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. Here, we hypothesise that this part of the genome should be considered as a potential target for the development of new drugs. Specifically, we propose a novel concept directed at the possible treatment of metastatic prostate cancer that is mostly based on epigenetics. Namely, metastatic prostate cancer is characterized by the strongly induced transcription of alpha satellite DNA located in pericentromeric heterochromatin and, according to our hypothesis, the stable controlled transcription of satellite DNA might be important in terms of the control of disease development. This can be primarily achieved through the epigenetic regulation of pericentromeric heterochromatin by using specific enzymes as well as their activators/inhibitors that could act as potential anti-prostate cancer drugs. We believe that our concept is innovative and should be considered in the potential treatment of prostate cancer in combination with other more conventional therapies.

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. By using the same modified primer in PCR amplification, only cDNA template is amplified since genomic DNA template is partially heterologous to the primer. In this way, amplification by PCR is unaffected by any potential DNA contamination since it is specific only for the cDNA template. Furthermore, it accurately reflects the initial RNA concentration of the sample, which is prone to changes due to various physical or enzymatic treatments commonly used by the current methodologies for DNA elimination. The method is particularly suitable for quantification of highly repetitive DNA transcripts, such as satellite 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 Escherichia coli SSB protein is encoded by an ssb gene. Although the ssb gene promoters harbor an SOS box, multiple studies over several decades failed to elucidate whether ssb gene expression is inducible and SOS dependent. The SOS regulon is comprised of about 50 genes, whose transcription is coordinately induced under stress conditions. Using quantitative real-time PCR, we determined the ssb gene expression kinetics in UV- and γ-irradiated E. coli and revealed that ssb gene expression is elevated in irradiated cells in an SOS-dependent manner. Additionally, the expression of the sulA gene was determined to indicate the extent of SOS induction. In a mutant with a constitutively induced SOS regulon, the ssb gene was overexpressed in the absence of DNA damage. Furthermore, we measured ssb gene expression by droplet digital PCR during unaffected bacterial growth and revealed that ssb gene expression was equal in wild-type and SOS^- bacteria, whereas sulA expression was higher in the former. This study thus reveals a complex pattern of ssb gene expression, which under stress conditions depends on the SOS regulon, whereas during normal bacterial growth it is unlinked to SOS induction. The E. coli ssb gene is SOS regulated in such a way that its basal expression is relatively high and can be increased only through stronger SOS induction. The remarkable SOS induction observed in undisturbed wild-type cells may challenge our notion of the physiological role of the SOS response in bacteria.

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. In this review, we focus on recent discoveries related to the regulation of satellite DNA expression and the role of their transcripts, either in heterochromatin establishment and centromere function or in gene expression regulation under various biological contexts. We discuss the role of satellite transcripts in the stress response and environmental adaptation as well as consequences of the dysregulation of satellite DNA expression in cancer and their potential use as cancer biomarkers.

mRNA vaccines: Why and how they should be modified

The COVID-19 pandemic has stimulated the production of different therapeutic approaches for the resolution of coronavirus infections. On one hand, nanobiomolecules have been proposed as bait material for viruses,1,2 on the other hand unconventional messenger RNA vaccines have been produced like SARS-CoV-2 mRNA vaccines (BioNTech/Pfizer BNT162b2 and Moderna mRNA-1273). [...]

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. Once inserted, the euchromatic ARs were stably transmitted to the descendant species, some exhibiting copy number variation, whereas their sequence divergence followed the species phylogeny. Many euchromatic ARs have sequence characteristics of (peri)centromeric alpha repeats suggesting heterochromatin as a source of dispersed euchromatic ARs. The majority of euchromatic ARs are inserted in the vicinity of other repetitive elements such as L1, Alu, and ERV or are embedded within them. Irrespective of the insertion context, each AR insertion seems to be unique and once inserted, ARs do not seem to be subsequently spread to new genomic locations. In spite of association with (retro)transposable elements, there is no indication that such elements play a role in ARs proliferation. The presence of short duplications at most of ARs insertion sites suggests site-directed recombination between homologous motifs in ARs and in the target genomic sequence, probably mediated by extrachromosomal circular DNA, as a mechanism of spreading within euchromatin.

