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Results for “structural genomics”

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PubMed2000

Genomic structure and chromosomal mapping of the human site-1 protease (S1P) gene.

Site-1 protease (S1P) is a subtilisin-related enzyme that cleaves sterol regulatory element-binding proteins (SREBPs) in the lumen of endoplasmic reticulum, thereby initiating the release of transcriptionally active NH2-terminal fragments of SREBPs from membranes. In the experiments reported here, we localized the human S1P gene to chromosome 16q24 by fluorescent in situ hybridization and radiation-hybrid mapping, and determined its genomic structure. This gene is more than 60 kb long and contains 23 exons and 22 introns. Its transcription-initiation site within exon 1 is separate from the initiation codon in exon 2. Analysis of the exon/intron structure revealed that the S1P gene consists of a mosaic of functional units: exon 1 encodes the 5' non-translated region; exon 2 encodes the NH2-terminal signal sequence; and exons 2 and 3 encode the pro-peptide sequence that is released when S1P is self-activated by intramolecular cleavage. Exons 5-10 encode the subtilisin-homology domain that is critical for catalytic activity, and exon 23 encodes the transmembrane region. Analysis of the putative promoter region revealed a highly G/C-rich region containing a binding site for ADD1/SREBP-1, as well as Sp1 and AP2 sites. Therefore, expression of the S1P gene may be under the control of SREBP-1, a key regulator of the expression of genes essential for intracellular lipid metabolism. Our data establish a basis for investigations to detect molecular variants in this gene that may alter levels of plasma lipoproteins and/or otherwise disrupt intracellular lipid metabolism.

Base Sequence↗

PubMed2006

Genomic structure of swine taste receptor family 1 member 3, TAS1R3, and its expression in tissues.

Taste receptor family 1 member 3, TAS1R3, is shown to be involved in sweet and umami tastes in mouse, and the nucleotide sequence of the gene has been reported in rat, gorilla, and human. Pigs are frequently used as models for human diseases, and are also considered to be source animals for xenotransplantation to humans due to their anatomical and physiological similarities to humans. Therefore, in the present study, the genomic structure of the swine TAS1R3 gene was determined, and TAS1R3 expression was studied in various swine tissues. The gene was shown to reside on swine chromosome 6q22-->q23, from which three types of mRNAs were generated: 3,752 bp derived from six exons in tongue, 3,704 bp from six exons and 3,630 bp from seven exons in testis. The 6 exons/5 introns were structurally similar to those of humans and mice, but the 7 exons/6 introns structure of TAS1R3 was first observed in swine. High expressions of TAS1R3 were revealed in tongue, kidney, and testis by real-time PCR. The expression profile of the tissues except for kidney was similar to that of mouse. When in situ hybridization using an RNA probe for TAS1R3 was performed on swine tongue and testis tissues, TAS1R3 expressions were revealed in tongue circumvallate papillae, fungiform papillae, mucosal epithelium, follicular B lymphocytes, lymphocytes in submucosal tissues of lingual tonsil, and spermatogenic cells. Using peripheral mature B lymphocytes, the expression of TAS1R3 in B lymphocytes was further confirmed by real-time PCR and sequencing of the real-time PCR product.

Animals↗

PubMed1992

Genomic structure and mapping of the chromosomal gene for transcobalamin I (TCN1): comparison to human intrinsic factor.

Transcobalamin I (TCI) is a vitamin B12 binding protein that is found in the secondary granules of mature neutrophils. The expression of the gene for TCI (TCN1) within neutrophils has been shown to be restricted to the later stages of myeloid development and can therefore be used as a marker for granulocyte differentiation. To study transcriptional control regions important in late stage myeloid gene regulation the genomic sequence for TCN1 has been cloned. Clones were isolated from a genomic library constructed in Charon 4A using homologous full-length cDNA probes. Southern blot analysis showed the gene to reside on five EcoRI fragments totaling 14 kb in length. Two overlapping phage clones, containing the entire 14 kb, were isolated and the introns and exons were mapped using Southern blotting and dideoxy sequencing of subclones. The cDNA is represented by nine exons contained within 12 kb of genomic DNA. Comparison of the genomic structure to gastric intrinsic factor (GIF), another vitamin B12 binding protein, revealed a strikingly similar intron/exon structure, with several positionally conserved splice sites. The gene was localized to chromosome 11 using in situ hybridization.

