ABSTRACT
The TRANSFAC database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER database on anatomical structures and developmental stages. The functionality of Match, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with Match Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER free download versions are available at http://www.biobase.de:8080/index.html.
Subject(s)
Databases, Genetic , Gene Expression Regulation , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription, Genetic , Animals , Binding Sites , Eukaryotic Cells/metabolism , Gene Expression Profiling , Gene Expression Regulation, Developmental , Humans , Mice , Promoter Regions, Genetic , Saccharomyces/genetics , Saccharomyces/metabolism , Tissue DistributionABSTRACT
In a search for genes involved in X-linked mental retardation we have analyzed the expression pattern and genomic structure of human MAGED2. This gene is a member of a new defined MAGE-D cluster in Xp11.2, a hot spot for X-linked mental retardation. Rat and mouse orthologues have been isolated. In contrast to the genes of the MAGE-A, MAGE- B and MAGE-C clusters, MAGED2 is expressed ubiquitously. High expression was detected in specific brain regions and in the interstitium of testes. Five SNPs in the coding region of human MAGED2 were characterized and their allele frequencies determined in a German and Turkish population.
Subject(s)
Antigens, Neoplasm/genetics , Exons/genetics , Gene Expression Profiling , Polymorphism, Single Nucleotide/genetics , Adaptor Proteins, Signal Transducing , Amino Acid Sequence , Animals , Antigens, Neoplasm/chemistry , Brain/metabolism , Cloning, Molecular , Gene Frequency , Germany , Haplotypes/genetics , Humans , Intellectual Disability/genetics , Introns/genetics , Male , Mice , Molecular Sequence Data , Rats , Sequence Alignment , Sequence Homology, Nucleic Acid , Testis/metabolism , Turkey , X Chromosome/geneticsABSTRACT
The cDNA sequence and expression profile of a novel human gene, encoding a new member of the immunoglobulin superfamily, is reported. The gene is localized in the pericentromeric region of human X chromosome between the markers DXS1213 and DXS1194. Abundant expression of transcripts was detected in several human fetal tissues, whereas among adult tissues lung and placenta express highest levels of Z39Ig mRNA.
Subject(s)
Immunoglobulins/genetics , X Chromosome , Amino Acid Sequence , Base Sequence , Chromosome Mapping , Cloning, Molecular , DNA, Complementary/analysis , Humans , Immunoglobulins/chemistry , Immunoglobulins/metabolism , Molecular Sequence Data , Receptors, Complement , Tissue DistributionSubject(s)
Chromosome Deletion , X Chromosome/genetics , Adolescent , Adult , Child , Family Health , Female , Humans , Karyotyping , Male , Pedigree , Phenotype , Turner Syndrome/genetics , Turner Syndrome/pathologyABSTRACT
The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes was found. The information will permit the conversion of those markers to STS markers and allow their use in PCR-based mapping experiments. Furthermore, it will facilitate the comparative mapping of genes across distantly related plant species by direct comparison of DNA sequences and map positions. [cDNA sequence data reported in this paper have been submitted to the EMBL database under accession nos. AA824695-AA825005 and the dbEST_Id database under accession nos. 1546519-1546862.]
Subject(s)
DNA, Plant/genetics , Genes, Plant , Plant Proteins/genetics , Sequence Analysis, DNA , Solanum lycopersicum/genetics , Arabidopsis/genetics , Chromosome Mapping , Cloning, Molecular , DNA, Complementary , Databases, Factual , Genetic Markers , Molecular Sequence Data , Plant Proteins/chemistry , Polymorphism, Restriction Fragment Length , Sequence Homology, Amino Acid , Sequence Homology, Nucleic Acid , Sequence Tagged Sites , Transcription, GeneticABSTRACT
The Wieacker-Wolff syndrome (WWS, MIM* 314580), first described clinically in 1985, is an X-linked recessive disorder. In earlier studies, linkage between the WWS gene and DXYS1 at Xq21.2 and DXS1 at Xq11 as well as AR at Xq12 was reported. Here we report on a linkage analysis using highly polymorphic, short terminal repeat markers located in the segment from Xp21 to Xq24. No recombination between the WWS locus and ALAS2 or with AR (z = 4.890 at theta = 0.0) was found. Therefore, the WWS locus was assigned to a segment of approximately 8 cM between PFC (Xp11.3-Xp 11.23) and DXS339 (Xq11.2-Xq13).
