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PubMed1988

Primary structure of the human follistatin precursor and its genomic organization.

Follistatin is a single-chain gonadal protein that specifically inhibits follicle-stimulating hormone release. By use of the recently characterized porcine follistatin cDNA as a probe to screen a human testis cDNA library and a genomic library, the structure of the complete human follistatin precursor as well as its genomic organization have been determined. Three of eight cDNA clones that were sequenced predicted a precursor with 344 amino acids, whereas the remaining five cDNA clones encoded a 317 amino acid precursor, resulting from alternative splicing of the precursor mRNA. Mature follistatins contain four contiguous domains that are encoded by precisely separated exons; three of the domains are highly similar to each other, as well as to human epidermal growth factor and human pancreatic secretory trypsin inhibitor. The genomic organization of the human follistatin is similar to that of the human epidermal growth factor gene and thus supports the notion of exon shuffling during evolution.

Adult↗

PubMed2002

Human Ro60 (SSA2) genomic organization and sequence alterations, examined in cutaneous lupus erythematosus.

BACKGROUND: The Ro 60 kDa protein (Ro60 or SSA2) is the major component of the Ro ribonucleoprotein (Ro RNP) complex, to which an immune response is a specific feature of several autoimmune diseases. The genomic organization and any sequence variation within the DNA encoding Ro60 are unknown. OBJECTIVES: To characterize the Ro60 gene structure and to assess whether any sequence alterations might be associated with serum anti-Ro antibody in subacute cutaneous lupus erythematosus (SCLE), thus potentially providing new insight into disease pathogenesis. METHODS: The cDNA sequence for Ro60 was obtained from the NCBI database and used for a BLAST search for a clone containing the entire genomic sequence. The intron-exon borders were confirmed by designing intronic primer pairs to flank each exon, which were then used to amplify genomic DNA for automated sequencing from 36 caucasian patients with SCLE (anti-Ro positive) and 49 with discoid LE (DLE, anti-Ro negative), in addition to 36 healthy caucasian controls. RESULTS: Heteroduplex analysis of polymerase chain reaction (PCR) products from patients and controls spanning all Ro60 exons (1-8) revealed a common bandshift in the PCR products spanning exon 7. Sequencing of the corresponding PCR products demonstrated an A > G substitution at nucleotide position 1318-7, within the consensus acceptor splice site of exon 7 (GenBank XM001901). The allele frequencies were major allele A (0.71) and minor allele G (0.29) in 72 control chromosomes, with no significant differences found between SCLE patients, DLE patients and controls. CONCLUSIONS: The genomic organization of the DNA encoding the Ro60 protein is described, including a common polymorphism within the consensus acceptor splice site of exon 7. Our delineation of a strategy for the genomic amplification of Ro60 forms a basis for further examination of the pathological functions of the Ro RNP in autoimmune disease.

Antibodies, Antinuclear↗

PubMed2000

Criteria for gene identification and features of genome organization: analysis of 6.5 Mb of DNA sequence from human chromosome 21.

To establish criteria for and the limitations of novel gene identification, to identify novel genes of potential relevance to Down Syndrome and to investigate features of genome organization, 6. 550kb. In total, 41 novel gene models were predicted, and for a subset of these, RT-PCR experiments helped to verify and refine the models, and were used to assess expression in early development and in adult brain regions of potential relevance to Down syndrome. Results suggest generally low and/or restricted patterns of expression, and also reveal examples of complex alternative processing, especially in brain, that may have important implications for regulation of protein function. Analysis of complete gene structures of the known genes identified a number of very large introns, a number of very short intergenic distances, and at least one potentially bi-directional promoter. At least 3/4 of known genes and 1/2 of predicted genes are associated with CpG islands. For novel genes, three cases of overlapping genes are predicted. Results of these analyses illustrate some of the complexities inherent in mammalian genome organization and some of the limitations of current sequence analysis technologies. They also doubled the number of potential genes within the region.

Adult↗

PubMed2000

The mitochondrial genome of the stramenopile alga Chrysodidymus synuroideus. Complete sequence, gene content and genome organization.