Amino Acid Sequence↗

PubMed2002

Genomic structure of the sponge, Halichondria okadai calcyphosine gene.

Calcyphosine is an EF-hand Ca(2+)-binding protein, which was first isolated from the canine thyroid. It is phosphorylated in a cyclic AMP (cAMP)-dependent manner; then it is thought to be implicated in the cross-signaling between the cAMP and calcium-phosphatidylinositol cascades. Here, we isolated the DNA complementary to RNA (cDNA) of an EF-hand Ca(2+)-binding protein from the sponge, Halichondria okadai and determined its genomic structure. The deduced sequence of the sponge Ca(2+)-binding protein showed significant similarity (about 40% identity) with those of mammal calcyphosines, and the intron positions were well conserved between the sponge and human calcyphosine genes. We considered that the isolated cDNA was that of sponge calcyphosine, and that sponge and mammalian calcyphosines evolved from a common ancestor gene. Recent cDNA projects have revealed that a calcyphosine cDNA is also expressed by human, mouse, and the ascidia. These cDNAs have more than 60% identity with sponge calcyphosine and each other, and all are composed of 208 amino acid residues. On the constructed phylogenetic trees, calcyphosines are essentially divided into two groups, types-I and -II calcyphosines. Type-I calcyphosine may be specific to mammals, and type-II is widely distributed among metazoan species. This suggests that type-II calcyphosine is a rather ancient gene with some essential function.

Amino Acid Sequence↗

PubMed1995

Further elucidation of the genomic structure of PAX3, and identification of two different point mutations within the PAX3 homeobox that cause Waardenburg syndrome type 1 in two families.

Waardenburg syndrome is an autosomal dominant disorder characterized by sensorineural deafness and pigmentary disturbances. Previous work has linked the disease to PAX3 on chromosome 2, and several mutations within the highly conserved paired-box and octapeptide motifs, but not the homeobox, have been reported. In this report, we have used the published cDNA sequence to further define the genomic structure of PAX3, using inverse PCR. We have identified exon/intron boundaries between exons 5 and 6 and between exons 6 and 7. Further, we have identified the first two mutations within the homeobox in two different families with type 1 Waardenburg syndrome. The first is a point mutation (G-->T) at the first base of exon 6, which substitutes phenylalanine for valine. In another family, we have identified a point mutation (C-->G) within the homebox, in exon 6, which substitutes a glycine for arginine at a highly conserved site. The homeodomain is important in binding of DNA and in effecting transcriptional control. These mutations likely result in structural change within the homeodomain that either change the DNA-binding specificity of the homedomain or reduce the affinity of the PAX3 protein for DNA. These homeodomain mutations should aid in elucidating the role of the homeodomain in the function of the PAX3 protein.

Amino Acid Sequence↗

PubMed1996

Genomic structure and chromosomal assignment of the mouse Ku70 gene.

DNA-dependent protein kinase (DNA-PK) consists of three polypeptide subunits: Ku70, Ku80, and the DNA-PK catalytic subunit (DNA-PKcs). Mammalian mutants deficient in either Ku80 or DNA-PKcs function have been shown to be lacking in DNA double-strand break repair and V(D)J recombination, respectively. The precise role of the Ku70 gene in this process has not yet been determined, in part because no cell lines, animals, or human diseases involved with deficiencies in this gene have yet been identified. Both the human and the mouse Ku70 cDNAs have been cloned, and the human gene has been mapped to chromosome 22q13. The original mouse cDNA clones, however, lacked a complete 5'-region, and none of the mammalian Ku70 genomic sequences have been characterized. This report contains an analysis of the 5'-region of the mouse cDNA sequence, a characterization of the mouse Ku70 genomic structure, and fluorescence in situ hybridization data that map the mouse gene to chromosome 15. The deduced amino acid sequence of the mouse gene consists of 608 amino acids compared to 609 for the human gene. The genomic sequence is 24 kb and consists of 13 exons, including an untranslated first exon. Sequences from the upstream region of exon 1 revealed four consensus GC box sequences and a strong transcription initiation site at a reasonable location. The assignment of the mouse Ku70 gene to chromosome 15 is consistent with the syntenic relationship of this gene in human (chromosome 22q13) and mouse and adds to the comparative mapping data for the genes involved in the SCID phenotype.

