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At least 487 records · Page 27Linked to original sources
PubMed2002

A novel porcine gene, alpha-1-antichymotrypsin 2 (SERPINA3-2): sequence, genomic organization, polymorphism and mapping.

A novel porcine gene, alpha-1-antichymotrypsin 2 (SERPINA3-2), a member of the serpin superfamily, was isolated from a porcine genomic library and sequenced. The genomic organization of the approximately 9.0 kb gene was determined on the basis of the porcine liver cDNA of SERPINA3-1 and SERPINA3-2, and comprises five exons and four introns. The coding sequence of SERPINA3-2 shares 86% identity with the paralogue, SERPINA3-1. Porcine SERPINA3-2 was found to be an orthologue of human SERPINA3 (71% identity of the coding sequences) and both genes have a similar genomic organization. Polymorphisms were found in intron 4 of the porcine gene using polymerase chain reaction-restriction fragment length polymorphism. The gene was mapped by linkage analysis and radiation hybrid mapping to the distal end of chromosome 7q, to the gene cluster of the protease inhibitors including PI1 (SERPINA1), PI2, PI3, PI4 (apparently paralogues of SERPINA3), and PO1A and PO1B. SERPINA3-2 is the first porcine serpin gene whose genomic organization has been determined.

Amino Acid Sequence↗
PubMed1993

Isolation and characterization of the human diacylglycerol kinase gene.

The 80 kDa diacylglycerol kinase (DGK) is abundantly expressed in oligodendrocytes and lymphocytes but not to a detectable extent in other cells such as neurons and hepatocytes. As an initial attempt to delineate the mechanism of the transcriptional control of the DGK gene, we have cloned from a human genomic library a 22 kb genomic fragment. The genomic clone consists of the 5'-flanking region and 17 exons coding for approx. 53% of the total exons of human DGK, including those encoding EF-hand and zinc-finger regions. The translation initiation site is located in the second exon. S1 nuclease mapping and primer extension analysis of the human DGK mRNA identified a major transcription initiation site (position +1) at 264 bp upstream from the initiator ATG. In the 5'-flanking sequence we detected a single GC box at -35 but no canonical TATA and CAAT sequences. However, the sequence starting from the cap site (AGTTCCTGCCA) is very similar to the initiator element that specifies the transcription initiation site of some housekeeping genes. In addition, the 5'-upstream region contains several putative cis-elements. Jurkat and HepG2 cells were transfected with various 5'-deletion mutants of the upstream region fused to the structural gene of chloramphenicol acetyltransferase (CAT). The CAT assay revealed that among constructs containing up to 3.4 kb of the 5'-flanking region, a fragment of 263 bp from the transcription initiation site contains a basic promoter that is active in both types of cells. Moreover, the region between -263 and -850 contains a negative element that is active in HepG2 but not in Jurkat cells. This negative element may, at least in part, be responsible for the cell type-specific expression of the DGK gene.

Animals↗
PubMed2000

Genomic structure and promoter analysis of the mouse EphA8 receptor tyrosine kinase gene.

The gene encoding the mouse EphA8 receptor tyrosine kinase has been isolated from a mouse genomic library, and its complete genomic structure has been determined. This gene spans approximately 28 kb and consists of 17 exons. This gene structure is similar to the structure of the chick EphB2 (Cek5) gene, except for one intron present between the first two exons encoding the EphA8 kinase domain. This difference may reflect an evolutionary divergence of the catalytic domain between EphA and EphB subgroup receptors. The site for transcription initiation has been mapped to the 19th nucleotide upstream from the translation start codon ATG. A feature of this gene is an unmethylated CpG island spanning exon 1 and the flanking sequence. The putative promoter of the EphA8 gene lacks a TATA box and contains multiple copies of the sequence GGGCGG, the core sequence of the putative Sp1-binding site. The 3.5-kb upstream genomic region containing part of the first exon showed strong promoter activity in NG108-15 neuroblastoma cells but much less in 293T cells, suggesting that this fragment is sufficient for neural cell-directed promoter activity. By deleting the genomic region containing the five GC boxes, it was shown that the minimal promoter region is primarily comprised of five copies of the Sp1-binding site located upstream from the transcription initiation site. Finally, in situ RNA hybridization studies revealed a very specific pattern of EphA8 gene expression restricted to the rostral region of midbrain tectum during embryonic development. Isolation of a functional promoter for the EphA8 gene is a first step in understanding how expression of this gene is controlled at the molecular level.

Amino Acid Sequence↗
PubMed2001

Characterization of a PR-10 pathogenesis-related gene family induced in rice during infection with Magnaporthe grisea.

