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PubMed2003

Telomere and ribosomal DNA repeats are chromosomal targets of the bloom syndrome DNA helicase.

BACKGROUND: Bloom syndrome is one of the most cancer-predisposing disorders and is characterized by genomic instability and a high frequency of sister chromatid exchange. The disorder is caused by loss of function of a 3' to 5' RecQ DNA helicase, BLM. The exact role of BLM in maintaining genomic integrity is not known but the helicase has been found to associate with several DNA repair complexes and some DNA replication foci. RESULTS: Chromatin immunoprecipitation of BLM complexes recovered telomere and ribosomal DNA repeats. The N-terminus of BLM, required for NB localization, is the same as the telomere association domain of BLM. The C-terminus is required for ribosomal DNA localization. BLM localizes primarily to the non-transcribed spacer region of the ribosomal DNA repeat where replication forks initiate. Bloom syndrome cells expressing the deletion alleles lacking the ribosomal DNA and telomere association domains have altered cell cycle populations with increased S or G2/M cells relative to normal. CONCLUSION: These results identify telomere and ribosomal DNA repeated sequence elements as chromosomal targets for the BLM DNA helicase during the S/G2 phase of the cell cycle. BLM is localized in nuclear bodies when it associates with telomeric repeats in both telomerase positive and negative cells. The BLM DNA helicase participates in genomic stability at ribosomal DNA repeats and telomeres.

Adenosine Triphosphatases↗
PubMed1986

Genomic variability of selected LAV-related AIDS retroviruses.

All AIDS retroviruses isolated from different patients have shown degrees of heterogeneity as defined by restriction fragment polymorphisms. Despite this variability, all these virus isolates share a number of structural features, including immunological cross-reactivity of virally encoded proteins. In this paper, we compare restriction patterns of integrated proviral DNA from viral isolates of patients belonging to different geographical groups, at risk or not for the disease. We confirm the existence of different clones in the same isolate of the Lymphadenopathy-associated virus (LAV) and of Human T lymphotropic virus (HTLV-III), which are identical. One of these forms is very similar to a Haitian isolate, as well as to an isolate from an early recognized New York case, suggesting a common origin for these viruses. More variation is apparent with Zairian viral isolates, and one of two clones found in a virus from a child who received an allogeneic bone marrow transplant. Greater disparity was also found in the restriction pattern of an isolate from an individual belonging to none of the so-called high-risk groups. We also show that this variation occurs mainly but not only in the env region of the genome, as previously described.

Adult↗
PubMed1985

Structural basis for restriction-site polymorphism at the albumin locus in inbred strains of rats.

Two types of variant EcoRI restriction enzyme patterns of albumin-gene DNA fragments are found in different inbred strains of rats and reflect allelic polymorphism. The structural basis of the two allelic forms has been analyzed by mapping the EcoRI fragments using cloned albumin cDNA probes corresponding to the 5' or 3' end of the rat albumin mRNA and different genomic subclones. Additional restriction fragment length polymorphism has been detected using the restriction endonucleases HindIII and MspI. The results suggest that the two allelic variants differ from each other by multiple cleavage-site variations (base-pair substitutions) and by an insertion or deletion of DNA sequences. An extensive DNA sequence variation appears to exist between the two forms of the albumin gene; we have estimated that as much as 4% of the nucleotides in this region varied between the two alleles. All of this genetic variation is found in the intervening sequences of the gene and has no phenotypic manifestation.

Alleles↗
PubMed2006

Planning for intracavitary anti-EGFR radionuclide therapy of gliomas. Literature review and data on EGFR expression.

Targeting with radionuclide labelled substances that bind specifically to the epidermal growth factor receptor, EGFR, is considered for intracavitary therapy of EGFR-positive glioblastoma multiforme, GBM. Relevant literature is reviewed and examples of EGFR expression in GBM are given. The therapeutical efforts made so far using intracavitary anti-tenascin radionuclide therapy of GBM have given limited effects, probably due to low radiation doses to the migrating glioma cells in the brain. Low radiation doses might be due to limited penetration of the targeting agents or heterogeneity in the expression of the target structure. In this article we focus on the possibilities to target EGFR on the tumour cells instead of an extracellular matrix component. There seems to be a lack of knowledge on the degree of intratumoral variation of EGFR expression in GBM, although the expression seemed rather homogeneous over large areas in most of the examples (n=16) presented from our laboratory. The observed homogeneity was surprising considering the genomic instability and heterogeneity that generally characterises highly malignant tumours. However, overexpression of EGFR is, at least in primary GBMs, one of the steps in the development of malignancy, and tumour cells that lose or downregulate EGFR will probably be outgrown in an expanding tumour cell population. Thus, loss of EGFR expression might not be the critical factor for successful intracavitary radionuclide therapy. Instead, it is likely that the penetration properties of the targeting agents are critical, and detailed studies on this are urgent.