Animals↗

PubMed2000

Human KLRF1, a novel member of the killer cell lectin-like receptor gene family: molecular characterization, genomic structure, physical mapping to the NK gene complex and expression analysis.

The human NK gene complex localized on chromosome 12p12.3 - p13.2 codes for several lectin-like receptor genes expressed by NK cells as well as by other hematopoietic cells. In this study, by using the expressed sequence tag database we identified a novel receptor gene, designated as killer cell lectin-like receptor, subfamily F, member 1 (KLRF1), encoding a putative type II transmembrane glycoprotein. The KLRF1 gene has been localized on the high-resolution physical map of chromosome 12p. The genomic structure of the KLRF1 gene and the existence of one spliced variant are also described. KLRF1 was expressed at the mRNA level in peripheral blood leukocytes, activated NK cells, monocytes and NK and myeloid cell lines. The presence of two immunoreceptor tyrosine-based inhibitory-like motifs within the cytoplasmic tail of KLRF1 suggests an inhibitory role in NK cell and monocyte activity.

Amino Acid Sequence↗

PubMed1998

Genomic structure and physical mapping of C17orf1: a gene associated with the proximal element of the CMT1A-REP binary repeat.

C17orf1, a gene expressed in skeletal muscle and heart, was initially isolated from a fetal brain cDNA library and localized centromeric to and partially within the proximal CMT1A-REP element. A second gene, COX10, spans the distal CMT1A-REP element, and a duplicated exon of this gene is present in the proximal CMT1A-REP element. C17orf1 includes this duplicated COX10 exon within its sequence; however, the DNA strand opposite to that of the COX10 gene is utilized. We have determined the genomic organization of C17orf1 and found it to be oriented in the direction opposite to COX10. Analysis of the genomic structure of C17orf1 has revealed that it contains at least six exons and spans a length of at least 17 kb. All but one of the splice sites conform to the GT/AG rule, and in this case the splice acceptor site within intron 1 is GA instead of the expected AG. Sequencing and mapping analyses have shown that the centromeric boundary of the proximal CMT1A-REP element lies within intron 5. A 7-bp insertion, identified from genomic sequencing of cosmid clones and verified in the original cDNA clone and RT-PCR products, has extended the previously reported open reading frame from 591 to 756 bp. C17orf1 therefore encodes a 252-amino-acid protein.

Alkyl and Aryl Transferases↗

PubMed1999

Rat osteotesticular phosphatase gene (Esp): genomic structure and chromosome location.

Osteotesticular phosphatase (OST-PTPase) is a class III receptor-type tyrosine phosphatase (RPTPase). It has 10 tandem fibronectin III-like (FN-III) repeats in the extracellular region and two phosphatase domains in the intracellular region. The expression of the rat OST-PTPase gene, Esp, is restricted to osteoblasts and Sertoli cells, and the transcript level in osteoblasts is highly up-regulated by parathyroid hormone and cAMP treatment. We report here the cloning and characterization of the rat Esp gene, including a 2.9-kb 5' flanking region sequence. Two potential binding sites for Osf2/Cbfa1, an osteoblast-specific transcription factor, are present in the promoter. Esp is composed of 35 exons, but spans merely 20 kb, making it the most compact RPTPase gene identified. Each FN-III repeat is encoded by a single exon flanked with phase 1 introns. Two phosphatase domains are encoded by 16 exons in a genomic organization similar to those in RPRPalpha, RPTPgamma, and Ptprc genes. Esp was mapped by fluorescence in situ hybridization to rat chromosome 13q1. These results represent the first genomic structure of a mammalian class III RPTPase gene.