This is the first report of a complete mitochondrial genome sequence from a photosynthetic member of the stramenopiles, the chrysophyte alga Chrysodidymus synuroideus. The circular-mapping mitochondrial DNA (mtDNA) of 34 119 bp contains 58 densely packed genes (all without introns) and five unique open reading frames (ORFs). Protein genes code for components of respiratory chain complexes, ATP synthase and the mitoribosome, as well as one product of unknown function, encoded in many other protist mtDNAs (YMF16). In addition to small and large subunit ribosomal RNAs, 23 tRNAs are mtDNA-encoded, permitting translation of all codons present in protein-coding genes except ACN (Thr) and CGN (Arg). The missing tRNAs are assumed to be imported from the cytosol. Comparison of the C.SYNUROIDEUS: mtDNA with that of other stramenopiles allowed us to draw conclusions about mitochondrial genome organization, expression and evolution. First, we provide evidence that mitochondrial ORFs code for highly derived, unrecognizable versions of ribosomal or respiratory genes otherwise 'missing' in a particular mtDNA. Secondly, the observed constraints in mitochondrial genome rearrangements suggest operon-based, co-ordinated expression of genes functioning in common biological processes. Finally, stramenopile mtDNAs reveal an unexpectedly low variability in genome size and gene complement, testifying to substantial differences in the tempo of mtDNA evolution between major eukaryotic lineages.

Algal Proteins↗

PubMed2002

Genome organization of Casphalia extranea densovirus, a new iteravirus.

The viral genome of Casphalia extranea densovirus (CeDNV) has been cloned and sequenced. It was 5002 nucleotides long and contained inverted terminal repeats of 230 nucleotides. Their distal 159 nucleotides formed imperfect palindromes in two orientations. Three large open reading frames (ORFs) were identified on the same strand, two in the left-hand half and one in the right-hand half. Each of the five structural proteins, expressed from the right-hand ORF in the baculovirus system, autoassembled into capsids. The two left-hand ORFs overlapped and code for nonstructural (NS) proteins. NS1 protein was shown to contain replicator protein and helicase/ATPase motifs. The PGY region in VP1 capsid protein is conserved among most parvoviruses and contained a phospholipase A(2) motif, a novel viral enzyme. This domain was expressed and its enzyme activity was demonstrated. The approximate 75% sequence identity between the DNAs from CeDNV and BmDNV-1 and identical genome organization indicated that CeDNV should be classified in the Iteravirus genus.

Amino Acid Sequence↗

PubMed1997

Genomic organization and chromosome localization of the human cathepsin K gene (CTSK).

Human cathepsin K is a recently described cysteine protease with high sequence homology to cathepsins S and L, members of the papain superfamily of cysteine proteases. Cathepsin K is abundantly and selectively expressed in osteoclasts and may perform a specialized role in osteoclast-mediated bone resorption. In the present study, the genomic organization and chromosomal localization of human cathepsin K (HGMW-approved symbol CTSK) were determined. Intron-exon boundaries were identified by PCR on human genomic DNA, and subsequently a P1 genomic clone containing the full-length gene was isolated. Cathepsin K spans approximately 12.1 kb of genomic DNA and is composed of eight exons and seven introns. The genomic organization of cathepsin K is similar to that of cathepsins S and L. The gene was mapped to chromosome 1q21 by fluorescence in situ hybridization. Primer walking on the P1 genomic clone identified 1108 bp of 5' flanking sequence and 459 bp of 3' flanking sequence. Ribonuclease protection assay and 5' RACE indicated a single transcriptional start site 49 bp upstream of the initiator Met codon. Analysis of the 5' flanking region indicates that this gene lacks canonical TATA and CAAT boxes and contains multiple potential transcription regulatory sites. The characterization of the cathepsin K gene and its promoter may provide valuable insights not only into its osteoclast-selective expression, but also into the molecular mechanisms responsible for osteoclast activation.

Base Sequence↗

PubMed2001

Comparative analysis of the genomic organization of Pax9 and its conserved physical association with Nkx2-9 in the human, mouse, and pufferfish genomes.

As a first step towards the identification of cis-regulatory elements of Pax9 by means of comparative genomics, we have analyzed genome regions encompassing the Pax9 gene in three vertebrate species, humans, mice (Mus musculus), and the Japanese pufferfish (Fugu rubripes). We show the genomic organization of Pax9 and its physical association with Nkx2-9 conserved in the three species. We discuss about possible implications of the conserved synteny between Pax9 and Nkx2-9 in a context of vertebrate evolution. This report also includes the first description of the primary structures of Fugu Pax9 and Nkx2-9. Furthermore, we report the identification of a novel upstream exon and putative transcription start sites in mouse Pax9. Our results suggest that transcription of Pax9 may be initiated at two alternative start sites and driven by TATA-less promoters.

