Single-strand DNA-binding protein suppresses illegitimate recombination in Escherichia coli, acting in synergy with RecQ helicase.

Single-strand DNA-binding proteins SSB/RPA are ubiquitous and essential proteins that bind ssDNA in bacteria/eukaryotes and coordinate DNA metabolic processes such as replication, repair, and recombination. SSB protects ssDNA from degradation by nucleases, while also facilitating/regulating the activity of multiple partner proteins involved in DNA processes. Using Spi assay, which detects aberrantly excised λ prophage from the E.

Alpha Satellite DNA in Targeted Drug Therapy for Prostate Cancer.

Prostate cancer is the most common solid cancer in men and, despite the development of many new therapies, metastatic castration-resistant prostate cancer still remains a deadly disease. Therefore, novel concepts for the treatment of metastatic prostate cancer are needed. In our opinion, the role of the non-coding part of the genome, satellite DNA in particular, has been underestimated in relation to diseases such as cancer.

Reverse transcription-quantitative PCR (RT-qPCR) without the need for prior removal of DNA.

The procedure illustrated in this paper represents a new method for transcriptome analysis by PCR (Polymerase Chain Reaction), which circumvents the need for elimination of potential DNA contamination. Compared to the existing methodologies, our method is more precise, simpler and more reproducible because it preserves the RNA's integrity, does not require materials and/or reagents that are used for elimination of DNA and it also reduces the number of samples that should be set up as negative controls. This novel procedure involves the use of a specifically modified primer during reverse transcription step, which contains mismatched bases, thus producing cDNA molecules that differ from genomic DNA.

Regulation of ssb Gene Expression in Escherichia coli.

Bacterial SSB proteins, as well as their eukaryotic RPA analogues, are essential and ubiquitous. They avidly bind single-stranded DNA and regulate/coordinate its metabolism, hence enabling essential DNA processes such as replication, transcription, and repair. The prototypic SSB protein is encoded by an gene.

Satellite DNAs in Health and Disease.

Tandemly repeated satellite DNAs are major components of centromeres and pericentromeric heterochromatin which are crucial chromosomal elements responsible for accurate chromosome segregation. Satellite DNAs also contribute to genome evolution and the speciation process and are important for the maintenance of the entire genome inside the nucleus. In addition, there is increasing evidence for active and tightly regulated transcription of satellite DNAs and for the role of their transcripts in diverse processes.

Alpha Satellite RNA Levels Are Upregulated in the Blood of Patients with Metastatic Castration-Resistant Prostate Cancer.

The aberrant overexpression of alpha satellite DNA is characteristic of many human cancers including prostate cancer; however, it is not known whether the change in the alpha satellite RNA amount occurs in the peripheral tissues of cancer patients, such as blood. Here, we analyse the level of intracellular alpha satellite RNA in the whole blood of cancer prostate patients at different stages of disease and compare it with the levels found in healthy controls. Our results reveal a significantly increased level of intracellular alpha satellite RNA in the blood of metastatic cancers patients, particularly those with metastatic castration-resistant prostate cancer relative to controls.

Distinct Regulation of the Expression of Satellite DNAs in the Beetle .

In the flour beetle, (peri)centromeric heterochromatin is mainly composed of a major satellite DNA TCAST1 interspersed with minor satellites. With the exception of heterochromatin, clustered satellite repeats are found dispersed within euchromatin. In order to uncover a possible satellite DNA function within the beetle genome, we analysed the expression of the major TCAST1 and a minor TCAST2 satellite during the development and upon heat stress.

Evolutionary History of Alpha Satellite DNA Repeats Dispersed within Human Genome Euchromatin.

Major human alpha satellite DNA repeats are preferentially assembled within (peri)centromeric regions but are also dispersed within euchromatin in the form of clustered or short single repeat arrays. To study the evolutionary history of single euchromatic human alpha satellite repeats (ARs), we analyzed their orthologous loci across the primate genomes. The continuous insertion of euchromatic ARs throughout the evolutionary history of primates starting with the ancestors of Simiformes (45-60 Ma) and continuing up to the ancestors of Homo is revealed.

Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats.

Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of "silent" H3K9me3 and "active" H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats.

The pulmonary-proteoliposome as a new therapeutic approach for Coronaviruses.

We are proposing the use of pulmonary-proteoliposome as a new therapeutic approach for Coronaviruses. The designed strategy represents a potential treatment to reduce the overall viral load in the lungs and to help the immune system to successfully stave off the infection.

RecF, UvrD, RecX and RecN proteins suppress DNA degradation at DNA double-strand breaks in Escherichia coli.

Double strand breaks (DSBs) in E. coli chromosome (such as those induced by gamma rays) are repaired by recombination repair, during which a certain amount of DNA gets degraded. We monitored DNA degradation in gamma-irradiated cells to assess processing of DSBs.

Dispersion Profiles and Gene Associations of Repetitive DNAs in the Euchromatin of the Beetle .