Animals↗

PubMed2006

Comparison of the genome structure of the self-incompatibility (S) locus in interspecific pairs of S haplotypes.

The determinants of recognition specificity of self-incompatibility in Brassica are SRK in the stigma and SP11/SCR in the pollen, both of which are encoded in the S locus. The nucleotide sequence analyses of many SRK and SP11/SCR alleles have identified several interspecific pairs of S haplotypes having highly similar sequences between B. oleracea and B. rapa. These interspecific pairs of S haplotypes are considered to be derived from common ancestors and to have maintained the same recognition specificity after speciation. In this study, the genome structures of three interspecific pairs of S haplotypes were compared by sequencing SRK, SP11/SCR, and their flanking regions. Regions between SRK and SP11/SCR in B. oleracea were demonstrated to be much longer than those of B. rapa and several retrotransposon-like sequences were identified in the S locus in B. oleracea. Among the seven retrotransposon-like sequences, six sequences were found to belong to the ty3 gypsy group. The gag sequences of the retrotransposon-like sequences were phylogenetically different from each other. In Southern blot analysis using retrotransposon-like sequences as probes, the B. oleracea genome showed more signals than the B. rapa genome did. These findings suggest a role for the S locus and genome evolution in self-incompatible plant species.

Brassica↗

PubMed2000

Genomic structure, chromosomal localization and identification of mutations in the xeroderma pigmentosum variant (XPV) gene.

The xeroderma pigmentosum variant (XP-V) is one of the most common forms of this cancer-prone syndrome. XP groups A through G are characterized by defective nucleotide excision repair, whereas the XP-V phenotype is proficient in this pathway. The XPV gene encodes DNA polymerase eta, which catalyzes an accurate translesion synthesis, indicating that the XPV gene contributes tumor suppression in normal individuals. Here we describe the genomic structure and chromosomal localization of the XPV gene, which includes 11 exons covering the entire coding sequence, lacks a TATA sequence in the upstream region of the transcription-initiation, and is located at the chromosome band 6p21.1-6p12. Analyses of patient-derived XP-V cell lines strongly suggested that three of four cell lines carried homozygous mutations in the XPV gene. The fourth cell line, XP1RO, carried heterozygous point mutations in the XPV gene, one of which was located at the splice acceptor site of exon 2, resulting in the omission of exon 2 from the mature mRNA. These findings provide a basis for diagnosis and therapy of XP-V patients.

Alleles↗

PubMed1998

Nucleotide sequence and genome structure of grapevine rupestris stem pitting associated virus-1 reveal similarities to apple stem pitting virus.

Rupestris stem pitting (RSP), a component of the rugose wood complex, is one of the most widespread graft-transmissible diseases of grapevines. Here we report on the consistent association of a high molecular mass dsRNA (ca. 8.7 kbp) with RSP. The dsRNA was reverse-transcribed and cDNAs generated were cloned into Lambda ZAP II. Sequence analysis of the cDNA clones showed that the dsRNA was of viral origin and the putative virus was designated rupestris stem pitting associated virus-1 (RSPaV-1). The genome of RSPaV-1 consists of 8726 nt excluding a poly(A) tail at the 3' terminus. It has five potential open reading frames which have the capacity to code for the replicase (ORF1), the triple gene block (ORF2-4) and the coat protein (ORF5). Comparison of the genome structure and nucleotide and amino acid sequences indicated similarities of RSPaV-1 to apple stem pitting virus, and to a lesser extent, to potato virus M carlavirus. The possibility that different strains of RSPaV-1 or other viruses are associated with RSP is discussed.

Amino Acid Sequence↗

PubMed2001

SAG/ROC2/Rbx2/Hrt2, a component of SCF E3 ubiquitin ligase: genomic structure, a splicing variant, and two family pseudogenes.

