ABSTRACT
Five greenhouse experiments were conducted in southeastern Sicily (Italy) from 2000 to 2009 to evaluate the effectiveness of soil solarization in reducing natural infections of tomato corky root caused by Pyrenochaeta lycopersici. Tests were performed with clear, traditional, and innovative plastic films and fumigant applications. In all the trials, soil solarization was effective in controlling corky root disease relative to an untreated control. Although inducing different thermal regimes in the soil, the use of different greenhouse covering and mulching films for solarization proved effective in reducing corky root severity relative to the untreated control. Solarization reduced infections caused by P. lycopersici comparable with methyl bromide fumigation and greater than metham sodium and metham potassium. Among the tested films, green coextruded film may be most attractive because it can be left on after solarization as mulch.
ABSTRACT
Two novel mouse genes and one novel human gene that define distinctive eukaryotic nucleotide-binding proteins (NUBP) and are related to the mrp gene of prokaryotes are characterized. Phylogenetic analyses of the genes, encoding a short form (Nubp2) and a long form (Nubp1) of NUBP, clearly establish them as a new NUBP/MRP gene family that is well conserved throughout phylogeny. In addition to conserved ATP/GTP-binding motifs A (P-loop) and A', members of this family share at least two highly conserved sequence motifs, NUBP/MRP motifs alpha and beta. Only one type of NUBP/MRP gene has been observed thus far in prokaryotes, but there are two types in eukaryotes. One group includes mouse Nubp1, human NBP, yeast NBP35, and Caenorhabditis elegans F10G8.6 and is characterized by a unique N-terminal sequence with four cysteine residues that is lacking in the other group, which includes mouse Nubp2, human NUBP2, and yeast YIA3w. Northern blot analyses of the two mouse genes show distinctive patterns consistent with this classification. Mouse Nubp2 is mapped to the t-complex region of mouse Chromosome 17, whereas Nubp1 is mapped to the proximal region of mouse Chromosome 16. Interestingly, both regions are syntenic with human chromosome 16p13.1-p13.3, suggesting that a chromosomal breakage between Nubp2 and Nubp1 probably occurred during the evolution of mouse chromosomes.
Subject(s)
GTP-Binding Proteins/genetics , Multigene Family , Nucleotides/metabolism , Amino Acid Sequence , Animals , Base Sequence , Caenorhabditis elegans/genetics , Carrier Proteins/genetics , Chromosome Mapping , Consensus Sequence , DNA Primers/genetics , DNA, Complementary/genetics , Humans , Intracellular Signaling Peptides and Proteins , Mice , Molecular Sequence Data , Phylogeny , Saccharomyces cerevisiae/genetics , Sequence Homology, Amino Acid , Species SpecificitySubject(s)
Apoptosis/genetics , Nuclear Proteins , Physical Chromosome Mapping , Proteins/genetics , X Chromosome/genetics , Apoptosis Regulatory Proteins , Chromosomes, Artificial, Yeast/genetics , Cloning, Molecular , Expressed Sequence Tags , Female , Humans , Hybrid Cells , Hydrolases , Intracellular Signaling Peptides and Proteins , Male , Open Reading Frames/genetics , Sequence Homology, Amino Acid , Tumor Cells, CulturedABSTRACT
Methylation of CpG islands is an established transcriptional repressive mechanism and is a feature of silencing in X chromosome inactivation. Housekeeping genes that are subject to X inactivation exhibit differential methylation of their CpG islands such that the inactive alleles are hypermethylated. In this report, we examine two contrasting X-linked genes with CpG islands for regulation by DNA methylation: SYBL1, a housekeeping gene in the Xq pseudoautosomal region, and GPC3, a tissue-specific gene in Xq26 that is implicated in the etiology of the Simpson-Golabi-Behmel overgrowth syndrome. We observed that in vitro methylation of either the SYBL1 or the GPC3 promoter resulted in repression of reporter constructs. In normal contexts, we found that both the Y and inactive X alleles of SYBL1 are repressed and hypermethylated, whereas the active X allele is expressed and unmethylated. Furthermore, the Y and inactive X alleles of SYBL1 were derepressed by treatment with the demethylating agent azadeoxycytidine. GPC3 is also subject to X inactivation, and the active X allele is unmethylated in nonexpressing leukocytes as well as in an expressing cell line, suggesting that methylation is not involved in the tissue-specific repression of this allele. The inactive X allele, however, is hypermethylated in leukocytes, presumably reflecting early X inactivation events that become important for gene dosage in expressing lineages. These and other data suggest that all CpG islands on Xq, including the pseudoautosomal region, are subject to X inactivation-induced methylation. Additionally, methylation of SYBL1 on Yq may derive from a process related to X inactivation that targets large chromatin domains for transcriptional repression.