Amino Acid Sequence↗

PubMed2001

The genomic organization of the gene encoding the vanilloid receptor: evidence for multiple splice variants.

Vanilloid receptor subtype-1 (VR1) is a nonselective cation channel that is expressed in sensory neurons and is activated by multiple noxious stimuli. Rat Vr1, stretch-inactivated channel (SIC), and vanilloid receptor 5' splice variant (VR.5'sv) have been hypothesized to be derived from a common VR gene. Characterization of the genomic structure encoding the 5' portion of rat Vr1 confirmed that VR.5'sv is derived from the VR gene; however, SIC seemed to be derived from two related but independent genes. We also deduced the genomic organization of the human gene VR1. Comparative studies of rat and human VR genes showed substantial conservation in genomic organization. The splice site flanking exon-intron 7 in rat and human VR1 diverged from the expected consensus sequence; this may help to explain the skipping of exon 7 within VR.5'sv and other VR splice variants.

5' Untranslated Regions↗

PubMed1996

The genome organization and affinities of an Australian isolate of carrot mottle umbravirus.

The genomic sequence of an Australian isolate of carrot mottle umbravirus (CMoV-A) was determined from cDNA generated from dsRNA. This provides the first data on the genome organization and phylogeny of an umbravirus. The 4201-nucleotide genome contains four major open reading frames (ORFs). Analysis suggests that ORF2 encodes an RNA-dependent RNA polymerase, that ORF4 encodes a movement protein, and that the virus has no coat protein gene. The functions of ORFs 1 and 3 remain unknown. ORF2 is probably translated following ribosomal frameshifting. ORFs 3 and 4 are probably translated from a subgenomic mRNA. Sequence comparisons showed CMoV-A to be closely related to pea enation mosaic RNA2 (PEMV-RNA2), but also to have affinities with the Bromoviridae. These findings shed light on the relationships between the luteoviruses, PEMV, and the umbraviruses and on the relationships between the carmo-like viruses and the Bromoviridae.

Australia↗

PubMed2004

The complete genomic organization of the human MUC6 and MUC2 mucin genes.

The complete genomic organization of the two mucin genes MUC2 and MUC6 was obtained by comparison of new and published mRNA sequences with newly available human genomic sequence. The two genes are located 38.5 kb apart in a head-to-head orientation within a gene complex on chromosome 11p15.5. The N-terminal organization of MUC6 is highly similar to that of MUC2, containing the D1, D2, D', and D3 Von Willebrand factor domains followed by the large tandem repeat domains located in exons 31 and 30, respectively. MUC6 has a much smaller C-terminal domain (101 amino acids) encoded by 2 exons containing only the CK domain, compared with MUC2, which has a C-terminal domain of 859 amino acids containing the D4, C, D, and CK domains, encoded by 19 exons. The gene structures agreed partially but not completely with predictions from gene prediction programs.

Chromosomes, Human, Pair 11↗

PubMed1995

Cloning of a cDNA coding for porcine zona pellucida glycoprotein ZP1 and its genomic organization.

The zona pellucida composed of three or four glycoproteins plays important roles in fertilization. Our previous study showed that porcine ZP1, one of the major glycoproteins of porcine zona pellucida, was divided into two components (porcine ZP4 and ZP2), and suggested it was a homologue of mouse ZP2. In this paper we report the cloning of a cDNA for porcine ZP1 and its genomic organization. The deduced amino acid sequence of porcine ZP1 shared a 54% and 63% identity with those of mouse and human ZP2, respectively. Genomic organization of porcine ZP1 was also similar to that of mouse ZP2. The transcript of porcine ZP1 gene was detected only in growing oocytes.

Amino Acid Sequence↗

PubMed2003

A new virus infecting Myzus persicae has a genome organization similar to the species of the genus Densovirus.

The genomic sequence of a new icosahedral DNA virus infecting Myzus persicae has been determined. Analysis of 5499 nt of the viral genome revealed five open reading frames (ORFs) evenly distributed in the 5' half of both DNA strands. Three ORFs (ORF1-3) share the same strand, while two other ORFs (ORF4 and ORF5) are detected in the complementary sequence. The overall genomic organization is similar to that of species from the genus DENSOVIRUS: ORFs 1-3 most likely encode the non-structural proteins, since their putative products contain conserved replication motifs, NTP-binding domains and helicase domains similar to those found in the NS-1 protein of parvoviruses. The deduced amino acid sequences from ORFs 4 and 5 show sequence similarities with the structural proteins of the members of the genus DENSOVIRUS: These data indicate that this virus is a new species of the genus Densovirus in the family PARVOVIRIDAE: The virus was tentatively named Myzus persicae densovirus.

