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J Filipski

Publications and source records attributed to J Filipski.

At least 19 recordsLinked to original sources
PubMed2003

Mapping candidate hotspots of meiotic recombination in segments of human DNA cloned in the yeast Saccharomyces cerevisiae.

The hotspots of meiotic recombination in the human genome can be localized by genetic techniques. The resolution of these techniques is in the range of kilobases and depends on the density of the physical markers identifying allelic variants of the chromosomal loci. We thought it would be interesting to localize these sites with higher resolution. Assuming that some human chromosomal sites conserve their propensity for recombination when cloned in yeast, we localized the hotspots of recombination in several yeast artificial chromosomes (YACs) carrying human DNA. A number of potential recombination hotspots could be identified in the clones studied. Among them there are two classes of sites that are particularly recombination prone also in human meiotic cells: sites associated with CpG islands and sites located in the vicinity of long minisatellite sequences.

Base Sequence↗
PubMed2000

Nuclease-hypersensitive chromatin formed by a CpG island in human DNA cloned as an artificial chromosome in yeast.

CpG islands are mostly unmethylated GC-, and CpG-rich chromosomal segments overlapping promoter sequences in all housekeeping and many tissue-specific genes in vertebrates. Typically, these islands show an open chromatin structure, low in histone H1 and rich in acetylated histones. We have previously found that the island-like CGCG-rich sites in human DNA are hypersensitive to DNase I upon cloning in Saccharomyces cerevisiae. Here we studied, with a higher resolution, the chromatin formed in yeast by one such site, the CpG island accompanying the human glucose-6-phosphate dehydrogenase gene. We have found two strong hypersensitive sites and several positioned nucleosomes flanking the island despite the absence in yeast of such chromatin fiber-shaping factors as histone H1, methyltransferase, and the tissue-specific transcription factors. This finding, together with similar observations from our laboratories and others supports the idea that variations in GC and/or CpG content substantially contribute to the DNA sequence features modulating the structure of the chromatin. The composition-dependent fluctuations in the accessibility of DNA in the chromatin may constitute an evolutionary advantage and may explain the surprising compositional selection that acts in both the coding and non-coding segments of some genes during mammalian evolution.

Chromatin↗
PubMed1998

Meiotic double-strand breaks in yeast artificial chromosomes containing human DNA.

Meiotic recombination in the yeast Saccharomyces cerevisiae is initiated by double-strand breaks (DSB) in chromosomal DNA. These DSB, which can be mapped in the rad 50S mutant yeast strain, are caused by a topoisomerase II-like enzyme, the protein Spo11. Evidence suggests that this protein is located in the axial element of the meiotic chromosome which implies that the DSB are located in these chromosomes in the vicinity of the bases of the DNA loops. We have found that in the yeast artificial chromosomes carrying human DNA, at the level of resolution obtained by pulsed field gel electrophoresis (PFGE), the meiotic DSB in the diploid yeast are co-localized with the DNase I hypersensitive sites (HS) in a haploid strain of yeast. These HS are located close to sequences which, under stress, have the potential to form secondary structures containing unpaired nucleotides. Clusters of such sequences could be a hallmark of the bases of the chromatin loops.

Chromatin↗
PubMed1998

DNase-hypersensitive sites in yeast artificial chromosomes containing human DNA.

We have mapped the DNase I-hypersensitive sites (HSs) in Yeast Artificial Chromosomes (YACs) containing segments of human chromosomal DNA. One of the five HSs found in a YAC carrying the beta-globin gene cluster has been localised in the region, termed HS2, that is DNase I hypersensitive in most human cells. We have also identified a class of HSs in YACs containing DNA from the q11.2 band of human chromosome 21, which are located close to, or within, segments of the chromosome that are sensitive to restriction enzymes recognizing CGCG tetranucleotides.

Chromosome Mapping↗
PubMed1997

Pharmacologic modulation of reduced glutathione circadian rhythms with buthionine sulfoximine: relationship with cisplatin toxicity in mice.