Subject(s)
DNA Methylation , Gene Expression Regulation/genetics , Heparan Sulfate Proteoglycans , Heparitin Sulfate/genetics , Membrane Proteins/genetics , Proteoglycans/genetics , Transcription, Genetic/genetics , X Chromosome/genetics , Aza Compounds/pharmacology , Cell Line , CpG Islands/genetics , Deoxycytidine/analogs & derivatives , Dosage Compensation, Genetic , Glypicans , Leukocytes/metabolism , Molecular Sequence Data , Polymerase Chain Reaction/methods , Promoter Regions, Genetic/genetics , R-SNARE Proteins , Sequence Analysis, DNA , Transfection/genetics , Y Chromosome/geneticsABSTRACT
As large-scale sequencing accumulates momentum, an increasing number of instances are being revealed in which genes or other relatively rare sequences are duplicated, either in tandem or at nearby locations. Such duplications are a source of considerable polymorphism in populations, and also increase the evolutionary possibilities for the coregulation of juxtaposed sequences. As a further consequence, they promote inversions and deletions that are responsible for significant inherited pathology. Here we review known examples of genomic duplications present on the human X chromosome and autosomes.
Subject(s)
Gene Duplication , Genetic Predisposition to Disease/genetics , Genome, Human , X Chromosome/genetics , X Chromosome/pathology , Humans , Repetitive Sequences, Nucleic Acid/geneticsABSTRACT
We have developed an approach to identify and localize cDNAs encoded by YACs. In this scheme, a YAC truncation vector containing a cDNA library is used to interrupt the YAC by homologous recombination in yeast. This approach generates YACs truncated at the site of recombination between the cDNA and the cognate YAC sequence and thus localizes the gene in the YAC. This method results in the production of a large percentage of true recombinants identifying gene encoding regions of the genome. This approach is shown to identify an unique EST sequence from a YAC in Xp22, the recently described transketolase-like gene in a YAC from Xq28 and a putative kinesin-like gene in Xq13. This system should also be useful in the mapping of YACs by targeted integration. We have constructed a new telomere truncation vector, pGR8, which incorporates two selectable markers, HIS5 and LYS2. This vector overcomes problems of previous vectors including: incompatibility with most YAC libraries, vector homology with the YAC arms and high backgrounds resulting from the use of a single selectible marker. A third counterselection with 5-fluoroorotic acid (5FOA) against yeast clones retaining the URA3 gene was also employed to reduce background further. Therefore, this vector and approach should be useful to the transcriptional analysis of YAC maps of any genome.
Subject(s)
Chromosomes, Artificial, Yeast/chemistry , Chromosomes, Artificial, Yeast/genetics , Cloning, Molecular/methods , DNA, Complementary/genetics , DNA, Complementary/isolation & purification , Genetic Vectors/chemical synthesis , Recombination, Genetic , Embryo, Mammalian , Gene Library , Genetic Vectors/genetics , Humans , Molecular Sequence Data , Polymerase Chain Reaction/methodsABSTRACT
We have isolated a novel full-length cDNA for a gene (IGSF1) located in distal Xq25. This transcript is highly expressed in adult testis and fetal liver but is undetectable in adult liver. A smaller alternate form is highly expressed in adult heart. The gene encodes a protein of 1327 amino acids with several recognizable functional domains. The protein has a putative signal peptide and transmembrane region, 15 potential sites for N-linked glycosylation, and 12 C2-type immunoglobulin (Ig)-like domains. All of the Ig-like domains contain the two conserved cysteine residues that form intradomain disulfide bonds typical of this superfamily. These features are consistent with a possible role for this molecule in cell surface recognition or cell-cell interaction.