A partial cDNA with homology to the PR-10 class of pathogenesis-related proteins was used to screen a rice genomic library. One 16-kb genomic clone contained three genes with PR-10 similarity. These genes, RPR10a, RPR10b, and RPR10c, were arranged in tandem and separated by approximately 2.5 kb. RPR10a cDNA was obtained by reverse transcription-polymerase chain reaction, and sequence analysis revealed that RPR10a and RPR10b encode predicted proteins of 158 and 160 amino acids, respectively, and share 71% amino acid identity. RPR10c appears to be a nonfunctional pseudogene. Gene-specific probes were used to study transcript accumulations of the three RPR10 genes in rice plants following inoculation with Magnaporthe grisea. RPR10a transcripts were induced from a low basal level within 12 h after inoculation and showed a second higher level induction at 48 h, which continued throughout the 144 h it was examined. In addition, RPR10a was induced strongly by salicylic and jasmonic acid applications to rice plants. Transcripts of RPR10b also were enhanced by M. grisea, but were not strongly visible until 48 h after inoculation. Tissue prints of M. grisea-infected rice leaves when the RPR10a-specific probe was used indicate that RPR10a is expressed most strongly in a localized fashion in response to the pathogen.

Base Sequence↗
PubMed1990

Characterization of a sperm-specific nuclear autoantigenic protein. I. Complete sequence and homology with the Xenopus protein, N1/N2.

In our studies on specific sperm proteins that function in fertilization, an autoantigenic, postacrosomal sperm protein has been found to originate in the testis as a nuclear-associated protein. This nuclear autoantigenic sperm protein (NASP) contains a C-terminal nuclear translocation signal and has structural similarities to the lamins and other nuclear proteins; and its 2.5 kb mRNA is apparently tissue-, but not species-, specific. DNA clones from a rabbit testis cDNA library and a rabbit genomic library were sequenced in order to characterize NASP. The polyadenylated mRNA has 39 bases of 5' untranslated sequence, an open reading frame of 2043 bases encoding 680 amino acids, and a 104 base 3' untranslated region (2,186). The encoded polypeptide has a calculated molecular weight of 73,533 and a pI = 4.06, containing 25% acidic residues. One clone (R1.2) expressing the C-terminal 446 amino acids was used to express a fusion protein. The expressed R1.2/beta-galactosidase fusion protein was found to be autoantigenic. Secondary structure predictions for NASP showed that 69% of the molecule had a high probability of forming alpha-helices and that several alpha-helical regions had a characteristic repeating heptad pattern that in the intermediate filaments and nuclear lamins is involved in coiled-coil interactions with other molecules. In addition to the nuclear translocation signal common to many nuclear proteins, NASP also showed homology with the Xenopus histone-binding protein, N1/N2.

Amino Acid Sequence↗
PubMed1998

The heat shock 70 gene family in the Mediterranean fruit fly Ceratitis capitata.

The cloning and the characterization of the heat shock 70 (hsp70) genes of the medfly C. capitata, a major agricultural pest, are presented. Six genomic clones were isolated by screening a medfly genomic library with an hsp70 genomic fragment of Drosophila melanogaster. They form two 30 kb contigs, both of which map cytogenetically in a single major heat shock puff (3L:24C) of the salivary gland polytene chromosomes. Restriction mapping and blot hybridization indicated the presence of six putative hsp70 genes in these two closely linked regions. The sequence of one of these genes suggests that it is a heat-inducible hsp70 gene. The 638-codon open reading frame shows 84% identity at the amino acid level (73.5% at the nucleotide level), relative to corresponding D. melanogaster sequences. The 5' untranslated leader sequence, approximately 200 bp long, is not interrupted by introns and is very rich (48%) in adenine residues, resembling Drosophila heat-inducible hsp70 genes. Furthermore, the promoter of this gene contains two characteristic heat shock elements close upstream from the TATA box. The levels of the hsp70 transcripts are very low at 25-30 degrees C, increase significantly at 33 degrees C and reach maximum at 39 degrees C.

Amino Acid Sequence↗
PubMed1995

Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain.