Satellite DNA-Mediated Gene Expression Regulation: Physiological and Evolutionary Implication

Satellite DNAs are tandemly repeated sequences organized in large clusters within (peri)centromeric and/or subtelomeric heterochromatin. However, in many species, satellite DNAs are not restricted to heterochromatin but are also dispersed as short arrays within euchromatin. Such genomic organization together with transcriptional activity seems to be a prerequisite for the gene-modulatory effect of satellite DNAs which was first demonstrated in the beetle Tribolium castaneum upon heat stress. Namely, enrichment of a silent histone mark at euchromatic repeats of a major beetle satellite DNA results in epigenetic silencing of neighboring genes. In addition, human satellite III transcripts induced by heat shock contribute to genome-wide gene silencing, providing protection against stress-induced cell death. Gene silencing mediated by satellite RNA was also shown to be fundamental for the early embryonic development of the mosquito Aedes aegypti. Apart from a physiological role during embryogenesis and heat stress response, activation of satellite DNAs in terms of transcription and proliferation can have an evolutionary impact. Spreading of satellite repeats throughout euchromatin promotes the variation of epigenetic landscapes and gene expression diversity, contributing to the evolution of gene regulatory networks and to genome adaptation in fluctuating environmental conditions.

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.

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. Our results show enhanced suppression of activity of TCAST1-associated genes and slower recovery of their activity after long-term heat stress relative to the same genes without associated TCAST1 satellite DNA elements. The level of gene suppression is not influenced by the distance of TCAST1 elements from the associated genes up to 40 kb from the genes' transcription start sites, but it does depend on the copy number of TCAST1 repeats within an element, being stronger for the higher number of copies. The enhanced gene suppression correlates with the enrichment of the repressive histone marks H3K9me2/3 at dispersed TCAST1 elements and their flanking regions as well as with increased expression of TCAST1 satellite DNA. The results reveal transient, RNAi based heterochromatin formation at dispersed TCAST1 repeats and their proximal regions as a mechanism responsible for enhanced silencing of TCAST1-associated genes. Differences in the pattern of distribution of TCAST1 elements contribute to gene expression diversity among T. castaneum strains after long-term heat stress and might have an impact on adaptation to different environmental conditions.

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. Here, we characterize minor TCAST2 satellite DNA of the red flour beetle Tribolium castaneum and follow its dynamics among wild-type strains originating from diverse geographic locations. The investigation revealed presence of three distinct subfamilies of TCAST2 satellite DNA which differ in monomer size, genome organization, and subfamily specific mutations. Subfamilies Tcast2a and Tcast2b are tandemly arranged within pericentromeric heterochromatin whereas Tcast2c is preferentially dispersed within euchromatin of all chromosomes. Among strains, TCAST2 subfamilies are conserved in sequence but exhibit a significant content variability. This results in overrepresentation or almost complete absence of particular subfamily in some strains and enables discrimination between strains. It is proposed that homologous recombination, probably stimulated by environmental stress, is responsible for the emergence of TCAST2 satellite subfamilies, their copy number variation and dispersion within genome. The results represent the first evidence for the existence of population-specific satellite DNA profiles. Partial organization of TCAST2 satellite DNA in the form of single repeats dispersed within euchromatin additionally contributes to the genome divergence at the population level.