Subject(s)
Genes, Immunoglobulin/genetics , Immunoglobulins/genetics , Membrane Proteins/genetics , X Chromosome/genetics , Amino Acid Sequence , Base Sequence , Cloning, Molecular , Gene Expression Regulation, Developmental , Gene Library , Humans , Immunoglobulins/biosynthesis , Immunoglobulins/chemistry , Membrane Proteins/biosynthesis , Membrane Proteins/chemistry , Models, Molecular , Molecular Sequence Data , Organ Specificity/genetics , TeratocarcinomaABSTRACT
We report the cloning of a novel Xp/Yp pseudoautosomal gene called PGPL , and demonstrate that PGPL , like other pseudoautosomal genes, escapes X inactivation and has a functional homologue on the Y chromosome. This gene is expressed in all the tissues examined and is highly conserved across several species. The PGPL gene encodes a protein of 442 amino acids and shows the consensus sequences of a series of motifs of the GTP-binding protein domain. Using fluorescence in situ hybridization analysis on normal males and on patients with rearrangements in the pseudoautosomal region, the gene was localized within 500 kb of the telomere. Further refinement using a cosmid contig of the region places this novel gene within 80-110 kb of the telomere, making this the most telomeric gene on the short arms of the sex chromosomes.
Subject(s)
GTP-Binding Proteins/genetics , Gene Rearrangement , Telomere/genetics , X Chromosome , Y Chromosome , Amino Acid Sequence , Animals , Base Sequence , Chromosome Mapping , Cloning, Molecular , Consensus Sequence , Female , GTP-Binding Proteins/biosynthesis , GTP-Binding Proteins/chemistry , Genetic Markers , Humans , In Situ Hybridization, Fluorescence , Male , Mice , Molecular Sequence Data , Muscle, Skeletal/metabolism , Organ Specificity , Polymerase Chain Reaction , Sequence Alignment , Sequence Homology, Amino Acid , Species SpecificityABSTRACT
Recently, we have shown that mutations in the X-linked glypican 3 (GPC3) gene cause the Simpson-Golabi-Behmel overgrowth syndrome (SGBS; ). The next centromeric gene detected is another glypican, glypican 4 (GPC4), with its 5' end 120763bp downstream of the 3' terminus of GPC3. One recovered GPC4 cDNA with an open reading frame of 1668nt encodes a putative protein containing three heparan sulfate glycosylation signals and the 14 signature cysteines of the glypican family. This protein is 94.3% identical to mouse GPC4 and 26% identical to human GPC3. In contrast to GPC3, which produces a single transcript of 2.3kb and is stringently restricted in expression to predominantly mesoderm-derived tissues, Northern analyses show that GPC4 produces two transcripts, 3.4 and 4.6kb, which are very widely expressed (though at a much higher level in fetal lung and kidney). Interestingly, of 20 SGBS patients who showed deletions in GPC3, one was also deleted for part of GPC4. Thus, GPC4 is not required for human viability, even in the absence of GPC3. This patient shows a complex phenotype, including the unusual feature of hydrocephalus; but because an uncle with SGBS is less affected, it remains unclear whether the GPC4 deletion itself contributes to the phenotype.