Human DNA-binding proteins, dbpA and dbpB (YB-1), are members of a protein family containing a cold-shock domain, and are regarded as transcriptional regulators. Here, we isolated genomic fragments of these genes and characterized their transcriptional regulation. Analysis of lambda phage genomic clones revealed that the dbpA gene consists of 10 exons spanning a 24-kb genomic region. The cold-shock domain, composed of about 70 amino acid residues, is encoded separately by exons 2-5. The exon 6, encoding 69 amino acid residues, was found to be an alternative exon. Northern-blot analysis showed that both genes were highly expressed in skeletal muscle and heart compared with in other tissues. The dbpA gene contains no typical TATA box or CAAT box at the immediate 5' region, but a sequence similar to an initiator consensus sequence was revealed at a major transcription-start site. A transient expression assay using the chloramphenicol acetyltransferase reporter gene revealed that the sequence located at positions -17 to +70 relative to the major transcription-start site was critical for promoter function. Within this region, the consensus sequence for serum-response element, CC(A/T)6GG, is present at positions -13 to -4 in addition to the initiator sequence. Immunofluorescence showed the cellular localization of dbpA to be both in the cytoplasm and nucleus, particularly at the perinuclear region. In situ hybridization demonstrated the localization of the dbpA gene on chromosome 12 band p13.1, whereas dbpB-(YB-1)-related genes were dispersed on many chromosomes with strongest hybridization signals on chromosome 1. All 16 dbpB (YB-1) clones, isolated from the same genomic library used for dbpA genomic cloning, were processed genes because of their intronless structures and multiple mutations. One of these processed genes possesses an open reading frame, which encodes most of the amino acid residues of dbpB (YB-1). These results indicate that dbpA and dbpB (YB-1) genes evolved in different fashions after deviation from a common ancestral gene.

Amino Acid Sequence↗
PubMed1991

gamma-Aminobutyric acidA receptor heterogeneity is increased by alternative splicing of a novel beta-subunit gene transcript.

DNA sequences encoding two variants of a novel gamma-aminobutyric acidA (GABAA) receptor beta subunit were isolated from an embryonic chicken whole-brain cDNA library and a chicken genomic library. The coding regions of these variants only differ from each other by the absence or presence of 12 bp in the region that encodes the presumed intracellular loop between transmembrane domains M3 and M4; the encoded subunits have been named beta 4 and beta 4', respectively. The predicted mature polypeptides are 72-77% identical to the previously characterized mammalian and chicken beta 1, beta 2, and beta 3 subunits. Analysis of the beta 4-subunit gene reveals that the different transcripts encoding the two variants arise by the use of one of two 5'-donor splice sites that are separated by 12 bp. This is the first demonstration of alternative splicing of a GABAA receptor subunit gene transcript and represents a further mechanism for the generation of GABAA receptor heterogeneity.

Animals↗
PubMed2006

Global mapping of transposon location.

Transposable genetic elements are ubiquitous, yet their presence or absence at any given position within a genome can vary between individual cells, tissues, or strains. Transposable elements have profound impacts on host genomes by altering gene expression, assisting in genomic rearrangements, causing insertional mutations, and serving as sources of phenotypic variation. Characterizing a genome's full complement of transposons requires whole genome sequencing, precluding simple studies of the impact of transposition on interindividual variation. Here, we describe a global mapping approach for identifying transposon locations in any genome, using a combination of transposon-specific DNA extraction and microarray-based comparative hybridization analysis. We use this approach to map the repertoire of endogenous transposons in different laboratory strains of Saccharomyces cerevisiae and demonstrate that transposons are a source of extensive genomic variation. We also apply this method to mapping bacterial transposon insertion sites in a yeast genomic library. This unique whole genome view of transposon location will facilitate our exploration of transposon dynamics, as well as defining bases for individual differences and adaptive potential.

Chromosome Mapping↗
PubMed1997

Molecular structure of the human gonadotropin-releasing hormone receptor gene.

GnRH receptors belong to the family of G protein-coupled receptor proteins and have been localized to the anterior pituitary, brain and reproductive organs as well as many steroid-dependent tumor tissues. Recently, cDNAs for the GnRH receptors of several species including the human have been cloned. To determine the structure of the gene encoding the human GnRH receptor, we isolated the receptor gene clones from the human genomic libraries. Comparison of the genomic and cDNA sequences revealed that the human GnRH receptor gene is composed of three exons and two introns and spans over 20 kb in size. Exon 1 encodes the 5' untranslated sequence and nucleotide +1 to +522 in the open reading frame, exon 2 encodes nucleotide +523 to +742 and exon 3 encodes nucleotide +743 to +987 in the open reading frame as well as the 3' untranslated sequence. Southern blot analysis of genomic DNA and localization of the GnRH receptor gene to a single site on human chromosome 4 (4q13) indicate the presence of a single copy of the gene in the human genome. Several regulatory sequences for various hormones and other regulatory factors were identified, including PEA-3, AP-1, AP-2, and Pit-1 sites. In addition, glucocorticoid/progesterone response element thyroid hormone response element, and cAMP response element sequences were identified. Reverse transcriptase-primer extension and 5' RACE analysis of the human pituitary RNA demonstrated the presence of multiple transcriptional start sites upstream of the translational start site. Analysis of the 5' flanking region of the gene also revealed the presence of multiple TATA and CAAT sequences. The finding of multiple transcriptional start sites raises the possibility of tissue-specific regulation and the existence of variable size transcripts. Chimeras containing 1.26 kb (-534 to 728) of the 5' flanking region of the receptor gene and the luciferase (Luc) gene expressed a significant luciferase activity when transfected into a human endometrial tumor cell line (HEC-1A) and a breast tumor cell line (MCF-7) but not in a mouse pituitary gonadotrope cell line (alpha T3-1), suggesting the existence of multiple promoter elements in the gene. These findings indicate a multiplicity of regulation of expression of the GnRH receptor and provide the substrate for detailed investigation in the reproductive system.