Subject(s)
Intellectual Disability/genetics , X Chromosome , Centromere , Chromosome Mapping , Female , Haplotypes , Humans , Male , Pedigree , SyndromeABSTRACT
In situ localization of short low- or single-copy sequences is still difficult in plants. One solution to this problem could be the use of large yeast artificial chromosomes (YACs) for fluorescence in situ hybridization. Two YACs specific for a single copy marker on the long arm of the NOR-chromosome 2 of tomato (Lycopersicon esculentum) were selected. Both probes hybridized exclusively to this chromosome, although one produced a slightly dispersed hybridization signal. Hybridization of these YACs onto potato chromosome showed a clear single locus on the homoeologous potato chromosome in both cases.
Subject(s)
Chromosomes, Artificial, Yeast , DNA Probes , In Situ Hybridization, Fluorescence/methods , Solanum lycopersicum/genetics , Solanum tuberosum/genetics , Chromosome Mapping/methods , DNA, Plant/genetics , Nucleolus Organizer Region/genetics , Repetitive Sequences, Nucleic Acid , Sensitivity and SpecificityABSTRACT
Cotransformation frequencies of 16, 39, 51, and 60% were observed when donor alleles were separated by distances of 9.2, 7.4, 6.3, and 5.1 kb, respectively, in donor Acinetobacter calcoaceticus DNA. A different and unexpected pattern was observed when the distance between recipient alleles was reduced from 9.2 to 5.1 kb. Ligation of unlinked chromosomal DNA fragments allowed them to be linked genetically through natural transformation.
Subject(s)
Acinetobacter calcoaceticus/genetics , Genetic Linkage , Transformation, Genetic , Alleles , Genes, Bacterial , Sequence DeletionABSTRACT
Two novel conditional broad-host-range cell lysis systems have been developed for the study of natural transformation in bacteria and the environmental fate of DNA released by cell death. Plasmid pDKL02 consists of lysis genes S, R, and Rz from bacteriophage lambda under the control of the Ptac promoter. The addition of inducer to Escherichia coli, Acinetobacter calcoaceticus, or Pseudomonas stutzeri containing plasmid pDKL02 resulted in cell lysis coincident with the release of high amounts of nucleic acids into the surrounding medium. The utility of this lysis system for the study of natural transformation with DNA released from lysed cells was assessed with differentially marked but otherwise isogenic donor-recipient pairs of P. stutzeri JM300 and A. calcoaceticus BD4. Transformation frequencies obtained with lysis-released DNA and DNA purified by conventional methods and assessed by the use of antibiotic resistance (P. stutzeri) or amino acid prototrophy (A. calcoaceticus) for markers were comparable. A second cell lysis plasmid, pDKL01, contains the lysis gene E from bacteriophage phi X174 and causes lysis of E. coli and P. stutzeri bacteria by activating cellular autolysins. Whereas DNA released from pDKL02-containing bacteria persists in the culture broth for days, that from induced pDKL01-containing bacteria is degraded immediately after release. The lysis system involving pDKL02 is thus useful for the study of both the fate of DNA released naturally into the environment by dead cells and gene transfer by natural transformation in the environment in that biochemically unmanipulated DNA containing defined sequences and coding for selective phenotypes can be released into a selected environment at a specific time point. This will allow kinetic measurements that will answer some of the current ecological questions about the fate and biological potential of environmental DNA to be made.
