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PubMed1993

Cloning and chromosome mapping of the human Mel-18 gene which encodes a DNA-binding protein with a new 'RING-finger' motif.

It has recently been reported that there exists a new 'RING-finger' protein family among the zinc-finger (Zf) proteins. Previously, we had isolated the mouse Mel-18 cDNA (mMel-18) encoding the nuclear RING-finger protein that exhibits an ability to bind to a nonspecific DNA column. Here, we have isolated and characterized the human Mel-18 cDNA (hMel-18) using the mMel-18 cDNA as a probe. The deduced hMel-18 protein contains 344 amino acids (38 kDa) with a RING-finger motif, a helix-loop-helix (HLH)-like structure and a Pro/Ser-rich region. The hMel-18 gene is conserved among vertebrates. Its mRNA is highly expressed in placenta, lung and kidney, but the level is low in liver, pancreas and skeletal muscle. Using in situ hybridization, we mapped hMel-18 to band q22 of chromosome 12. It is possible that the Mel-18/bmi-1 gene family represents a mammalian homologue of the Drosophila polycomb gene group.

Amino Acid Sequence↗
PubMed1998

Chromosome mapping of Rett syndrome: a likely candidate region on the telomere of Xq.

Rett syndrome (RS) is a disease of neurological development. First reported 30 years ago in 1966, its biological and genetic basis remains obscure. RS is commonly thought of as an X linked dominant disorder lethal to hemizygous males. The few familial cases would arise through mosaicism or because of occasional females failing to manifest the disorder through skewed X inactivation in relevant cell types. We have one family where the mother and daughter are affected with RS, and which can be explained according to this hypothesis. If the alternative proposal of Thomas (1996) is correct, that the lack of males affected by such disorders is the result of a high male to female ratio of germline mutations rather than of gestational lethality, then the RS gene should be located on the grandpaternal chromosome. Genomic screening with markers covering the whole X chromosome has been performed. Studies using multiple informative markers indicate that the RS locus is likely to be located close to one of the X chromosome telomeres. Further investigations in eight additional families suggest the most likely region for the RS gene to be is the distal part of Xq (Xq28).

Chromosome Mapping↗
PubMed1992

Genomic structure and chromosomal mapping of the murine CD40 gene.

The B cell-associated surface molecule, CD40, is likely to play a central role in the expansion of Ag-stimulated B cells, and their interaction with activated Th cells. In our study we have isolated genomic clones of murine CD40 from a mouse liver genomic DNA library. Comparison with the murine CD40 cDNA sequence revealed the presence of nine exons that together contain the entire murine CD40 coding region, and span approximately 16.3 kb of genomic DNA. The intron/exon structure of the CD40 gene resembles that of the low affinity nerve growth factor receptor gene, a close homolog of both human and murine CD40. In both cases the functional domains of the receptor molecules are separated onto different exons throughout the genes. Southern blot analysis demonstrated that murine CD40 is a single copy gene that maps in the distal region of mouse chromosome 2.

Amino Acid Sequence↗
PubMed1983

Chromosomal mapping of Xenopus 5S genes: somatic-type versus oocyte-type.

Xenopus 5S RNA genes exhibit a pattern of differential expression during development in which some members (oocyte-type) are transcribed only in oocytes, while others (somatic-type) are expressed in both oocytes and somatic cells. Using cloned DNA probes specific for each gene type, we determined the positions of these genes on Xenopus metaphase chromosomes by in situ hybridization. Somatic-type 5S genes in both X. laevis and X. borealis are located at the distal end of the long arm of only one chromosome (number 9). The oocyte-type 5S RNA genes are found at the distal ends of the long arms of most Xenopus chromosomes, including chromosome 9. Thus, large scale differences in chromosomal location cannot explain the selective expression of these genes, as suggested previously.

Animals↗
PubMed1989

Isolation, chromosomal mapping, and expression of the mouse tyrosinase gene.