The relationship between the rhythm in reduced glutathione (GSH) and that in cisplatin (CDDP) toxicity was investigated in a total of 560 male B6D2F1 mice, using buthionine sulfoximine (BSO). GSH was measured by high-performance liquid chromatography (HPLC) in four tissues, at each of six sampling times, 4 hr apart. A significant 24-hr rhythm was statistically validated in liver, jejunum, and colon, but not in bone marrow. Relative to liver, glutathione content was 56% in colon, 38% in bone marrow, 25% in jejunum, and negligible in kidney, where cysteine, a final product of GSH catabolism, displayed a 12-hr rhythmic variation. This rhythm may reflect that in the activity of GSH-degrading enzymes. BSO (450 mg/kg ip, 4 hr before sampling) reduced liver GSH threefold and kidney cysteine content was halved, but this pretreatment had no significant effect upon GSH content in the other organs. Furthermore, the period of the physiologic liver GSH rhythm changed from 24 hr to a composite (24 + 12 hr) period. This change in the period may result from an unmasking of the 12-hr rhythm in GSH-degrading enzyme activity by GSH synthesis blockade. Maximal values occurred in the mid-rest span and in the mid-active span after BSO administration. In the other tissues, the 24-hr period remained unchanged. BSO injection largely enhanced CDDP toxicity (as assessed by survival, leukopenia, and histologic lesions in kidney and bone marrow) and kidney mean platinum concentration. Furthermore, BSO pretreatment modified the period of CDDP toxicity rhythm: survival followed a significant 12-hr-rhythm, instead of a 24-hr rhythm. The cycling of GSH concentration results from a balance between synthesis and catabolism and likely constitutes one of the main components of the circadian rhythm in CDDP toxicity in mice.

Animals↗
PubMed1997

Modification of the apoptotic-like effects of MBP protein overexpression in E. coli by fusion with 14-3-3 derived polypeptides.

Overexpression of even non-toxic proteins in bacteria causes a starvation-like response: the arrest of bacterial proliferation and apoptotic-like suicidal cell death. We have shown here that, as in the cells of higher organisms, these effects are accompanied by DNA degradation. The fusion with the bacterial MBP of a polypeptide, belonging to the 14-3-3 family and normally expressed in pumpkin (C. pepo), modifies the apoptotic-like effects of overexpression of this protein in E. coli. Fusion of the full length 14-3-3 protein with the MBP considerably slows down the DNA degradation caused by overexpression of the unmodified MBP. Overexpression of the construct containing a truncated version of the 14-3-3 polypeptide causes immediate arrest of bacterial growth and rapid degradation of the chromosomal DNA. This result suggests that the DNA degradation in bacteria is an active process which can be modified to some extent by an endogenous protein.

Journal Article↗
PubMed1996

Modulation of cisplatin chronotoxicity related to reduced glutathione in mice.

Intracellular reduced glutathione (GSH) concentrations were measured according to the tissue sampling-time along the 24 h scale in male B6D2F1 mice. A significant circadian rhythm in GSH content was statistically validated in liver, jejunum, colon and bone-marrow (P < or = 0.02) but not in kidney. Tissue GSH concentration increased in the dark-activity span and decreased in the light-rest span of mice. The minimum and maximum of tissue GSH content corresponded respectively to the maximum and minimum of cisplatin (CDDP) toxicity. The role of GSH rhythms with regard to CDDP toxicity was investigated, using a specific inhibitor of GSH biosynthesis, buthionine sulfoximine (BSO). Its effects were assessed on both tissue GSH levels and CDDP toxicity at three circadian times. BSO resulted in a 10-fold decrease of the 24 h-mean GSH in kidney. However a moderate GSH decrease characterized liver (-23%) and jejunum (-30%). BSO pretreatment largely enhanced CDDP toxicity which varied according to a circadian rhythm. Although BSO partly and/or totally abolished the tissue GSH rhythms, it did not modify those in CDDP toxicity. We conclude that GSH have an important influence on CDDP toxicity but not in the circadian mechanism of such platinum chronotoxicity.

Animals↗
PubMed1996

New approaches to the mapping of chromosomal domains.

Although it is generally accepted that the chromosome is divided into elementary subunits, the structural and functional domains, the organisation of these structures at the molecular level is not well understood. In particular, the domain boundaries are not easily identifiable. Several possible candidates such as MARs/SARs, insulators, LCRs, palindromic sequences, or easily melting sequences have been found in the regions having properties one would except for boundaries. None of these elements, however, has been found in all of the constructs functioning as boundaries in tests in vivo. Recent work suggests that the common denominator might be the presence og GC-rich oligonucleotide stretches and the formation of the chromatin hypersensitive sites. A model is discussed in which "unusual" structures, in particular the four-stranded DNA sequence elements containing unpaired bases, play the role of domain boundaries.

Animals↗
PubMed1995

Loop-size spacings between CGCG clusters in long segments of human DNA.

The CGCG tetranucleotides are clustered inside the CpG islands in the genomes of vertebrates. In order to study the distribution of the islands in the human chromosome we have mapped the loci sensitive to the CGCG specific restriction nuclease, in a 1.5 Mb long DNA segment cloned as Yeast Artificial Chromosome (YAC). The sites most sensitive to Bsh 1236 I nuclease show chromosomal loop-size spacing. This result, as well as the result of nucleotide sequence analysis of long genomic segments, suggests that the CGCG are organised in clusters (not always undermethylated) which are coincident with GC peaks on the sine wave-like curve representing DNA composition along the mammalian chromosome.