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. In this paper, a cytosine methylation in Tribolium castaneum embryos was detected by methylation sensitive restriction endonucleases and immuno-dot blot assay. DNA methylation in embryos is followed by a global demethylation in larvae, pupae and adults. DNA demethylation seems to proceed actively through 5-hydroxymethylcytosine, most probably by the action of TET enzyme. Bisulfite sequencing of a highly abundant satellite DNA located in pericentromeric heterochromatin revealed similar profile of cytosine methylation in adults and embryos. Cytosine methylation was not only restricted to CpG sites but was found at CpA, CpT and CpC sites. In addition, complete cytosine demethylation of heterochromatic satellite DNA was induced by heat stress. The results reveal existence of DNA methylation cycling in T. castaneum ranging from strong overall cytosine methylation in embryos to a weak DNA methylation in other developmental stages. Nevertheless, DNA methylation is preserved within heterochromatin during development, indicating its role in heterochromatin formation and maintenance. It is, however, strongly affected by heat stress, suggesting a role for DNA methylation in heterochromatin structure modulation during heat stress response.

Satellite DNA-mediated effects on genome regulation

Being the major heterochromatin constituents, satellite DNAs serve important roles in heterochromatin establishment and regulation. Their transcripts act as epigenetic signals required for organization of pericentromeric heterochromatin during embryogenesis and are necessary for developmental progression. In addition, satellite DNAs and their transcripts potentially play an active role in modulating gene expression and epigenetic states of a genome. Due to the presence of promoter elements and transcription factor binding sites within a sequence, satellite DNAs can interfere with the expression of nearby genes. Gene activity can be directly controlled by the number of repeats in a section of satellite DNA. In the case of stress, transcriptional activation of pericentromeric satellite DNAs seems to be part of a general stress response program activated by environmental stimuli. Such diverse forms of genome regulation modulated by satellite DNAs may be controlled by selective pressures and could influence the adaptability of the organism.

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. Using direct sequencing of genomic PCR products we show that the TCAST satellite exists in the form of two related subfamilies: Tcast1a and Tcast1b that make up 20 and 15% of the genome, respectively. Tcast1a and Tcast1b have consensus sequences of 377 and 362 bp respectively, share an average similarity of 79% and are characterized by a divergent, subfamily specific region of approximately 100 bp. The two subfamilies are prevalently organized in the interspersed form, although a portion exists in the form of homogenous tandem arrays composed of only Tcast1a or Tcast1b. The pattern of restriction enzyme digestion indicates that Tcast1a and Tcast1b are organized in composite higher order repeats. Comparison of sequence variability of Tcast1a and Tcast1b among ten strains reveals a difference in the frequency of particular mutations present at some positions. However, no difference in the organization and in the amount of subfamilies was detected among strains. The results show that direct genomic sequencing can be a useful method for the detection of population specific features of satellite DNA. In the case of TCAST satellite DNA, changes in the mutational profiles seem to represent the first step in the genesis of a population specific satellite profile.

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. dalmatina has a pericentromeric location on ten chromosome pairs and presents two homologous repeats S1a (494 bp) and S1b (332 bp), mostly organized as composite S1a-S1b repetitive units. In other brown frog species, both repeats have different sequences and locations, and are usually organized as separate arrays, although composite S1a-S1b repeats represent a minor, widely variable component in Rana italica. The average genomic sequences indicate that the species contains an enormous number of variants of each repeat derived from a unique, species-specific common sequence. The repeat variability is restricted to specific base changes in specific sequence positions in all population samples. Our data show that the structure and evolution of S1 satellite family is not due to crossing-over and gene conversion, but to a mechanism that maintains the ability of the satellite DNA to assemble in constitutive heterochromatin by replacing altered satellite segments with new arrays generated by rolling circle amplification. The mode of action of this repair process not only directly explains the intra- and inter-specific variability of the structure and organization of the S1 satellite repeats from European brown frogs, but also accounts for all general features of satellite DNA in eukaryotes, including its discontinuous evolution. This repair mechanism can maintain the satellite structure in a species indefinitely, but also promote a rapid generation of new variants or types of satellite DNA when environmental conditions favor the formation of new species.