Animals↗
PubMed2000

Identification of Sp1 as the transcription factor for the alternative promoter P2 of the bovine growth hormone receptor gene.

Growth hormone receptor (GHR) mRNA variants that differ in the 5'-untranslated regions (5'-UTR) have been isolated in various species. These 5'-UTR variants are generated from the use of alternative promoters and/or alternative splicing. The 5'-UTR 1B is one of the GHR 5'-UTR variants isolated in the bovine but its homologues are also present in other species. The 5'-UTR 1B is a predominant GHR 5'-UTR expressed in many tissues. In the present study, we screened a bovine genomic library and isolated a 1.7 kb bovine GHR genomic sequence including exon 1B and its 5' flanking region from which the GHR 5'-UTR 1B is generated. Using primer extension, two major transcription start sites were mapped in the bovine exon 1B. Transient transfection analysis of the 5' flanking region of exon 1B confirmed its promoter activity (termed P2) in both Hep G2 and BHK-21 cells. Furthermore, analysis of deletion promoter-reporter constructs found that the basal activity of P2 resided in the proximal region of P2. DNase I footprinting analysis and electromobility shift assay (EMSA) identified the ubiquitous transcription factor Sp1 as the binding protein to a GC box-containing DNA element within the proximal P2. Deletion of the GC box greatly reduced the activity of P2 in cell lines. The GC box-containing site also appeared to bind Sp1 in the nuclear extracts from diverse bovine tissues. This suggests that interactions of Sp1 with the GC box-containing element in the proximal region of P2 may be part of the mechanism for the expression of the bovine GHR 5'-UTR 1B in diverse tissues.

5' Untranslated Regions↗
PubMed1995

Isolation and characterization of the human muscle glycogen synthase gene.

Impaired glycogen synthase (GS) activity in skeletal muscle has been considered to be an inherited trait in patients with non-insulin-dependent diabetes mellitus (NIDDM). We therefore isolated the human muscle GS gene from genomic libraries and determined the genomic structure. The entire coding region, the 5'-flanking region, and the exon-intron boundaries were sequenced. The gene consists of 16 exons spanning approximately 27 kb of DNA and exists as a single copy in the human genome. The negatively charged parts with all known phosphorylation sites were coded by the first and the last exon. A single transcription initiation site was located 167 nucleotides upstream of the initiation codon. All of the exons and the putative promoter region were analyzed by single-strand conformation polymorphism in 30 insulin-resistant Finnish NIDDM patients, and three polymorphic sites were found. A missense mutation Gly464/Ser in exon 11 was found in 2 of 228 NIDDM patients screened but in 0 of 154 control subjects. These two patients were characterized further by severe insulin resistance and premature arteriosclerosis. The characterization of the genomic structure of the human muscle GS gene will facilitate studies of its role in the development of insulin resistance and NIDDM.

Adult↗
PubMed1999

Differential mRNA display cloning and characterization of a Cryptosporidium parvum gene expressed during intracellular development.

