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F Galibert

Publications and source records attributed to F Galibert.

At least 37 records · Page 2Linked to original sources
PubMed2001

Chromosome-specific single-locus FISH probes allow anchorage of an 1800-marker integrated radiation-hybrid/linkage map of the domestic dog genome to all chromosomes.

We present here the first fully integrated, comprehensive map of the canine genome, incorporating detailed cytogenetic, radiation hybrid (RH), and meiotic information. We have mapped a collection of 266 chromosome-specific cosmid clones, each containing a microsatellite marker, to all 38 canine autosomes by fluorescence in situ hybridization (FISH). A 1500-marker RH map, comprising 1078 microsatellites, 320 dog gene markers, and 102 chromosome-specific markers, has been constructed using the RHDF5000-2 whole-genome radiation hybrid panel. Meiotic linkage analysis was performed, with at least one microsatellite marker from each dog autosome on a panel of reference families, allowing one meiotic linkage group to be anchored to all 38 dog autosomes. We present a karyotype in which each chromosome is identified by one meiotic linkage group and one or more RH groups. This updated integrated map, containing a total of 1800 markers, covers >90% of the dog genome. Positional selection of anchor clones enabled us, for the first time, to orientate nearly all of the integrated groups on each chromosome and to evaluate the extent of individual chromosome coverage in the integrated genome map. Finally, the inclusion of 320 dog genes into this integrated map enhances existing comparative mapping data between human and dog, and the 1000 mapped microsatellite markers constitute an invaluable tool with which to perform genome scanning studies on pedigrees of interest.

Animals↗
PubMed2001

DNA sequence and physical mapping of the canine transglutaminase 1 gene.

The transglutaminase 1 gene (TGM1) encodes an enzyme necessary for cross-linking the structural proteins that form the cornified envelope, an essential component of the outermost layer of the skin, the stratum corneum. Reported here is the complete coding region of canine TGM1, its chromosome localization, and its map position in the integrated canine linkage-radiation hybrid map. Canine TGM1 consists of 2,448 nucleotides distributed over 15 exons. The nucleotide sequence has 90% identity to human TGM1. The deduced canine TGM1 protein is 816 amino acids long and is 92% identical to human TGM1. Using fluorescence in situ hybridization, we localized canine TGM1 to dog (Canis familiaris) chromosome 8 (CFA 8q). Canine TGM1 localized to CFA 8 on the integrated linkage-radiation hybrid map in the interval FH2149-MYH7. Characterizing the coding region of canine TGM1 is a first step in examining the role of this enzyme in normal and defective cornification in the dog.

Amino Acid Sequence↗
PubMed2000

From sequence to chromosome: the tip of the X chromosome of D. melanogaster.

One of the rewards of having a Drosophila melanogaster whole-genome sequence will be the potential to understand the molecular bases for structural features of chromosomes that have been a long-standing puzzle. Analysis of 2.6 megabases of sequence from the tip of the X chromosome of Drosophila identifies 273 genes. Cloned DNAs from the characteristic bulbous structure at the tip of the X chromosome in the region of the broad complex display an unusual pattern of in situ hybridization. Sequence analysis revealed that this region comprises 154 kilobases of DNA flanked by 1.2-kilobases of inverted repeats, each composed of a 350-base pair satellite related element. Thus, some aspects of chromosome structure appear to be revealed directly within the DNA sequence itself.

Animals↗
PubMed2000

High-resolution physical map of the pSymb megaplasmid and comparison of the three replicons of Sinorhizobium meliloti strain 1021.

A high-resolution physical map of the larger megaplasmid (pSymb) of Sinorhizobium meliloti strain 1021 has been constructed by using BAC libraries and an original two-step PCR screening method. This method, previously used to map both the chromosome and the smaller megaplasmid (pSyma), allowed us to position over the genome a total of 842 markers with an average density of one marker every 8.3 kb. In addition, we used BLASTX and PRODOM analysis to predict a function for a number of STSs. This work led to the discovery of several interesting loci and to a comparison of the genetic information carried by each replicon. The two main results emerging from this study are (i) a biased distribution of housekeeping genes, mainly detected on chromosome, and (ii) the presence of an unexpected number of transporters, mainly belonging to the ABC superfamily. These are broadly distributed across the whole genome, but particularly found on pSymb.