Subject(s)
Heparan Sulfate Proteoglycans/genetics , Heparitin Sulfate/genetics , Proteoglycans/genetics , X Chromosome/genetics , Abnormalities, Multiple/genetics , Amino Acid Sequence , Animals , Base Sequence , Centromere , DNA/genetics , Gene Expression Regulation, Developmental , Glypicans , Humans , Mice , Molecular Sequence Data , Physical Chromosome Mapping , RNA, Messenger/genetics , RNA, Messenger/metabolism , Sequence Alignment , Sequence Deletion , Sequence Homology, Amino Acid , Tissue Distribution , Transcription, Genetic , Tumor Cells, CulturedABSTRACT
GPC3, the gene modified in the Simpson-Golabi-Behmel gigantism/overgrowth syndrome (SGBS), is shown to span more than 500 kb of genomic sequence, with the transcript beginning 197 bp 5' of the translational start site. The Xq26.1 region containing GPC3 as the only known gene has been extended to > 900 kb by sequence analysis of flanking BAC clones. Two GC isochores (40.6 and 42.6% GC) are observed at the 5' and 3' ends of the locus, with a large repertoire of repetitive sequences that includes an unusual cluster of four L1 elements > 92% identical over 2.8 kb. Eight exons, accounting for the full 2.4-kb GPC3 cDNA, have been sequenced along with neighboring intronic regions. PCR assays have been developed to amplify each exon and exon/intron junction sequence, to help discriminate instances of SGBS among individuals with overgrowth syndromes and to facilitate mutational analysis of lesions in the gene.
Subject(s)
Exons , Heparan Sulfate Proteoglycans , Heparitin Sulfate/genetics , Introns , Promoter Regions, Genetic , Proteoglycans/genetics , Amino Acid Sequence , Base Sequence , Chromosome Mapping , DNA, Complementary , Glypicans , Humans , Molecular Sequence Data , Polymorphism, Single-Stranded Conformational , Sequence Homology, Nucleic Acid , X ChromosomeABSTRACT
We have isolated a full-length cDNA corresponding to the XAP5 gene in Xq28. An unusual feature of the cDNA is that it contains runs of CCG repeats in the 5' untranslated region, typical of genes that exhibit anticipation. It has a striking pattern of differential expression and is greatly enhanced in various fetal tissues. This predicted protein encodes a unique 339-amino-acid polypeptide that contains a large percentage of highly charged residues and a possible nuclear localization signal. A comparison to genomic sequence shows that XAP-5 comprises 13 exons spanning 6.5 kb. An examination of the human population indicates that the longest CCG run is polymorphic and varies in length from 8 to 12 repeats.
Subject(s)
Nuclear Proteins/genetics , Amino Acid Sequence , Base Sequence , DNA, Complementary , Humans , Molecular Sequence Data , Polymorphism, Genetic , Trinucleotide Repeats , X ChromosomeABSTRACT
The recently discovered second pseudoautosomal region (XqPAR) contains at least two genes, IL9R and SYBL1. Recent findings show that, like XpPAR genes, IL9R escapes X inactivation and its Y allele is also expressed, but SYBL1 seems to act like an X-linked gene, expressed from the active X chromosome but not from the inactive X or Y. Here we show that differences are also seen in the evolution of the sex chromosome locations of IL9R and SYBL1. IL9R is known to be autosomal in mice, and is X-linked only in primates. SYBL1, however, has been found to be on the X chromosome in all mammals tested, from marsupials to humans. Both genes were duplicated on the Y homologue of the terminal portion of the X chromosome during the evolution of Homo sapiens from other higher primates. The inactivation pattern of SYBL1 may be correlated with its longer history of X linkage, and at a more centromeric chromosomal position during evolution; the more recent X linkage and more telomeric position of the IL9R gene may explain its autosomal, 'uninactivated' transcriptional status.
Subject(s)
Evolution, Molecular , Gene Expression Regulation , Membrane Proteins/genetics , Receptors, Interleukin/genetics , X Chromosome , Animals , Base Sequence , Chromosome Mapping , DNA, Complementary , Genome , Humans , Marsupialia/genetics , Mice , Mice, Inbred C57BL , Molecular Sequence Data , Primates/genetics , R-SNARE Proteins , Receptors, Interleukin-9ABSTRACT
Human Xp22.1 contains genes involved in mineral balance that are implicated in X-linked hypophosphatemia (XLH) in humans, its murine homologue (Hyp), and another distinct murine hypophosphatemic disorder (Gy). In XLH, a gene, PEX, has been found to be mutated in up to 83% of patients but the sequences of the promoter and 5' end have not been characterized. To further the understanding of this genomic region, 139,454 bp in Xp22.1 have been sequenced. Our analysis confirms the three most 5' published exons of PEX and extends through a putative PEX promoter region. The 5' untranslated sequence of PEX and the mouse and rat equivalents are very highly homologous, implying a conserved functional significance. In addition, we mapped and analyzed another gene 5' of PEX, spermine synthase (SpS), which encodes a ubiquitous enzyme of polyamine metabolism that may contribute to the pathophysiology of Gy. SpS consists of 11 exons spread over 54 kb. The definition of the locations of SpS and the putative promoter region of PEX will facilitate functional analysis of these genes.