Differential mRNA display was used to detect differences in gene expression between mock-infected and Cryptosporidium parvum-infected human adenocarcinoma cells. A reproducible band present only in C. parvum-infected cells, ddHC-10 was isolated and cloned. Northern blot analysis was used to confirm the differential expression of the HC-10 mRNA. As differential mRNA display does not differentiate between parasite and host mRNAs, Southern blot analysis was used to demonstrate that ddHC-10 represented a C. parvum gene. Northern blot analysis demonstrated that HC-10 mRNA is expressed by sporozoites prior to invasion of host cells. Screening of a C. parvum genomic library identified 2 different genomic clones, HC-10-13C and HC-10-6C. The combined genomic sequence contained a predicted open reading frame of 2,952 base pairs (bp), coding for a protein of 984 amino acids with a predicted molecular weight of approximately 106 kDa. Reverse transcription polymerase chain reaction mapping of the HC-10 transcript demonstrated that the HC-10 gene lacks introns, and the approximately 4,789-bp mRNA contains relatively large 5' (approximately 1,390-bp) and 3' (approximately 440-bp) untranslated regions. The predicted polypeptide contained a high proportion of polar amino acids, with the most abundant amino acids being serine (10.5%), threonine (9.8%), and cysteine (7.6%). The C-terminal region of the predicted polypeptide is characterized by a threonine-rich region containing multiple repeats of the sequence TTTTRP. This repeat motif is similar to that found in the mucin-like genes of vertebrates and lower eukaryotes that have been shown to play important roles in cell-cell interactions in multicellular organisms and invasion of host cells by unicellular parasites.

Amino Acid Sequence↗
PubMed1990

Genomic organization and chromosomal localization of the human nucleolin gene.

Nucleolin, a eukaryotic nucleolar phosphoprotein, is involved in the synthesis and maturation of ribosomes. To characterize the genomic organization and regulatory sequences of this gene, two overlapping lambda clones containing the human nucleolin gene plus flanking regions were isolated from a genomic library using human nucleolin cDNA. Southern blots of genomic DNA from human, several mammals, chicken, and yeast revealed that the nucleolin gene is well conserved across these species. The gene consists of 14 exons with 13 intervening sequences and spans approximately 11 kilobases of DNA. Analysis of the splice junctions indicated that the amino-terminal domain and the four RNA binding domains plus the nuclear localization signal are split into adjacent exons. Sequences from the 5'-flanking and the first intron contain a high content of GC residues which is consistent with nucleolin being a "housekeeping" gene. Promoter elements include an atypical TATA box (GTTA), one CCAAT box much further from the initiation site, three reverse compliments of CCAAT (ATTGG), and two pyrimidine-rich nucleotide stretches. In addition, this region and the first intron contain numerous potential Sp1, GCF, CRE-fos, GCN, AP-1, AP-2, UCE, and sequences similar to the glucocorticoid receptor binding site. The transcription start site was determined by primer extension and S1 nuclease mapping of RNA from human liver. One Kpn and three Alu repeats were found within two of the middle introns. The 3'-untranslated portion of the gene contains five homology blocks in a 100-base pair region that are highly conserved among human, mouse, and hamster genomes. Finally, we have determined that the human nucleolin gene is located on chromosome 2q12-qter and is present at one copy per haploid genome. A restriction fragment length polymorphism with EcoRI has been detected in the gene.

Amino Acid Sequence↗
PubMed1989

[Cloning and analysis of the primary structure of an element, related to the murine mammary cancer virus, from the genome of the Djungarian hamster].

11 recombinant bacteriophages from the genomic library of Djungarian hamster genome, that carry MMTV-related sequences (MRS-Ps), have been cloned with the murine mammary cancer virus (MMTV) as a hybridization probe. The sequences are repeated 50 times in the genome. MRS-Ps contain the tracts of homology with the long end repeat MMTV, the genes pol and, possibly, env, but not with the gag gene. Sequencing of the 0,87 kb restrict, common to all EcoRI-BamHI clones, and the analysis of the sequence have demonstrated the high level of homology with the pol gene of MMTV and its origination from the somewhat functioning gene.

Animals↗
PubMed1986

Molecular biology of human serum cholinesterase.

More than 90% of the amino acid sequence of purified human serum cholinesterase has been determined in our laboratory. Purified enzyme was digested with several proteolytic enzymes; the resulting polypeptides were then separated, purified, and sequenced. Optimal sequence regions were identified and used as the basis for the synthesis of three 17-mer oligonucleotide probes. In addition, one long peptide of 58 amino acid residues was selected for construction of two unique sequence oligonucleotide probes of 39-mer and 53-mer; the peptide regions corresponding to the latter are six amino acids apart. The probes have been used to screen a human liver cDNA library and a human genomic library. Several positive clones to both types of probes have been identified. These are being characterized, and some of them have been or are now being sequenced. A high degree of homology in the amino acid sequence of the active center of human serum cholinesterase and that of acetylcholinesterase from the Torpedo fish has been noted. It appears that this region of cholinesterases has been conserved during evolution, and there may be an important, still unrecognized role for serum nonspecific cholinesterase in mammalian metabolism.

Amino Acid Sequence↗