Using a human tyrosinase cDNA probe, we have isolated mouse tyrosinase genomic clones and used them to map the mouse tyrosinase locus and to analyze the promoter sequence of the tyrosinase gene. Southern blot analyses of DNA from somatic cell hybrids, interspecies backcross mice, and albino deletion mice have revealed that the locus for mouse tyrosinase resides at or near the albino locus on mouse chromosome 7. There were three TATA-elements, but only one CAT-element, and the CAT-element appeared to be paired with the third TATA-element, located at the position farthest upstream. Mouse tyrosinase mRNA is approximately 2.4 Kb in size. The amount of tyrosinase mRNA reflects the levels of tyrosinase activity in normal melanocytes and Cloudman S-91 melanoma cell line.

Albinism↗
PubMed2000

Expression and comparative chromosomal mapping of MKP-5 genes DUSP10/Dusp10.

We have isolated a mouse cDNA for a novel MAPK phosphatase, designated as MKP-5. Two MKP-5 mRNA transcripts of 3.5 kb and 2.7 kb were detected. The 3.5-kb transcript was expressed in almost all the tissues examined, and was particularly abundant in cerebellum, skeletal muscle, and bone marrow. On the other hand, the 2.7-kb transcript was specifically and highly expressed in testis. The MKP-5 genes (DUSP10/Dusp10) were localized to chr 1q41, Chr 1H5 and chr 13q26 in human, mouse and rat, respectively. They were mapped in regions where conserved linkage homology has been identified among the three species.

Amino Acid Sequence↗
PubMed1999

Isolation of cDNA, chromosome mapping, and expression of the human TBP-like protein.

TBP is an essential factor for eukaryotic transcription. In this study, we identified a human cDNA encoding 21-kDa TBP-like protein (TLP). The TLP ORF, carrying 186 amino acids, covered the entire 180 amino acids of the C-terminal conserved domain of human TBP with 39% identity and 76% similarity. FISH determined that human tlp gene was located at chromosome 6 region q22.1-22.3. Northern blot analysis demonstrated that TLP mRNAs were expressed in various human tissues ubiquitously. We found that the TLP proteins exist in multiple mammalian cells and chicken cells. Although the Drosophila TBP-related factor (TRF) is a neurogenesis-related transcription factor, expression of TLP was nearly constant throughout the neural differentiation of P19 cells. Unlike TRF, TLP did not bind to the TATA-box nor direct transcription initiation in vitro. Similarity between TRF and TLP was considerably lower (35 in alignment score) than that between Drosophila TBP and human TBP (88 in alignment score). Multiple amino acids critical for the TBP function were deleted or substituted in TLP. We suggest that TLP is not a bona fide vertebrate counterpart nor a direct descendant of TRF.

Amino Acid Sequence↗
PubMed1999

Organization and chromosomal mapping of mouse Gh/tissue transglutaminase gene (Tgm2).

The mouse Gh/tissue transglutaminase gene (Tgm2), coding a dual-function protein that both binds guanosine triphosphate (GTP) and catalyzes the posttranslational modification of proteins by transamidation of glutamine residues, has been cloned. Sequence analysis of Tgm2 and comparison with the TGase sequences of other species allowed correction of several apparent sequencing artifacts in the Tgm2 cDNA. Tgm2 spans approximately 34 kb and has 13 exons and 12 introns. Although the structure of Tgm2 shows similarity to that of other transglutaminase genes, with introns ranging from 921 bp to >5 kb, several introns differ considerably in size from those of the human Gh gene, TGM2. Tgm2 maps to the distal region of mouse chromosome 2, a region syntenic to human chromosome 20q containing TGM2. Tgm2 is in the vicinity of two uncloned mouse mutations, diminutive (dm) and blind-sterile (bs). Genomic DNA from dm mice was unavailable; however, Southern blot analysis of bs DNA showed no gross rearrangements of Tgm2.

Amino Acid Sequence↗
PubMed2001

Cloning, genetic characterization, and chromosomal mapping of the mouse VDUP1 gene.