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. This indicates the presence in the species of an enormous number of repeats having a different distribution of bases in these variable positions. Individual genomes contain thousands of repeat variants, but these mixtures have very similar characteristics in all populations because they present the same type of restricted and species-specific variability. Southern blots analyses and sequences of cloned S1a repeats fully support this conclusion. The S1 satellite DNA of other European brown frog species also presents properties indicating the same type of variability. This first characterisation of the overall repeat variability of a satellite DNA in a species has revealed features that cannot be determined by gene conversion and crossing over. Our results suggest that a specific directional process based on rolling circle amplification should play a relevant role in the evolution of satellite DNA.

Pair-wise detection of eight common DNA polymorphisms of the human lipoprotein lipase gene by PCR-RFLP. Findings of the Olivetti Heart Study

We developed a rapid procedure to analyse simultaneously two different DNA polymorphisms of the human LPL gene by PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism). The method involves PCR amplification of the gene fragments encompassing two polymorphic sites, direct digestion in the same PCR-tube of the amplification mixture with two restriction enzymes, and the analysis of the resulting DNA fragments by gel electrophoresis. In 422 participants of the 1994 follow-up examination of the Olivetti Heart Study, a total of eight common LPL gene polymorphisms have been analysed in pairs by this procedure: -93 T/G and D9N; V108V and T361T; N291S and PvuII; HindIII and S447X. Two of these polymorphisms (V108V and T361T) were analysed for the first time. This method is suitable for the routine analysis of clinical samples of varying DNA content and practically halves the times and costs of screening for these LPL polymorphisms.

In vivo expression of the whole HOX gene network in human breast cancer

The HOX network contains 39 genes that act as transcriptional regulators and control crucial cellular functions during both embryonic development and adult life. Inside the network, this is achieved according to the rules of temporal and spatial co-linearity with 3' HOX genes acting on the anterior part of the body, central HOX genes on the thoracic part and lumbo-sacral HOX genes on the caudal region. We analysed HOX gene expression in normal breast tissue and in primary breast cancers by reverse-transcriptase-polymerase chain reaction (RT-PCR). 17 out of 39 HOX genes were expressed in the normal breast tissue. The expression of thoracic HOX genes tended to be similar in normal and neoplastic breast tissues suggesting that these genes are involved in breast organogenesis. In contrast, cervical and lumbo-sacral HOX gene expression was altered in the primary breast cancers with respect to normal breast tissue. This supports their involvement in breast cancer evolution and suggests they could be targets for future cancer therapies.

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. The satellite DNA from the Greek taxon contains two repetitive units (S1a (494 bp) and S1b (363 bp)) that could be sequenced after amplification from genomic DNA to directly yield their consensus sequences in each genome. These consensus sequences were very similar among the Greek populations, but differed either in sequence (in S1a) or in both size and sequence (in S1b) from the corresponding repeats of the Italian taxon. A mechanism of concerted evolution is likely responsible for the high homogeneity of S1a and S1b repeat sequences within each genome and species. The genomic content of S1 satellite DNA was lower in the Greek than in the Italian populations (0.5 vs. 1.9%) and fluorescence in situ hybridization (FISH) analysis showed the S1 satellite on only 4 chromosome pairs in the Greek taxon and on all 13 chromosome pairs in the Italian taxon. The completely different structure and genomic organization of the S1 satellite DNA indicate that the Greek and Italian taxa are distinct species: R. graeca and R. italica.

A family of centromeric satellite DNAs from the European brown frog Rana graeca italica

Digestion of Rana graeca italica DNA with Asp 718I produces highly repetitive fragments of 281 and 385 bp that were cloned and sequenced. The shorter fragment corresponds to the unit repeat (RgiS1b) of a satellite DNA. The longer fragment was found to be part of a 494-bp repeat of another satellite DNA (RgiS1a) that was cloned intact as an EcoRV fragment. RgiS1b is 97% homologous to RgiS1a, from which it seems to be derived by a single deletion. Among all species tested, only the related brown frog Rana dalmatina contained homologous repetitive DNA. The overall number of RgiS1a and RgiS1b repeats per R. graeca italica haploid genome was estimated to be 2.7 x 10(5). RgiS1a and RgiS1b repeats are organized in separate arrays, but repetitive units formed by various combinations of the two repeats were also observed on Southern blots. The amount of these extra repeats varies greatly among animals from the same population, representing a rare case of individual variability in the satellite DNA organization. FISH with probes specific for both satellites, or for RgiS1a only, labeled the centromeric and pericentromeric heterochromatin of all chromosomes. This indicated that RgiS1a and RgiS1b are interspersed within the same heterochromatic regions of the chromosomes.