Satellite DNAs are tandemly repeated sequences clustered within heterochromatin. However, in some cases, such as the major TCAST1 satellite DNA from the beetle , they are found partially dispersed within euchromatin. Such organization together with transcriptional activity enables TCAST1 to modulate the activity of neighboring genes.

S1 satellite DNA repetitive units display identical structure and overall variability in all Anatolian brown frog taxa.

S1 satellite DNA from Palearctic brown frogs has a species-specific structure in all European species. We characterized S1 satellite DNA from the Anatolian brown frogs Rana macrocnemis, R. camerani, and R.

Satellite DNA Modulates Gene Expression in the Beetle Tribolium castaneum after Heat Stress.

Non-coding repetitive DNAs have been proposed to perform a gene regulatory role, however for tandemly repeated satellite DNA no such role was defined until now. Here we provide the first evidence for a role of satellite DNA in the modulation of gene expression under specific environmental conditions. The major satellite DNA TCAST1 in the beetle Tribolium castaneum is preferentially located within pericentromeric heterochromatin but is also dispersed as single repeats or short arrays in the vicinity of protein-coding genes within euchromatin.

Satellite DNA as a driver of population divergence in the red flour beetle Tribolium castaneum.

Tandemly repeated satellite DNAs are among most rapidly evolving sequences in eukaryotic genome, usually differing significantly among closely related species. By inducing changes in heterochromatin and/or centromere, satellite DNAs are expected to drive population and species divergence. However, despite high evolutionary dynamics, divergence of satellite DNA profiles at the level of natural population which precedes and possibly triggers speciation process is not readily detected.

First evidence of DNA methylation in insect Tribolium castaneum: environmental regulation of DNA methylation within heterochromatin.

DNA methylation has been studied in many eukaryotic organisms, in particular vertebrates, and was implicated in developmental and phenotypic variations. Little is known about the role of DNA methylation in invertebrates, although insects are considered as excellent models for studying the evolution of DNA methylation. In the red flour beetle, Tribolium castaneum (Tenebrionidae, Coleoptera), no evidence of DNA methylation has been found till now.

Satellite DNA-like elements associated with genes within euchromatin of the beetle Tribolium castaneum.

In the red flour beetle Tribolium castaneum the major TCAST satellite DNA accounts for 35% of the genome and encompasses the pericentromeric regions of all chromosomes. Because of the presence of transcriptional regulatory elements and transcriptional activity in these sequences, TCAST satellite DNAs also have been proposed to be modulators of gene expression within euchromatin. Here, we analyze the distribution of TCAST homologous repeats in T.

Structure and population dynamics of the major satellite DNA in the red flour beetle Tribolium castaneum.

In the beetle genus Tribolium, satellite DNAs comprise a significant amount of pericentromeric heterochromatin and are characterized by rapid turnover resulting in species specific profiles. In the present work we characterize the major pericentromeric satellite DNA TCAST of the beetle T. castaneum and analyse its population dynamics.

Transcription of Satellite DNAs in Insects.

The very complex life cycle and extreme diversity of insect life forms require a carefully regulated network of biological processes to switch on and off the right genes at the right time. Chromatin condensation is an important regulatory mechanism of gene silencing as well as gene activation for the hundreds of functional protein genes harbored in heterochromatic regions of different insect species. Being the major heterochromatin constituents, satellite DNAs (satDNAs) serve important roles in heterochromatin regulation in insects in general.

Intra-specific variability and unusual organization of the repetitive units in a satellite DNA from Rana dalmatina: molecular evidence of a new mechanism of DNA repair acting on satellite DNA.

We have characterized the S1 satellite from eight European populations of Rana dalmatina by Southern blot, cloning and a new method that determines the sequence variability of repetitive units in the genome. This report completes our previous studies on this satellite DNA family, thus providing the first characterization of the overall variability of the structure and genomic organization of a satellite DNA within a species and among related species. The S1 satellite from R.

The first characterisation of the overall variability of repetitive units in a species reveals unexpected features of satellite DNA.

We investigated the overall variability of the S1a satellite DNA repeats in ten European populations of Rana temporaria by a new procedure that determines the average sequence of the repeats in a genome. The average genomic sequences show that only 17% of the S1a repeat sequence (494 bp) is variable. The variable positions contain the same major and minor bases in all or many of the population samples tested, but the percentages of these bases can greatly vary among populations.

S1 satellite DNA as a taxonomic marker in brown frogs: molecular evidence that Rana graeca graeca and Rana graeca italica are different species.

The brown frog Rana graeca was believed to be present in two areas, the Balkan Peninsula and the Italian Apennines. We have characterised the S1 satellite DNA family from Rana graeca graeca and compared it with that of Rana graeca italica. On Southern blots, the patterns of S1 satellite DNA bands are very different between Italian and Greek specimens, but homogeneous among various populations of the same taxon.