Antibodies↗
PubMed1984

Murine leukemia virus-induced T-cell lymphomagenesis: integration of proviruses in a distinct chromosomal region.

A number of mink cell focus-forming (MCF) proviruses was molecularly cloned from mouse lymphoma DNA. From each clone, flanking probes were prepared to detect common integration regions in other MuLV-induced lymphomas. One clone frequently revealed variations in the molecular structure of the corresponding region (Pim-1) in other lymphomas. The results show the following. Changes in the Pim region are seen in 24 out of 93 lymphomas tested. Over 50% of the early T-cell lymphomas show integration in the Pim-1 region. The alterations are seen in different mouse strains and with various MuLVs. The observed variations are caused by the integration of predominantly MCF genomes. All integrations occur in a region spanning less than 20 kb and are associated with the transcriptional activation of a distinct region within the Pim-1 domain. The activated region does not show any homology with 13 known and three putative oncogenes.

Animals↗
PubMed1988

Long-range restriction maps of Plasmodium falciparum chromosomes: crossingover and size variation among geographically distant isolates.

Homologous chromosomes from the human malaria parasite Plasmodium falciparum exhibit striking size polymorphism from isolate to isolate. To examine the structural basis for these variations, we have determined full-length restriction maps of chromosome 4 from three P. falciparum clones. Two clones, HB3 and 3D7, are derived from geographically distant strains, while the third, XP5, is the product of an HB3/3D7 cross. The restriction maps show that, while the overall structure and organization of chromosome 4 from each clone are similar, large-scale variations occur within a few hundred kilobase pairs of the chromosome ends. An apparent crossover between the 3D7 and the HB3 parent chromosomes accounts for a chromosome of intermediate size in clone XP5. Similar restriction studies extended to other parasite chromosomes will ultimately yield a long-range physical map of the P. falciparum genome.

Animals↗
PubMed2001

Molecular cloning, phylogenetic analysis and three-dimensional modeling of Cu,Zn superoxide dismutase (CnSOD1) from three varieties of Cryptococcus neoformans.

Cryptococcus neoformans (Cn), causal agent of fungal meningoencephalitis, has three varieties with variable host predilection. To explore mechanisms for these pathogenic differences, we have characterized Cu,Zn SOD gene (CnSOD1). A Saccharomyces cerevisiae sod1Delta mutant was complemented with Cn var. grubii yeast expression library. The complementing clone had an ORF of 462 bp and the deduced 154 aa sequence showed 61% identity with S. cerevisiae SOD1 and 53-65% with other eukaryotic SOD1s. Cn var. grubii CnSOD1 cDNA was used to clone corresponding cDNAs from var. neoformans and var. gattii. ORFs from three varieties revealed 20-29% differences in deduced aa (s) with a significant 6% non-synonymous aa substitution between Cn var. grubii and Cn var. gattii. Cosmid library screening and PCR cloning were used to obtain genomic SOD1, which was split by five introns with identical placements and a typical 5' splice junction sequence, GTNNGY. These introns also showed a large nt variation among the three Cn varieties. Phylogenetic analyses revealed CnSOD1 to be in a group distinct from other eukaryotic SOD1s and with a significant divergence of the var. grubii from var. gattii. The CnSOD1 -deduced protein was modeled based on the crystal structure of S. cerevisiae SOD1, which showed an excellent fit. Most of the non-synonymous aa substitutions occurred on the outside of the molecule and these may contribute to differences in antigenicity among the three varieties. Notably, Cn var. neoformans and var. gattii Cu,Zn SOD had three substitutions of glycine (Gly26, Gly92 and Gly123 for Asn26, Ser92 and Ser123) that may contribute to the observed lower thermostability of this enzyme vis-a-vis Cn var. grubii. This is the first nucleotide and structural comparison of a protein-encoding gene from the three Cn varieties, which may provide a framework for future studies on the role of Cu,Zn SOD in Cn pathogenesis.