We have recently cloned and characterized an evolutionarily conserved gene, Sensitive to Apoptosis Gene (SAG), which encodes a redox-sensitive antioxidant protein that protects cells from apoptosis induced by redox agents. The SAG protein was later found to be the second family member of ROC/Rbx/Hrt, a component of the Skp1-cullin-F box protein (SCF) E3 ubiquitin ligase, being required for yeast growth and capable of promoting cell growth during serum starvation. Here, we report the genomic structure of the SAG gene that consists of four exons and three introns. We also report the characterization of a SAG splicing variant (SAG-v), that contains an additional exon (exon 2; 264 bp) not present in wildtype SAG. The inclusion of exon 2 disrupts the SAG ORF and gives rise to a protein of 108 amino acids that contains the first 59 amino acids identical to SAG and a 49-amino acid novel sequence at the C terminus. The entire RING-finger domain of SAG was not translated because of several inframe stop codons within the exon 2. The SAG-v protein was expressed in multiple human tissues as well as cell lines, but at a much lower level than wildtype SAG. Unlike SAG, SAG-v was not able to rescue yeast cells from lethality in a ySAG knockout, nor did it bind to cullin-1 or have ligase activity, probably because of the lack of the RING-finger domain. Finally, we report the identification of two SAG family pseudogenes, SAGP1 and SAGP2, that share 36% or 47% sequence identity with ROC1/Rbx1/Hrt1 and 30% or 88% with SAG, respectively. Both genes are intronless with two inframe stop codons.

Alternative Splicing↗

PubMed1996

The genomic structure and chromosomal localization of the mouse STAT3 gene.

A variety of cytokines induce the tyrosine phosphorylation of signal transducers and activators of transcription (STATs). Activation of the same STAT proteins by distinct cytokines and activation of different STAT proteins by each cytokine are thought to contribute to redundancy and pleiotropy of cytokine actions respectively. STAT3 is rapidly tyrosine phosphorylated in response to IL-6, ciliary neurotrophic factor, oncostatin M, leukemia inhibitory factor, IL-11, granulocyte colony stimulation factor and epidermal growth factor. In this report we have isolated and characterized the mouse genomic structure of STAT3. The mouse STAT3 gene consisted of 24 exons which spanned > 37 kb. The structure of the mouse STAT3 gene was almost identical to that of the human STAT2 gene, including the number and size of exons, indicating that the exon-intron organization had already been accomplished before these two genes duplicated, and then these genes evolved to respond to different ligands. By molecular linkage analysis with interspecific backcross mice the STAT3 gene mapped at 1.4 cM proximal to D11Mit59 on mouse chromosome 11. The promoter region contained potential regulatory elements such as GATA, NF-IL-6, PEBP2, Sp-1, AP-2 binding sites, cAMP response element, CAAT box and E-box. Transient expression of constructs harboring the 5' flanking region of the STAT3 gene fused to the luciferase gene showed that a 160 bp sequence upstream of the transcription start site conferred a basal and an IL-6-inducible promoter activity.

Animals↗

PubMed1997

Genomic structure and parent-of-origin-specific methylation of Peg1.

We previously identified Peg1/Mest as a novel paternally expressed gene in the developing mouse embryo. The human PEG1 gene was recently assigned to 7q32 and shown to be imprinted and paternally expressed. Therefore, PEG1 deficiency could participate in the aetiology of pre- and post-natal growth retardation associated with maternal uniparental disomy 7 in humans. We have now initiated the characterization of the Peg1 locus in order to identify and dissect cis-acting elements implicated in its imprinted monoallelic expression. The genomic structure of Peg1 as well as the DNA sequence of the 5'-end of the gene, including 2.4 kb of promoter sequences and covering the first 2 exons, have been determined. Important sequence elements, such as a CpG island spanning exon 1 and direct repeats, are identified and discussed. To address the role of epigenetic modifications in the imprinting of Peg1, a methylation analysis of the Peg1 gene is presented. Partially methylated cytosine residues in 13.5 d.p.c. embryos and undifferentiated ES cells were identified. Using embryos carrying a targetted mutation at the Peg1 locus, we show that this partial promoter methylation pattern reflects a strict parent-of-origin-specific differential methylation: the expressed paternal allele is unmethylated, whereas the silenced maternal allele is fully methylated at the CpG sites studied. That the gametes carry the epigenetic information necessary to lay down this allele-specific methylation pattern is suggested by analysis of DNA isolated from sperm and parthenogenetic embryos.