ATP-Binding Cassette Transporters↗
PubMed2000

POL32, a subunit of the Saccharomyces cerevisiae DNA polymerase delta, defines a link between DNA replication and the mutagenic bypass repair pathway.

Pol32 is a subunit of Saccharomyces cerevisiae DNA polymerase delta required in DNA replication and repair. To gain insight into the function of Pol32 and to determine in which repair pathway POL32 may be involved, we extended the analysis of the pol32delta mutant with respect to UV and methylation sensitivity, UV-induced mutagenesis; and we performed an epistasis analysis of UV sensitivity by combining the pol32delta with mutations in several genes for postreplication repair (RA D6 group), nucleotide excision repair (RAD3 group) and recombinational repair (RAD52 group). These studies showed that pol32delta is deficient in UV-induced mutagenesis and place POL32 in the error-prone RAD6/ REV3 pathway. We also found that the increase in the CAN1 spontaneous forward mutation of different rad mutators relies entirely or partially on a functional POL32 gene. Moreover, in a two-hybrid screen, we observed that Pol32 interacts with Srs2, a DNA helicase required for DNA replication and mutagenesis. Simultaneous deletion of POL32 and SRS2 dramatically decreases cellular viability at 15 degrees C and greatly increases cellular sensitivity to hydroxyurea at the permissive temperature. Based on these findings, we propose that POL32 defines a link between the DNA polymerase and helicase activities, and plays a role in the mutagenic bypass repair pathway.

DNA Polymerase III↗
PubMed2000

An integrated linkage-radiation hybrid map of the canine genome.

Purebred dogs are a unique resource for dissecting the molecular basis of simple and complex genetic diseases and traits. As a result of strong selection for physical and behavioral characteristics among the 300 established breeds, modern dogs are characterized by high levels of interbreed variation, complemented by significant intrabreed homogeneity. A high-resolution map of the canine genome is necessary to exploit the mapping power of this unusual resource. We describe here the integration of an expanded canine radiation hybrid map, comprised of 600 markers, with the latest linkage map of 341 markers, to generate a map of 724 markers-the densest map of the canine genome described to date. Through the inclusion of 217 markers on both the linkage and RH maps, the 77 RH groups are reduced to 44 syntenic groups, thus providing comprehensive coverage of most of the canine genome.

Animals↗
PubMed2000

Transcriptional analysis of the 69-kb sequence centromeric to HLA-J: a dense and complex structure of five genes.

Performed within the framework of the sequencing of the 356-kb MHC class I distal region, systematic bioinformatic annotation and preliminary experiments conducted on the whole sequence indicate a high level and a complex pattern of expression. In this paper, we analyze a particular stretch of 69 kb centromeric to the HLA-J gene, in which we identify 21 different mRNAs mainly expressed in testis, and characterize five different transcription units, HZFw, HZFc, HCGV, HTEX6, and HTEX4. These tightly linked genes form a cluster conserved between human and mouse and displaying a high gene density of about one every 14 kb. Alternative splicing processes are observed for all the genes, together with an alternative polyadenylation event for gene HTEX4, sense/antisense mRNA overlaps for HZFw and HZFc, for HZFw and HCGV at their 3' end, and for HTEX6 and HTEX4 at their 5' end. This complex genomic structure suggests a mechanism of coregulation by cis-interaction in gene expression.

Base Sequence↗
PubMed2000

Canine genetics comes of age.

The dog, as human's favored companion, is unique among animal species in providing new insights into human genetic disease. In this review, we will discuss both the breed and the population structure of dogs and why that makes canines amenable to genetic studies. We will review the current state of the map and discuss the particular disease states in which canines stand to make the greatest contribution to medical genetics.