Hierarchical order in a satellite DNA from the European brown frog Rana dalmatina

We have cloned and sequenced a 341 bp EcoRV fragment of a repetitive DNA from the European brown frog Rana dalmatina. This fragment contained 11 copies in tandem of the 31 bp long repeat of a satellite DNA, that was named RdS2. RdS2 is species-specific, is not A+T rich and represents about 0.24% of the frog genome (3.5 x 10(5) copies of repeats per haploid genome). Southern blots of Rana dalmatina. DNA partially digested with EcoRV and RsaI indicated that RdS2 also contains high-order repeats with periodicities varying from 10 to 26 copies of the 31 bp unit repeat. Thus, RdS2 appears to have a hierarchical order like a number of satellite DNAs from other vertebrate and invertebrate genomes.

Cloning and preliminary characterization of two satellite-like DNA sequences from the brown frog Rana graeca

Two repetitive DNA sequences of about 0.29 Kb and 0.39 Kb have been isolated from Rana graeca genomic DNA by digestion with Asp718I and have been cloned in pTZ18R. Hybridization data obtained with DNA probes derived from these clones indicate that: i) both sequences are highly repetitive and species-specific; ii) the two sequences are partially homologous; iii) the 0.29 Kb sequence is present in the frog genome with the typical tandem organization of satellite DNA; iv) the 0.39 Kb sequence is presumably part of a longer repetitive sequence of satellite DNA.

A modified alkaline lysis method for the preparation of highly purified plasmid DNA from Escherichia coli

We have developed a very efficient and rapid method for the preparation on a small or large scale of highly purified plasmid DNA from Escherichia coli. The procedure consists of five steps: (1) cell lysis by NaOH-SDS, (2) precipitation of cell lysate with 2 M potassium acetate-1 M acetic acid, (3) precipitation of the resulting supernatant with isopropanol, (4) treatment of the precipitate with RNase, and (5) a second isopropanol precipitation. The new procedure yields a plasmid DNA that is more than 90% in the supercoiled form and virtually free from proteins, RNA, and chromosomal DNA. We have thoroughly tested the method in the preparation of several thousand samples of different plasmids from various E. coli strains. We found that it consistently produced samples of plasmid DNA suitable for all routine uses such as restriction analysis, sequencing, and preparation of DNA probes for cloning and hybridization experiments. Moreover, plasmids purified by this procedure could fully replace plasmids purified on CsCl gradients for more demanding tasks such as the in vitro synthesis of RNA probes by phage RNA polymerases, the generation of deletion mutants with exonuclease III, and the transfection of mammalian cells by the calcium phosphate coprecipitation method, as tested on human fibroblasts and on CV-1 cells.

cDNA isolation, expression analysis, and chromosomal localization of two human zinc finger genes

On the basis of sequence similarity in the repeated zinc finger domain, we have identified and characterized two human cDNA clones (ZNF7 and ZNF8), both encoding proteins containing potential finger-like nucleic acid binding motifs. Northern blot analysis indicates that both genes are expressed as multiple transcripts and they are ubiquitously present in many human cell lines of different embryological derivation. Moreover, their expression is modulated during in vitro induced terminal differentiation of human myeloid cell line HL-60. By in situ hybridization experiments, we have localized the ZNF7 gene to chromosome 8 (region q24) and the ZNF8 gene to the terminal band of the long arm of chromosome 20 (20q13).