Subject(s)
Hypophosphatemia/genetics , Proteins/genetics , Spermine Synthase/genetics , X Chromosome/genetics , Amino Acid Sequence , Animals , Base Sequence , Chromosome Mapping , Cosmids , CpG Islands , DNA, Complementary/genetics , Exons , Genetic Linkage , Humans , Mice , Molecular Sequence Data , PHEX Phosphate Regulating Neutral Endopeptidase , Promoter Regions, Genetic , RatsABSTRACT
Most genes on the X chromosome undergo "inactivation," being transcribed from only one copy in female somatic cells, but several human genes have been shown to be expressed from both the active and the otherwise inactivated homologue. To assess further the fraction and location of genes that escape inactivation, we have analyzed the inactivation status of a set of 73 expressed sequence tags that were derived from the sequencing of cDNA collections and mapped to the X chromosome. Of 33 that were expressed in cultured cells, as assessed by reverse transcription and PCR, 4 (about 12%) were transcribed from both the active and the inactive X chromosome. Two, RPS4 and PCTAIRE1, are already known to escape inactivation; the other 2, of unknown function, include a short cDNA with a full open reading frame and a transcript with no detectable open reading frame. They map, respectively, to Xp11.3-p11.4 and Xp22.2; both regions were previously reported to encode sequences transcribed from the inactive X. Neither transcript has a corresponding sequence on the Y. Thus, they exhibit double dosage in females compared to males, and inactivation status may be inconsequential for these transcribed sequences.
Subject(s)
Dosage Compensation, Genetic , X Chromosome/genetics , Base Sequence , Blotting, Northern , Blotting, Southern , Chromosome Mapping , DNA, Complementary/genetics , Female , Gene Dosage , Gene Expression Regulation/genetics , Genetic Linkage/genetics , Genetic Markers , Humans , Information Systems , Molecular Sequence Data , Open Reading Frames/genetics , Polymerase Chain Reaction , RNA-Directed DNA Polymerase/genetics , RNA-Directed DNA Polymerase/metabolism , Y Chromosome/geneticsABSTRACT
A YAC/STS map of the X chromosome has reached an inter-STS resolution of 75 kb. The map density is sufficient to provide YACs or other large-insert clones that are cross-validated as sequencing substrates across the chromosome. Marker density also permits estimates of regional gene content and a detailed comparison of genetic and physical map distances. Five regions are detected with relatively high G + C, correlated with gene richness; and a 17-Mb region with very low recombination is revealed between the Xq13.3 [XIST] and Xq21.3 XY homology loci.
Subject(s)
Chromosome Mapping , X Chromosome/genetics , Base Composition/genetics , Chromosome Mapping/methods , Chromosomes, Artificial, Yeast/genetics , Cytosine Nucleotides/genetics , DNA, Complementary/genetics , Gene Expression/genetics , Genomic Library , Guanine Nucleotides/genetics , Humans , Sequence Tagged SitesABSTRACT
STSs, which have been used to build and format clone contigs, have been used here to assemble a transcriptional map across a cytogenetic band. Of fifty one STSs in Xq28, 20 were positive by RT-PCR. Thus, an additional 20 possible ESTs were detected among the STSs, and seven of these also identified cDNAs in at least one library. The transcripts confirm the high expression level of this region, correlated with its GC compositional map and CpG island content.