VDUP1 encodes a vitamin D3-inducible gene product that has been shown to be down-regulated in chemically-induced mammary tumors in rats. It has recently been reported to negatively regulate thioredoxin expression and function. We have cloned the mouse VDUP1 gene and characterized its genomic locus. The VDUP1 coding region spans eight exons within a total length of 2.3 kb located on mouse chromosome 3. Consensus sites for polyadenylation were identified 1.3 kb downstream of the gene, defining a long 3' untranslated region. The minimal functional VDUP1 promoter contains TATA and CCAAT boxes and transcription is initiated from two major start sites downstream. A direct repeat element located proximal to the TATA with homology to the USF binding site was identified as a potential regulator of VDUP1gene expression. Expression analysis determined that VDUP1 mRNA was markedly induced in myeloma cells in high density cell culture, but not in sub-confluent cells arrested by serum deprivation. All samples of a panel of mouse immortalized or transformed cell lines were shown to express abundant levels of VDUP1 mRNA.

Animals↗
PubMed1998

Structure, organization, and chromosomal mapping of the gene encoding macrosialin, a macrophage-restricted protein.

Murine macrosialin and its human homologue CD68 are heavily glycosylated transmembrane proteins expressed specifically in macrophages and macrophage-related cells. Macrosialin is predominantly a late endosomal protein but is also found on the cell surface where it binds oxidized LDL, an important factor in atherogenesis. We have cloned and sequenced the murine macrosialin gene (Cd68) and localized it by linkage analysis to chromosome 11. The gene is 1908 nucleotides long from the start site of transcription to the end of the 3'UTR. It has six exons, which range in size from 79 to 434 nucleotides. The promoter lacks a classical TATA box but contains other protein binding sites consistent with preferential monocyte/macrophage gene expression. Although the function of macrosialin is unknown, it might play a role in lipoprotein regulation given its binding of oxidized LDL in vitro and its colocalization to a region on chromosome 11 involved in the control of HDL levels.

Animals↗
PubMed2003

Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum.

The apicomplexan Cryptosporidium parvum is one of the most prevalent protozoan parasites of humans. We report the physical mapping of the genome of the Iowa isolate, sequencing and analysis of chromosome 6, and approximately 0.9 Mbp of sequence sampled from the remainder of the genome. To construct a robust physical map, we devised a novel and general strategy, enabling accurate placement of clones regardless of clone artefacts. Analysis reveals a compact genome, unusually rich in membrane proteins. As in Plasmodium falciparum, the mean size of the predicted proteins is larger than that in other sequenced eukaryotes. We find several predicted proteins of interest as potential therapeutic targets, including one exhibiting similarity to the chloroquine resistance protein of Plasmodium. Coding sequence analysis argues against the conventional phylogenetic position of Cryptosporidium and supports an earlier suggestion that this genus arose from an early branching within the Apicomplexa. In agreement with this, we find no significant synteny and surprisingly little protein similarity with Plasmodium. Finally, we find two unusual and abundant repeats throughout the genome. Among sequenced genomes, one motif is abundant only in C. parvum, whereas the other is shared with (but has previously gone unnoticed in) all known genomes of the Coccidia and Haemosporida. These motifs appear to be unique in their structure, distribution and sequences.

Animals↗
PubMed1990

Chromosomal mapping of a human phenol UDP-glucuronosyltransferase, GNT1.

A 5' fragment of a full-length cDNA clone encoding a human phenol UDP-glucuronosyltransferase was used to produce a specific probe for this gene. DNA isolated from a panel of 18 human-rodent somatic cell hybrids was analysed by Southern-blot hybridization. The results indicate that this UDP-glucuronosyltransferase is encoded by a single gene, designated GNT1, located on human chromosome 2.

Blotting, Southern↗
PubMedDate not supplied

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes.

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and AmphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.

Animals↗
PubMed1999

[Chromosomal mapping of ld gene which causes congenital limb deformity syndrome in KM-ld mouse].

Fourteen biochemical marker loci and 61 SSLP loci in congenic strain C57BL/6.KM-ld were screened to determine the loci linkage to ld gene, an autosomal recessive mutant gene in KM mouse which causes congenital limb deformity in mouse by means of electrophoresis and PCR amplification. The result showed that ld gene linked to D2Mit30, D2Mit62 and D2Mit63. To locate ld gene more accurately on chromosome 2, 86 backcross offsprings (C57BL/6 x KM-ld) F1 x KM-ld were produced for linkage analysis. From the backcross progeny genomic DNAs were amplified for D2Mit13, D2Mit30, D2Mit62 and D2Mit63 loci in vitro. According to phenotypes, the linkage between the four SSLP loci and ld gene was analysed by calculating genetic distance, ld gene was located exactly on Chr. 2, 76cM, with distances of 25.58cM to D2Mit30, D2Mit62 and D2Mit63, of 31.39cM to D2Mit13.