Animals↗
PubMed2000

Identification and characterization of a set of 100 tri- and dinucleotide microsatellites in the canine genome.

A set of 100 canine microsatellite markers--83 dinucleotides and 17 trinucleotides--is reported. A study of their frequency in the dog genome showed that, while the frequency of the CA repeats is one (CA)n every 47 kb, the 10 trinucleotidic frequencies vary from one every 117 kb (AGG)n to one every 875 kb (AGT)n. Polymorphism analysis performed on 16 unrelated mongrel dogs showed that 80% of dinucleotides are polymorphic, while only 30% of the trinucleotides are so. Of this set of 100 markers, 56 have been mapped on the RHDF5000 dog/hamster whole genome radiation hybrid panel. Moreover, through systematic BLAST analogy searches of the microsatellite-containing clone sequence, three new dog genes could be identified, based on their human ortholog. All of the markers presented may prove useful in physical mapping methods, and polymorphic microsatellites in genetic linkage studies or parentage controls in dog.

Animals↗
PubMed2000

High-resolution physical map of the Sinorhizobium meliloti 1021 pSyma megaplasmid.

To facilitate sequencing of the Sinorhizobium meliloti 1021 pSyma megaplasmid, a high-resolution map was constructed by ordering 113 overlapping bacterial artificial chromosome clones with 192 markers. The 157 anonymous sequence tagged site markers (81,072 bases) reveal hypothetical functions encoded by the replicon.

Chromosomes, Bacterial↗
PubMed2000

Using the fluorogenic 5' nuclease assay for high-throughput detection of (CA)n repeats in radiation hybrid mapping.

Here, the power of the 5' nuclease assay to detect PCR products containing (CA)n repeats was compared with that of the classical electrophoretic analysis. This assay, which relies on the use of a unique (CA)10 energy transfer-labeled probe and the 5' nuclease activity of Taq DNA polymerase, was used to construct a dog radiation hybrid map consisting of microsatellite markers. Data from over 7000 PCRs were analyzed in parallel by the fluorogenic assay and the conventional ethidium bromide-stained, agarose gel-based assay. We show that the fluorogenic assay provides a sensitive, reliable and specific method for detecting (CA)n amplimers. Moreover, as no processing is required after the PCR, the risk of carryover contamination and the time required for sample analysis are greatly reduced. All radiation hyrid (RH) assays can be performed using a single PCR protocol, and a standard analysis method has been developed that enables numerically automated data processing. On the whole, using this strategy greatly enhanced the rapidity, throughput and accuracy of the RH mapping of microsatellite markers.

5'-Nucleotidase↗
PubMed2000

Sequencing the Sinorhizobium meliloti genome.

The Sinorhizobium meliloti genome consists of three replicons. This bacterium forms an intricate symbiotic relationship with the roots of certain legumes and is considered as an agriculturally important nitrogen-fixer. A consortium of 6 European laboratories was organized to sequence its single chromosome (3.7 Mb), whereas the other two elements (pSyma 1.4 Mb and pSymb 1.7 Mb) will be sequenced by other groups.

Base Sequence↗
PubMed1999

A high-density physical map of Sinorhizobium meliloti 1021 chromosome derived from bacterial artificial chromosome library.

As part of the European Sinorhizobium meliloti (strain 1021) chromosome sequencing project, four genomic bacterial artificial chromosome (BAC) libraries have been constructed, one of which was mainly used for chromosome mapping. This library consists of 1,824 clones with an average insert size of 80 kilobases and represents approximately 20-fold total genome coverage [6.8 megabases (Mbs)]. PCR screening of 384 BAC clones with 447 chromosomal markers (PCR primer pairs), consisting of 73 markers representing 118 genes (40 individual genes and 78 genes clustered in 23 operons), two markers from the rrn operon (three loci), four markers from insertion sequences (approximately 16 loci) and 368 sequence-tagged sites allowed the identification of 252 chromosomal BAC clones and the construction of a high-density physical map of the whole 3.7-Mb chromosome of S. meliloti. An average of 5.5 overlapping and colinear BAC clones per marker, correlated with a low rate of deleted or rearranged clones (0.8%) indicate a solid BAC contigation and a correct mapping. Systematic BLASTX analysis of sequence-tagged site marker sequences allowed prediction of a biological function for a number of putative ORFs. Results are available at. This map, whose resolution averages one marker every 9 kilobases, should provide a valuable tool for further sequencing, functional analysis, and positional cloning.