Animals↗
PubMed1995

Correlation of GC content with replication timing and repair mechanisms in weakly expressed E.coli genes.

Regional variations of DNA GC content are observed in species as different as S.cerevisiae and humans. In vertebrates and yeast they are correlated with replication timing; late replicating chromosomal regions are more AT-rich than early replicating regions. We show here that gene composition in E.coli also has long range variations which are similarly correlated with replication timing. We suggest that the enrichment in AT base pairs in late replicating DNA reflects differences in DNA repair modes. These sequences, which are in single copy for a greater part of the cell cycle than origin-linked genes, have less opportunity to engage in repair via homologous recombination and therefore may resort more often to translesion synthesis involving the misincorporation of adenine opposite modified nucleotides.

Base Composition↗
PubMed1992

The distribution of 5-methylcytosine in the nuclear genome of plants.

We have determined the 5-methylcytosine (5mC) content in high molecular weight DNA, from two dicot (tobacco and pea) and two monocot (wheat and maize) plant species, fractionated according to base composition. The results show that the proportion of 5mC in the genomic fractions increases linearly with their guanine + cytosine (G + C) content while the proportion of non-methylated cytosine remains almost constant. This can be interpreted as a consequence of a difference in mutation pressure related to spontaneous deamination of 5mC to thymine between the different compartments of plant genomes.

5-Methylcytosine↗
PubMed1990

Periodicity of DNA folding in higher order chromatin structures.

Each level of DNA folding in cells corresponds to a distinct chromatin structure. The basic chromatin units, nucleosomes, are arranged into solenoids which form chromatin loops. To characterize better the loop organization of chromatin we have assumed that the accessibility of DNA inside these structures is lower than on the outside and examined the size distribution of high mol. wt DNA fragments obtained from cells and isolated nuclei after digestion with endogenous nuclease or topoisomerase II. The largest discrete fragments obtained contain 300 kbp of DNA. Their further degradation proceeds through another discrete size step of 50 kbp. This suggests that chromatin loops contain approximately 50 kbp of DNA and that they are grouped into hexameric rosettes at the next higher level of chromatin structure. Based upon these observations a model by which the 30 nm chromatin fibre can be folded up into compact metaphase chromosomes is also described.

Animals↗
PubMed1989

Chromosome localization-dependent compositional bias of point mutations in Alu repetitive sequences.

The Alu repetitive sequence family originated from a common ancestor. Its members, apparently free from functional constraints, are interspersed throughout primate genomes. We have found that base substitutions occurring during the evolution of primates caused a decrease in the average G + C content of those members of the family that are located in an A + T-rich region of the genome. The family members that are located in a G + C-rich genomic region have not changed their, already high, G + C content. This suggests that the regional differences in G + C content, which are responsible for chromosomal banding, are caused by an accumulation of mutations that, although selectively neutral in the majority, show different compositional bias in different regions of the vertebrate chromosome.

Animals↗
PubMed1988

Why the rate of silent codon substitutions is variable within a vertebrate's genome.

Different genes within the murine genome are diverging at different rates. The rate of synonymous codon substitutions in these genes is related to their base composition. It is proposed that the variabilities of rate of mutation accumulation, of codon choice and of average GC content within vertebrate genomes are caused by differences between DNA synthesis in repair and replication, as far as the frequency and compositional bias of mutations introduced by these systems are concerned. DNA repair contributes substantially to the evolution of the DNA domains, which are actively repaired in germline cells and which correspond to regions available for transcription in these cells and to Giemsa-negative bands in stained chromosomes.

Animals↗
PubMed1988

Development of a Salmonella-specific biotinylated DNA probe for rapid routine identification of Salmonella.

Classical microbiological techniques used in the detection and identification of Salmonella spp. in foods, drinking water and clinical samples are relatively lengthy. Immunoassays, on the other hand, have the major disadvantage of often generating false positives and false negatives. Recombinant DNA technology offers more efficient alternatives to the detection of a specific organism by employing cloned DNA sequences unique to the organism. Demonstration of a presence of complementary sequences among a heterogeneous population of molecules of DNA isolated from bacteria can be made by using a DNA-DNA hybridization technique. We have obtained a fragment of DNA from Salmonella typhimurium chromosomal DNA, cloned it in Escherichia coli plasmid and tested it in colony hybridization tests with 57 strains of Salmonella and other enterobacteriaceae. In all tests, the fragment was found to be Salmonella-specific in that it gave a positive reaction with all strains of Salmonella tested and was negative when tested against other Enterobacteriaceae.

Animals↗