Amino Acid Sequence↗
PubMed2003

Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units.

The study of genomic divergence between humans and primates may provide insight into the origins of human beings and the genetic basis of unique human traits and diseases. Chromosome 21 is the smallest chromosome in the human genome, and some of its regions have been implicated in mental retardation and other diseases. In this study, we sequenced the coding and regulatory regions of 127 known genes on human chromosome 21 in DNA samples from human and chimpanzees and a part of the corresponding genes from orangutan, gorilla, and macaque. Overall, 3,003 nucleotide differences between human and chimpanzee were identified over approximately 400 kb. The differences in coding, promoter, and exon-intron junction regions were 0.51 +/- 0.02%, 0.88 +/- 0.03%, and 0.85 +/- 0.02%, respectively, much lower than the previously reported 1.23% in genomic regions, which suggests the presence of purifying selection. Significant variation in substitution rate among genes was observed by comparing the divergence between human and chimpanzee. Furthermore, by implementing a bioinformatics-based approach, we showed that the identification of genetic variants specific to the human lineage might lead to an understanding of the mechanisms that are attributable to the phenotypes that unique to humans, by changing the structure and/or dosage of the proteins expressed. A phylogenetic analysis unambiguously confirms the conclusion that chimpanzees were our closest relatives to the exclusion of other primates and the relative divergence of the Homo-Pan and that of (Homo-Pan)-Gorilla are 4.93 million years and 7.26 million years, respectively.

3' Untranslated Regions↗
PubMed2005

Positive selection for indel substitutions in the rodent sperm protein catsper1.

Catsper1 is a voltage-gated calcium channel located in the plasma membrane of the sperm tail and is necessary for sperm motility and fertility in mice. We here examine the evolutionary pattern of Catsper1 from nine species of the rodent subfamily Murinae of family Muridae. We show that the rate of insertion/deletion (indel) substitutions in exon 1 of the gene is 4-15 times that in introns or neutral genomic regions, suggesting the presence of strong positive selection that promotes fixations of indel mutations in exon 1. The number of indel polymorphisms within species appears higher than expected from interspecific comparisons, although there are too little data to provide a statistically significant conclusion. These results, together with an earlier report in primates, indicate that positive selection promoting length variation in Catsper1 may be widespread in mammals. A structural model of Catsper1 suggested the importance of the exon 1-encoded region in regulating channel inactivation, which may affect sperm mobility and sperm competition. Our findings provide a necessary foundation for future experimental investigations of Catsper1's function in sperm physiology and role in sperm competition using rodent models.

Amino Acid Sequence↗
PubMed2025

Engineered histones reshape chromatin in human cells.

Histone proteins and their variants have been found to play crucial and specialized roles in chromatin organization and the regulation of downstream gene expression; however, the relationship between histone sequence and its effect on chromatin organization remains poorly understood, limiting our functional understanding of sequence variation between distinct subtypes and across evolution and frustrating efforts to rationally design synthetic histones that can be used to engineer specified cell states. Here, we make the first advance towards engineered histone-driven chromatin organization. By expressing libraries of sequence variants of core histones in human cells, we identify variants that dominantly modulate chromatin structure. We further interrogate variants using a combination of imaging, proteomics, and genomics to reveal both cis and trans-acting mechanisms of effect. Functional screening with transcription factor libraries identifies transcriptional programs that are facilitated by engineered histone expression. Double mutation screens combined with protein language models allow us to learn sequence-to-function patterns and design synthetic histone proteins optimized to drive specific chromatin states. This work establishes a foundation for the high-throughput evaluation and engineering of chromatin-associated proteins and positions histones as tunable nodes for understanding and modulating mesoscale chromatin organization.

Journal Article↗
PubMed2006

Genomics basics: DNA structure, gene expression, cloning, genetic mapping, and molecular tests.