Animals↗

PubMed2001

Optimal classification of protein sequences and selection of representative sets from multiple alignments: application to homologous families and lessons for structural genomics.

Hierarchical classification is probably the most popular approach to group related proteins. However, there are a number of problems associated with its use for this purpose. One is that the resulting tree showing a nested sequence of groups may not be the most suitable representation of the data. Another is that visual inspection is the most common method to decide the most appropriate number of subsets from a tree. In fact, classification of proteins in general is bedevilled with the need for subjective thresholds to define group membership (e.g., 'significant' sequence identity for homologous families). Such arbitrariness is not only intellectually unsatisfying but also has important practical consequences. For instance, it hinders meaningful identification of protein targets for structural genomics. I describe an alternative approach to cluster related proteins without the need for an a priori threshold: one, through its use of dynamic programming, which is guaranteed to produce globally optimal solutions at all levels of partition granularity. Grouping proteins according to weights assigned to their aligned sequences makes it possible to delineate dynamically a 'core-periphery' structure within families. The 'core' of a protein family comprises the most typical sequences while the 'periphery' consists of the atypical ones. Further, a new sequence weighting scheme that combines the information in all the multiply aligned positions of an alignment in a novel way is put forward. Instead of averaging over all positions, this procedure takes into account directly the distribution of sequence variability along an alignment. The relationships between sequence weights and sequence identity are investigated for 168 families taken from HOMSTRAD, a database of protein structure alignments for homologous families. An exact solution is presented for the problem of how to select the most representative pair of sequences for a protein family. Extension of this approach by a greedy algorithm allows automatic identification of a minimal set of aligned sequences. The results of this analysis are available on the Web at http://mathbio.nimr.mrc.ac.uk/~amay.

Algorithms↗

PubMed2002

Human aminopeptidase B (rnpep) on chromosome 1q32.2: complementary DNA, genomic structure and expression.

Aminopeptidase B (APB) is a Zn(2+)-metalloexopeptidase, which selectively removes Arg and/or Lys residues from the N-terminus of several peptide substrates. Several data strongly support the hypothesis that this enzyme could participate in the final stages of precursor processing mechanisms and/or in particular inflammatory processes and tumor developments. Therefore, we have cloned the complementary DNA encoding the human APB, a 658-residues protein, containing the canonical "HEXXH(X(18))E", a signature allowing its classification in the M1 family of metallopeptidases. The genomic structure of the human APB gene (rnpep; 1q32.1-q32.2) was also determined. rnpep is bracketed by pre-protein translocase of the inner mitochondrial membrane gene and ETS family transcription factor ELF3 gene. It spans more than 24 kbp and contains 11 exons ranging from 109 to 574 bp. Finally, expression of the human APB messenger RNA (mRNA) was investigated using a pre-made dot-blot. This mRNA seems to be ubiquitous although its expression level varies depending of the cells or tissues considered.

Amino Acid Sequence↗

PubMed1996

cDNA sequence and genomic structure of the murine p55 (Mpp1) gene.

MPP1 is an X-linked human gene encoding a heavily palmitoylated membrane protein (p55) with homology to the Drosophila tumor suppressor gene lethal(1) discs-large. As a first step toward studying the effects of mutations in this gene in a mammalian system, the nucleotide sequence of the mouse Mpp1 cDNA has been determined along with the intron-exon boundaries. Mpp1 is ubiquitously expressed and encodes a p55 protein of 466 amino acids with 93 and 65% identity to the human and puffer fish (Fugu rubripes) p55 sequences, respectively. The genomic structure of the Mpp1 gene is likewise conserved with 12 exons. The location of the Mpp1 gene, on the X chromosome, is also conserved between the human and the mouse. Conservation of the Mpp1 gene between mouse and human gives support to the notion that construction and study of a mouse knockout model may help establish the function of the human MPP1 gene, a potential tumor suppressor gene.

Amino Acid Sequence↗