Chromosome Mapping↗
PubMed1999

Characterization of 463 type I markers suitable for dog genome mapping.

In total, 463 canine gene markers were identified and characterized to serve as reagents in canine genome map projects. These markers are distributed over 221 canine gene markers, 139 TOASTs (Traced Orthologous Sequence Tags), 27 canine TOASTs, and 76 huESTs (human Expressed Sequence Tags). Out of 310 canine gene markers, 59%-84% were successfully amplified on dog DNA, the highest rates of success being observed when the exon/intron structure is known. Concerning TOASTs and human ESTs, of the 225 and 300 markers analyzed, 62% and 25% respectively were able to produce a dog positive amplification. As part of an ongoing project to map the canine genome using a dog/hamster radiation hybrid panel, these markers were tested for their specificity on dog versus hamster DNA. Thus 61%, 21%, and 12% of dog gene markers, TOASTs, and huESTs met the criteria required for radiation hybrid mapping, respectively. All of these 463 canine gene markers, however, are available and will be of value to any other mapping strategies.

Animals↗
PubMed1999

Construction and optimization of a dog whole-genome radiation hybrid panel.

A dog whole-genome radiation hybrid (WGRH) panel including 126 clones was constructed by fusing dog fibroblasts irradiated at 5000 rads with thymidine kinase-deficient hamster cells. The average retention frequency of the panel designated as RHDF5000 is 21%, and its resolution power is estimated at 600 kb. The data provided by typing 400 markers were used to estimate linkage power changes subsequent to panel reduction. These changes were analyzed by recomputing typing data from five reduced panels. From these simulations, the parameters allowing investigation of the evolution of the linkage power in the course of panel reduction were determined. Guidelines for constructing a WGRH panel are proposed.

Animals↗
PubMed1999

The Saccharomyces cerevisiae protein YJR043C (Pol32) interacts with the catalytic subunit of DNA polymerase alpha and is required for cell cycle progression in G2/M.

We have analysed the YJR043c gene of Saccharomyces cerevisiae, previously identified by systematic sequencing. The deletion mutant (yjr043cdelta) shows slow growth at low temperature (15 degrees C), while at 30 degrees C and 37 degrees C the growth rate of mutant cells is only moderately affected. At permissive and nonpermissive temperatures, mutant cells were larger and showed a high proportion of large-budded cells with a single duplicated nucleus at or beyond the bud neck and a short spindle. This phenotype was even more striking at low temperature, the mutant cells becoming dumbbell shaped. All these phenotypes suggest a role for YJR043C in cell cycle progression in G2/M phase. In two-hybrid assays, the YJR043c gene product specifically interacted with Pol1, the catalytic subunit of DNA polymerase alpha. The pol1-1 /yjr043cdelta double mutant showed a more severe growth defect than the pol1-1 single mutant at permissive temperature. Centromeric plasmid loss rate elevated in yjr043cdelta. Analysis of the sequence upstream of the YJR043c ORF revealed the presence of an MluI motif (ACGCGT), a sequence associated with many genes involved in DNA replication in budding yeast. The cell cycle phenotype of the yjr043cdelta mutant, the evidence for genetic interaction with Pol1, the presence of an MluI motif upstream and the elevated rate of CEN plasmid loss in mutants all support a function for YJR043C in DNA replication.

Catalytic Domain↗