Genomics is the study of the structure and function of the human genome including genes and their surrounding DNA sequences. The over 3 billion base pairs of the human genome have now been sequenced and approximately 25,000 genes acknowledged. However, only 1% of the entire genome has been assigned to protein coding and decades more work is anticipated to define the functional relevance of noncoding DNA as well as the basis and consequences of sequence variations among individuals. For medical scientists, the focus remains on discovering both disease-causing and disease-susceptibility genes. For pharmaceutical companies, the opportunity to develop molecularly targeted therapy is not going unnoticed. For the practicing physician, the prospect of genomic medicine that incorporates molecular diagnosis and pathogenesis-targeted therapy requires basic understanding of terminology and concepts in molecular biology and the corresponding laboratory tests.

Chromosome Mapping↗
PubMed2000

[Monomorphic species specific DNA, detected by polymerase chain reaction with random primers].

Intra- and interspecific variability of total DNA isolated from haploid megagametophytes of coniferous species was examined using polymerase chain reaction with random primers. Based on this technique, one can with certainty detect heterozygosity at gene loci carrying null alleles and thus reveal cryptic intraspecific genetic variation. Large population samples were used. Along with random amplified polymorphic DNA, i.e., widely known fragments (amplicons) polymorphic within a species, we found invariant loci lacking individual or geographic variability but differentiating species within genera and other taxa. This DNA was termed RAMD (random amplified monomorphic DNA) to distinguish it from polymorphic DNA. Our findings suggest that genetic monomorphism of species and the dual structure of the eukaryotic genome can be detected at the DNA level as was previously shown for protein gene markers.

DNA Primers↗
PubMed2002

Ribosomal and mitochondrial DNA sequence variation in Sarcoptes mites from different hosts and geographical regions.

In order to investigate the extent of the genetic variation in the DNA sequences of Sarcoptes scabiei, mite populations collected on Alpine chamois ( Rupicapra rupicapra), Pyrenean chamois ( Rupicapra pyrenaica) and red fox ( Vulpes vulpes) from different localities of Italy and Spain were studied. Sequence analyses were carried out on the second internal transcribed spacer of the nuclear ribosomal DNA and on the 16S mitochondrial rRNA gene. ITS-2 sequences showed a higher degree of genetic polymorphism, mostly randomly distributed in the isolates from different hosts and localities, although both genomic regions are characterised by fixed nucleotide substitutions which were able to discriminate the mites collected on Pyrenean chamois from north-western Spain and on foxes from north-eastern Spain and from north-western Italy with respect to the other isolates. These results suggest the existence of a limitation to free gene exchange between the studied populations, probably related to the genetic structuring of local populations rather than to a differential adaptation to host species.

Animals↗
PubMed1986

Fixation of mutations in the viral genome during an outbreak of foot-and-mouth disease: heterogeneity and rate variations.

Rates of fixation of mutations during the evolution of the foot-and-mouth disease virus (FMDV) C1 in nature have been estimated by hybridization of viral RNA to cloned cDNAs representing defined FMDV genome segments, and comparison of the selected RNAs by T1 RNase oligonucleotide fingerprinting. Values ranged from less than 0.04 X 10(-2) to 4.5 X 10(-2) substitutions per nucleotide per year (s/nt/yr), depending on the time period and the genomic segment considered. Rates for viral structural protein genes were up to sixfold higher than for nonstructural protein genes. Values in excess of 10(-2) s/nt/yr have been measured for the RNA region that encodes VP1-VP3. The nucleotide sequences of the major immunogenic region of capsid protein VP1 have been determined for six new FMDV C1 isolates, and they are compared with the two previously known sequences of FMDV C1 (C-S8 and C1-O). Both oligonucleotide fingerprinting of selected RNA fragments and direct nucleotide sequencing demonstrate that genetic heterogeneity exists among three viruses isolated on the same day, introducing a significant indetermination in the evaluation of fixation rates of mutations. During the FMDV C1 outbreak, amino acid substitutions did occur that are known to affect the immunological properties of the virus. The proportion of mutations between two viral RNAs does not increase significantly with the time elapsed between the two isolations, suggesting a cocirculation of multiple, related, nonidentical FMDVs ('evolving quasispecies') as the mode of evolution of this agent.

Amino Acid Sequence↗
PubMed1981

Structure and variation of human ribosomal DNA: molecular analysis of cloned fragments.