Amino Acid Sequence↗

PubMed1997

Genomic organization of the metal-mobilizing bacterium Thiobacillus cuprinus.

The genomic organization of Thiobacillus cuprinus, a facultative chemolithotrophic bacterium that preferentially solubilizes copper from complex ores, has been studied by Pulsed Field Gel Electrophoresis (PFGE). It has been determined that T. cuprinus has a circular chromosome of about 3.8 Mb in size as concluded by analysis of gamma-irradiated total DNA and restriction analysis. Macrorestriction patterns for several restriction enzymes have been generated. Restriction enzymes AseI, DraI, SpeI, SwaI and XbaI give a number of fragments that can be adequately resolved by PFGE and then be used for electrophoretic karyotyping and for the construction of physical maps of the chromosome. Such a map has been constructed for the endonucleases SpeI and SwaI. The localization of several heterologous and homologous genes on the physical map, including those for rRNA, has paved the way for the construction of a genetic map.

Chromosomes↗

PubMed1984

Cloning, physical mapping and genome organization of mitochondrial DNA from Cyprinus carpio oocytes.

The mitochondrial genome from Cyprinus carpio oocytes is a 10.5 megadalton, circular DNA molecule. The carp mitochondrial DNA was cloned in pBR325. Three recombinant plasmids accounted for the entire genome. Mapping of this DNA using 11 different restriction endonucleases is reported here. Both the large and small rRNA genes were then localized using Southern blot analysis. The subunit I of the cytochrome oxidase, the cytochrome b, the tRNAGlu and the URF 4 genes were localized by nucleotide sequence analysis and homology studies with human mtDNA. Our results suggest that a similar gene order has been maintained in the mitochondrial genomes of Chordata and support the hypothesis of a common ancestor for all vertebrate organelle genomes. This study constitutes the first report on the genome organization of a fish mtDNA and provides information for further investigation in connection with sequence determination, replication, and gene expression in carp mitochondria.

Animals↗

PubMed1995

The large-scale genomic organization of repetitive DNA families at the telomeres of rye chromosomes.

Repetitive DNA sequences in the terminal heterochromatin of rye (Secale cereale) chromosomes have consequences for the structural and functional organization of chromosomes. The large-scale genomic organization of these regions was studied using the telomeric repeat from Arabidopsis and clones of three nonhomologous, tandemly repeated, subtelomeric DNA families with complex but contrasting higher order structural organizations. Polymerase chain reaction analysis with a single primer showed a fraction of the repeat units of one family organized in a "head-to-head" orientation. Such structures suggest evolution of chromosomes by chromatid-type breakage-fusion-bridge cycles. In situ hybridization and pulse field gel electrophoresis showed the order of the repeats and the heterogeneity in the lengths of individual arrays. After Xbal digestion and pulse field gel electrophoresis, the telomeric and two subtelomeric clones showed strong hybridization signals from 40 to 100 kb, with a maximum at 50 to 60 kb. We suggest that these fragments define a basic higher order structure and DNA loop domains of regions of rye chromosomes consisting of arrays of tandemly organized sequences.

Arabidopsis↗

PubMed1998

Genomic organization and chromosomal localization of the murine epididymal retinoic acid-binding protein (mE-RABP) gene.

The murine epididymal retinoic acid-binding protein (mE-RABP) is specifically synthesized in the mouse mid/distal caput epididymidis and secreted in the lumen. In this report, we have demonstrated by Southern blot analysis of genomic DNA that mE-RABP is encoded by a single-copy gene. A mouse 129/SvJ genomic bacterial artificial chromosome (BAC) library was screened using a cDNA encoding the minor form of mE-RABP. One positive BAC clone was characterized and sequenced to determine the nucleotide sequence of the entire mE-RABP gene. The molecular cloning of the mE-RABP gene completes the characterization of the 20.5-kDa-predicted preprotein leading to the minor and major forms of mE-RABP. Comparison of the DNA sequence of the promoter and coding regions with that of the rat epididymal secretory protein I (ESP I) gene showed that the mE-RABP gene is the orthologue of the ESP I gene that encodes a rat epididymal retinoic acid-binding protein. