protein is a key tumor suppressor and the most commonly mutated and down-regulated protein in human tumors. It functions mainly through interaction with DNA, and p53 acts as a transcription factor that recognizes the so-called p53 target sites on the promoters of various genes. P53 has been shown to exist as many isoforms, including three C-terminal isoforms that are produced by alternative splicing. Because the C-terminal domain is responsible for sequence-nonspecific binding and regulation of p53 binding, we have analyzed DNA recognition by these C-terminal isoforms. Using atomic force microscopy, we show for the first time that all C-terminal isoforms recognize superhelical DNA. It is particularly noteworthy that a sequence-specific p53 consensus binding site is bound by p53α and β isoforms with similar affinities, whilst p53α shows higher binding to a quadruplex sequence than both p53β and p53γ, and p53γ loses preferential binding to both the consensus binding sequence and the quadruplex-forming sequence. These results show the important role of the variable p53 C-terminal amino acid sequences for DNA recognition.
Noncanonical secondary structures in nucleic acids have been studied intensively in recent years. Important biological roles of cruciform structures formed by inverted repeats (IRs) have been demonstrated in diverse organisms, including humans. Using Palindrome analyser, we analyzed IRs in all accessible bacterial genome sequences to determine their frequencies, lengths, and localizations. IR sequences were identified in all species, but their frequencies differed significantly across various evolutionary groups. We detected 242,373,717 IRs in all 1,565 bacterial genomes. The highest mean IR frequency was detected in the Tenericutes (61.89 IRs/kbp) and the lowest mean frequency was found in the Alphaproteobacteria (27.08 IRs/kbp). IRs were abundant near genes and around regulatory, tRNA, transfer-messenger RNA (tmRNA), and rRNA regions, pointing to the importance of IRs in such basic cellular processes as genome maintenance, DNA replication, and transcription. Moreover, we found that organisms with high IR frequencies were more likely to be endosymbiotic, antibiotic producing, or pathogenic. On the other hand, those with low IR frequencies were far more likely to be thermophilic. This first comprehensive analysis of IRs in all available bacterial genomes demonstrates their genomic ubiquity, nonrandom distribution, and enrichment in genomic regulatory regions. IMPORTANCE 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.
- MeSH
- Bacteria genetika MeSH
- fylogeneze MeSH
- genomika * MeSH
- lidé MeSH
- replikace DNA * MeSH
- sekvence nukleotidů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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 genome features and markers; and (5) enhanced visualization outputs. Our new R-loop tracker tool is freely accessible on the web pages of DNA Analyser tools, and its implementation on the web-based server allows effective analyses not only for DNA segments but also for full chromosomes and genomes.
- MeSH
- algoritmy * MeSH
- DNA chemie genetika MeSH
- genomika metody MeSH
- internet statistika a číselné údaje MeSH
- lidé MeSH
- nestabilita genomu * MeSH
- R-smyčka * MeSH
- software MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
G-quadruplexes contribute to the regulation of key molecular processes. Their utilization for antiviral therapy is an emerging field of contemporary research. Here we present comprehensive analyses of the presence and localization of putative G-quadruplex forming sequences (PQS) in all viral genomes currently available in the NCBI database (including subviral agents). The G4Hunter algorithm was applied to a pool of 11,000 accessible viral genomes representing 350 Mbp in total. PQS frequencies differ across evolutionary groups of viruses, and are enriched in repeats, replication origins, 5'UTRs and 3'UTRs. Importantly, PQS presence and localization is connected to viral lifecycles and corresponds to the type of viral infection rather than to nucleic acid type; while viruses routinely causing persistent infections in Metazoa hosts are enriched for PQS, viruses causing acute infections are significantly depleted for PQS. The unique localization of PQS identifies the importance of G-quadruplex-based regulation of viral replication and life cycle, providing a tool for potential therapeutic targeting.
- MeSH
- databáze nukleových kyselin * MeSH
- DNA virů genetika metabolismus MeSH
- G-kvadruplexy * MeSH
- genom virový * MeSH
- lidé MeSH
- virové nemoci * genetika metabolismus MeSH
- viry * genetika metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The importance of gene expression regulation in viruses based upon G-quadruplex may point to its potential utilization in therapeutic targeting. Here, we present analyses as to the occurrence of putative G-quadruplex-forming sequences (PQS) in all reference viral dsDNA genomes and evaluate their dependence on PQS occurrence in host organisms using the G4Hunter tool. PQS frequencies differ across host taxa without regard to GC content. The overlay of PQS with annotated regions reveals the localization of PQS in specific regions. While abundance in some, such as repeat regions, is shared by all groups, others are unique. There is abundance within introns of Eukaryota-infecting viruses, but depletion of PQS in introns of bacteria-infecting viruses. We reveal a significant positive correlation between PQS frequencies in dsDNA viruses and corresponding hosts from archaea, bacteria, and eukaryotes. A strong relationship between PQS in a virus and its host indicates their close coevolution and evolutionarily reciprocal mimicking of genome organization.
Popisujeme případ 74leté polymorbidní pacientky s těžkou kyfoskoliózou, která byla referována od praktického lékaře k provedení urgentní koronarografie pro akutní infarkt myokardu s elevacemi úseku ST (STEMI) na spodní a zadní stěně levé komory. Cestou pravé arteria radialis byla provedena pouze koronarografie pravé věnčité tepny (ACD), kde byl zjištěn uzávěr v její střední části, levou věnčitou tepnu bylo nutné zobrazit cestou levé arteria radialis pro extrémní vinutí aorty při deformitě páteře. Při následné sondáži ACD vodicím katétrem došlo k rozsáhlé disekci tepny s retrográdním šířením na ascendentní aortu. Případ jsme vyřešili implantací lékových stentů do proximálního a distálního segmentu ACD, další stent jsme implantovali do ostia ACD, čímž jsme pokryli reziduální disekci ACD a současně uzavřeli vstup do disekce ascendentní aorty. Depo kontrastní látky v ascendentní aortě zůstalo konstantní, bez progrese. Zvažovali jsme konzultaci kardiochirurgického pracoviště, nicméně s ohledem na těžkou kyfoskoliózu by případné operační řešení disekce nebylo možné, navíc pacientka byla již hemodynamicky a rytmicky stabilní, proto jsme volili konzervativní postup. Po třech dnech nekomplikované hospitalizace na koronární jednotce byla nemocná přeložena na spádové interní oddělení s duální protidestičkovou léčbou (DAPT). Dle praktického lékaře pacientka nadále žije a má minimální potíže.
We herein describe a case of a 74-year-old polymorbid patient with severe kyphoscoliosis who was referred by her general practitioner for an urgent coronary angiography for acute ST-elevation myocardial infarction (STEMI) of the inferior and posterior wall of the left ventricle. Coronary angiography of the right coronary artery (rCA) was performed via the right radial artery and showed an occlusion of its mid-portion. The left coronary artery had to be visualized through the left radial artery due to an extremely tortuous aorta and the spinal deformity. Extensive dissection with a retrograde flow to the ascending aorta occurred during probing the rCA using a guide catheter. We managed the case by implanting drug stents into the proximal and distal segments of the rCA; another stent was implanted into the ostium of the rCA, thus covering the residual dissection of the rCA and at the same time closing the entrance of the dissection of the ascending aorta. The deposit of the contrast agent in the ascending aorta remained constant and without progression. We considered consulting the department of cardiac surgery; however, with regard to the severe kyphoscoliosis, a surgical solution of the dissection would not be possible. Moreover, the patient was already hemody- namically and rhythmically stable, therefore we chose a conservative approach. After three days of uncomplicated hospitalization at the coronary care unit, the patient was transferred to a catchment department of internal medicine on dual antiplatelet therapy (DAPT). According to her general practitioner, the patient is still living and has minimal difficulties.
The importance of DNA structure in the regulation of basic cellular processes is an emerging field of research. Among local non-B DNA structures, inverted repeat (IR) sequences that form cruciforms and G-rich sequences that form G-quadruplexes (G4) are found in all prokaryotic and eukaryotic organisms and are targets for regulatory proteins. We analyzed IRs and G4 sequences in the genome of the most important biotechnology microorganism, S. cerevisiae. IR and G4-prone sequences are enriched in specific genomic locations and differ markedly between mitochondrial and nuclear DNA. While G4s are overrepresented in telomeres and regions surrounding tRNAs, IRs are most enriched in centromeres, rDNA, replication origins and surrounding tRNAs. Mitochondrial DNA is enriched in both IR and G4-prone sequences relative to the nuclear genome. This extensive analysis of local DNA structures adds to the emerging picture of their importance in genome maintenance, DNA replication and transcription of subsets of genes.
The importance of unusual DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes (G4s) have gained in popularity during the last decade, and their presence and functional relevance at the DNA and RNA level has been demonstrated in a number of viral, bacterial, and eukaryotic genomes, including humans. Here, we performed the first systematic search of G4-forming sequences in all archaeal genomes available in the NCBI database. In this article, we investigate the presence and locations of G-quadruplex forming sequences using the G4Hunter algorithm. G-quadruplex-prone sequences were identified in all archaeal species, with highly significant differences in frequency, from 0.037 to 15.31 potential quadruplex sequences per kb. While G4 forming sequences were extremely abundant in Hadesarchaea archeon (strikingly, more than 50% of the Hadesarchaea archaeon isolate WYZ-LMO6 genome is a potential part of a G4-motif), they were very rare in the Parvarchaeota phylum. The presence of G-quadruplex forming sequences does not follow a random distribution with an over-representation in non-coding RNA, suggesting possible roles for ncRNA regulation. These data illustrate the unique and non-random localization of G-quadruplexes in Archaea.
- MeSH
- Archaea klasifikace genetika metabolismus MeSH
- archeální proteiny genetika metabolismus MeSH
- cirkulární dichroismus MeSH
- DNA vazebné proteiny genetika metabolismus MeSH
- DNA chemie genetika metabolismus MeSH
- druhová specificita MeSH
- fylogeneze MeSH
- G-kvadruplexy * MeSH
- genom archeí genetika MeSH
- genomika metody MeSH
- konformace nukleové kyseliny MeSH
- RNA chemie genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
MOTIVATION: G-quadruplexes (G4) are important regulatory non-B DNA structures with therapeutic potential. A tool for rational design of mutations leading to decreased propensity for G4 formation should be useful in studying G4 functions. Although tools exist for G4 prediction, no easily accessible tool for the rational design of G4 mutations has been available. RESULTS: We developed a web-based tool termed G4Killer that is based on the G4Hunter algorithm. This new tool is a platform-independent and user-friendly application to design mutations crippling G4 propensity in a parsimonious way (i.e., keeping the primary sequence as close as possible to the original one). The tool is integrated into our DNA analyzer server and allows for generating mutated DNA sequences having the desired lowered G4Hunter score with minimal mutation steps. AVAILABILITY AND IMPLEMENTATION: The G4Killer web tool can be accessed at: http://bioinformatics.ibp.cz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- MeSH
- algoritmy MeSH
- DNA MeSH
- G-kvadruplexy * MeSH
- mutace MeSH
- sekvenční analýza DNA MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Akutní plicní embolie spojená s obstrukčním šokem patří mezi závažnéstavy s vysokou mortalitou. Lékem volby je v tomto případě systémová trombolýza, na kterou navazuje antikoagulační léčba. Tento postup umožní rychlézvládnutí hemodynamickénestability a zároveň zabrání časnérecidivě plicní embolie. V kazuistice popisujeme případ 80leté pacientky s časnou recidivou těžkéakutní plicní embolie krátce po úspěšnésystémovétrombolýze. Případ je zajímavý také tím, že v obou případech byla echokardiograficky dokumentována přítomnost mobilních trombů v pravostranných srdečních oddílech.
Acute pulmonary embolism associated with obstructive shock is a serious condition with high mortality. In this case, the treatment of choice is systemic thrombolysis, followed by anticoagulant treatment. This procedure will allow rapid management of hemodynamic instability while preventing early recurrence of pulmonary embolism. In our case report, we describe an 80-year-old patient suffering from early recurrence of severe acute pulmonary embolism, presenting shortly after successful systemic thrombolysis. The case is interesting thanks to the fact that the presence of mobile thrombi in the right heart compartments was documented by echocardiography.
- Klíčová slova
- altepláza,
- MeSH
- antikoagulancia aplikace a dávkování MeSH
- dyspnoe etiologie MeSH
- echokardiografie MeSH
- farmakoterapie metody MeSH
- heparin nízkomolekulární aplikace a dávkování MeSH
- hypotenze etiologie MeSH
- lidé MeSH
- plicní embolie * terapie MeSH
- recidiva * MeSH
- senioři MeSH
- sinusová tachykardie etiologie MeSH
- srdce diagnostické zobrazování patofyziologie MeSH
- trombolytická terapie MeSH
- trombóza diagnostické zobrazování farmakoterapie MeSH
- Check Tag
- lidé MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- kazuistiky MeSH