Animals↗
PubMed1986

Cloning and screening with nanogram amounts of immunopurified mRNAs: cDNA cloning and chromosomal mapping of cystathionine beta-synthase and the beta subunit of propionyl-CoA carboxylase.

We have developed conditions for efficient cDNA cloning of nanogram amounts of purified mRNAs coding for cystathionine beta-synthase [L-serine hydro-lyase (adding homocysteine), EC 4.2.1.22] and for the cytosolic precursors of mitochondrial ornithine transcarbamylase (carbamoylphosphate:L-ornithine carbamoyltransferase, EC 2.1.3.3) and the beta subunit of propionyl-CoA carboxylase [propanoyl-CoA: carbon-dioxide ligase (ADP-forming), EC 6.4.1.3]. The three mRNAs, prepared by sequential immunoselection from the same batch of rat liver polysomes, were pooled (20 ng each), and cDNA was synthesized by using avian reverse transcriptase. The second DNA strand was prepared by "nick-translation repair" of the cDNA . mRNA hybrid with RNase H, polymerase I, and DNA ligase from Escherichia coli. The double-stranded (ds) DNA was tailed with deoxycytidine residues, annealed with Pst I-cut/dG-tailed pBR322, and used to transform E. coli. The library generated by this three-step procedure contained 5000 independent colonies. A 550-base-pair (bp) cDNA clone of the beta subunit of propionyl-CoA carboxylase was detected by hybrid-selected translation; it was then used to screen the library for longer cDNAs. Two hybridizing cDNAs, 1200 and 1000 bp long with a 200-bp overlap, representing together a full-length copy of the coding region and 446 bp of 3' untranslated sequence, were recovered. Each plasmid mapped to the region q13.3----q22 of human chromosome 3. Cystathionine beta-synthase clones were obtained by screening the library with a single-stranded [32P]cDNA prepared directly from the highly purified synthase mRNA by reverse transcriptase. The longest hybridizing cDNA of 1700 bp was used in hybrid-selected translation and detected a polypeptide of 63 kDa, identical in size to rat liver synthase. In situ hybridization of this cDNA to q22 of human chromosome 21 confirmed two previous tentative assignments of the synthase locus to this chromosome.

Animals↗
PubMed1991

Human type VII collagen: cDNA cloning and chromosomal mapping of the gene.

A human keratinocyte cDNA expression library in bacteriophage lambda gt11 was screened with the purified IgG fraction of serum from a patient with epidermolysis bullosa acquisita, which had a high titer of anti-type VII collagen antibodies. Screening of approximately 3 x 10(5) plaques identified 8 positive clones, the largest one (K-131) being approximately 1.9 kilobases in size. Dideoxynucleotide sequencing of K-131 indicated that it consisted of 1875 base pairs and contained an open reading frame coding for a putative N-terminal noncollagenous domain of 439 amino acids and a collagenous C-terminal segment of 186 amino acids. The collagenous domain was characterized by repeating Gly-Xaa-Yaa sequences that were interrupted in several positions by insertions or deletions of 1-3 amino acids. The deduced amino acid sequence also revealed a peptide segment that had a high degree of identity with a published type VII collagen protein sequence. Northern hybridization of the K-131 cDNA with human epidermal keratinocyte and skin fibroblast RNA revealed an mRNA of approximately 8.5 kilobases. The fusion protein produced by the K-131 cDNA, when incubated with epidermolysis bullosa acquisita serum, bound to antibodies that reacted in Western blots with type VII collagen. The genomic location of the type VII collagen gene (COL7A1) was determined by chromosomal in situ hybridization with the K-131 cDNA. The results mapped the COL7A1 to the locus 3p21. The cDNA clones characterized in this study will be valuable for understanding the protein structure and gene expression of type VII collagen present in anchoring fibrils and its aberrations in the dystrophic forms of heritable epidermolysis bullosa.

Amino Acid Sequence↗