Eco-RI-A fragments of the human ribosomal RNA gene family from two types of tissue and three individuals were cloned in lambda vectors and compared by restriction enzyme digestion and electron microscopy. The EcoRI fragment A contains (i) 0.2 kb of the 3' end of the 18S rDNA, (ii) 2.5 kb of internal transcribed spacer and the 5.8S rDNA, and (iii) 4.6 kb of the 28S rDNA gene. All of the six cloned rDNA fragments isolated are identical by these analyses. Moreover, all contain a HincII site that is absent in about 50% of the rDNA identified by genomic blotting. Polymorphism in the nontranscribed spacer rDNA was studied in genomic blots of BamHI-digested DNA, using the 3' end of the 28S rDNA as a probe. The boundaries between the 18S rDNA, internal transcribed spacer, 28s rDNA, and external nontranscribed spacer were determined by R-loop analysis, further defining the organization of the ribosomal RNA precursor.

Bacteriophage lambda↗
PubMed2005

Environmental programming of stress responses through DNA methylation: life at the interface between a dynamic environment and a fixed genome.

Early experience permanently alters behavior and physiology. These effects are, in part, mediated by sustained alterations in gene expression in selected brain regions. The critical question concerns the mechanism of these environmental "programming" effects. We examine this issue with an animal model that studies the consequences of variations in mother-infant interactions on the development of individual differences in behavioral and endocrine responses to stress in adulthood. Increased levels of pup licking/grooming by rat mothers in the first week of life alter DNA structure at a glucocorticoid receptor gene promoter in the hippocampus of the offspring. Differences in the DNA methylation pattern between the offspring of high- and low-licking/grooming mothers emerge over the first week of life; they are reversed with cross-fostering; they persist into adulthood; and they are associated with altered histone acetylation and transcription factor (nerve growth factor-induced clone A [NGFIA]) binding to the glucocorticoid receptor promoter. DNA methylation alters glucocorticoid receptor expression through modifications of chromatin structure. Pharmacological reversal of the effects on chromatin structure completely eliminates the effects of maternal care on glucocorticoid receptor expression and hypothalamic-pituitary-adrenal (HPA) responses to stress, thus suggesting a causal relation between the maternally induced, epigenetic modification of the glucocorticoid receptor gene and the effects on stress responses in the offspring. These findings demonstrate that the structural modifications of the DNA can be established through environmental programming and that, in spite of the inherent stability of this epigenomic marker, it is dynamic and potentially reversible.

Animals↗
PubMed2000

Mitotic recombination in yeast: elements controlling its incidence.

Mitotic recombination is an important mechanism of DNA repair in eukaryotic cells. Given the redundancy of the eukaryotic genomes and the presence of repeated DNA sequences, recombination may also be an important source of genomic instability. Here we review the data, mainly from the budding yeast S. cerevisiae, that may help to understand the spontaneous origin of mitotic recombination and the different elements that may control its occurrence. We cover those observations suggesting a putative role of replication defects and DNA damage, including double-strand breaks, as sources of mitotic homologous recombination. An important part of the review is devoted to the experimental evidence suggesting that transcription and chromatin structure are important factors modulating the incidence of mitotic recombination. This is of great relevance in order to identify the causes and risk factors of genomic instability in eukaryotes.

Chromatin↗
PubMed1999

Genomic structure, promoter characterisation and mutational analysis of the S100A7 gene: exclusion of a candidate for familial psoriasis susceptibility.

We have recently assigned a locus for familial psoriasis (PS) susceptibility to the region containing the epidermal differentiation complex gene cluster on chromosome 1q21. Gene S10OA7 maps within this cluster and is reported to be markedly over-expressed in the skin lesions of psoriatic patients. In order to analyse S100A7 as a candidate for PS susceptibility, we have determined its genomic structure regarding exon-intron boundaries and the transcription start site. The gene is organised in three exons and two introns, spanning 2.7 kb. The 5' flanking region contains AP1- and Sp1-binding motifs and a TATA box. We have performed functional assays by using the beta-galactosidase gene as a reporter and have confirmed that this region has strong promoter activity. To search for nucleotide variation within S100A7, we have designed a set of primers to amplify each exon and the gene promoter. Polymerase chain reaction products from 15 unrelated PS patients selected from 1q-linked pedigrees and 25 normal controls have been characterised by single-strand conformation polymorphism and direct sequencing techniques. These analyses have revealed the presence of two polymorphisms in the promoter region (-559G/A and -563 A/G), neither of which shows preferential association with the disease. Our results indicate that S100A7 can be excluded as a candidate for PS susceptibility.

Base Sequence↗