Subject(s)
Sequence Tagged Sites , Transcription, Genetic , X Chromosome , Base Sequence , Blotting, Northern , DNA, Complementary , Gene Expression , Humans , Molecular Sequence Data , Sequence Homology, Nucleic AcidABSTRACT
X-linked hypophosphatemia (XLH), which is a heritable metabolic bone disease characterized biochemically by selective renal phosphate (Pi) wasting, is associated with mutations in the PEX (Phosphate-regulating gene with homologies to Endopeptidases on the X-chromosome) gene. To further explore the physiologic role of PEX and define its effect in XLH we have determined the expression and tissue distribution. Northern analysis found abundant PEX mRNA in a restricted pattern, predominantly in adult ovary and fetal lung. In addition, PEX expression was also found in adult lung and fetal liver. A PEX cDNA of 2550 basepairs, which contains the full PEX coding region, was isolated from a human ovary cDNA library. The PEX cDNA shows high homology to other membrane-bound zinc metallopeptidases. The presence of PEX in nonosseous tissues strongly suggests features of a systemic role, rather than a unique function in bone development.
Subject(s)
Hypophosphatemia/genetics , Proteins/genetics , Amino Acid Sequence , Base Sequence , Cloning, Molecular , DNA, Complementary/genetics , Gene Expression , Humans , Introns , Molecular Sequence Data , PHEX Phosphate Regulating Neutral Endopeptidase , Point Mutation , RNA, Messenger/genetics , Species Specificity , X ChromosomeABSTRACT
Seven thyroid function parameters (total T3, TT3; total T4, TT4; free T3, FT3; free T4, FT4; TSH; anti-thyroglobulin antibodies, TGAb; and anti-microsomal antibodies, TMAb) were studied in a series of 20 healthy centenarians in order to evaluate their thyroid function status. Our results showed that all the parameters were within normal range, with the exception of TT4 values which were reduced in 60% of centenarians examined. Therefore, the authors believe that the production of thyroid hormones seems to decrease in advanced years, but that this may not solely depend on thyroid parenchyma involution, but also on a lower demand by the hormone sensitive tissues. Centenarians seem to be adapted euthyroid subjects who present low, nonetheless adequate, levels of circulating thyroid hormone (T4).
ABSTRACT
Bone mineral density at medio distal (MD-BMD) and ultra distal (UD-BMD) sites of non dominant radius were studied, using a DEXA Mineralometer (TURBOSCAN-NIM) on a series of 20 patients, over 60 years old, all thyroidectomized for thyroid carcinoma and treated with levothyroxin replacement therapy. T3 and T4 (RIA method), TSH (IRMA method) and two cardiac parameters as TPER (time peak ejection rate) and TPFR (time peak filling rate) by angiocardioscintigraphy were also determined. Results showed that 19 patients considering MD-BMD values and ten considering UD-BMD values were at risk of fractures. Circulating T3 levels were within normal range in 17 patients, elevated in two cases and reduced in one case. Circulating T4 levels were within normal range in 15 patients, increased in four cases and reduced in one case. Circulating TSH levels were within normal range in 17 patients, reduced in two cases and elevated in one case. TPER were reduced in 18 patients and normal in two cases. TPFR were reduced in six patients and normal in fourteen cases. The authors administered alendronate (10 mg/day) which seems to prevent bone loss, especially at the level of the trabecular bone. Bone loss reverted at 6 and 12 months, confirming that disphosphonates slow down this phenomenon in a situation of increased bone turnover (e.g. patients on long-term L-T4 therapy).
ABSTRACT
Genome mapping efforts and the initial sequencing of large segments of human DNA permit ongoing assessment of the patterns and extent of sequence duplication and divergence in the human genome. Initial sequence data indicate that the most highly repetitive sequences show isochore-related enrichment and clustering produced by successive insertional recombination and local duplication of particular repetitive elements. Regional duplication is also observed for a number of otherwise unique genomic sequences and thereby makes these segments become repetitive. The consequences of these duplication events are: (1) clustering of related genes, along with a variety of coregulatory mechanisms; and (2) recombinations between the nearby homologous sequences, which can delete genes in individuals and account for a significant fraction of human genetic disease.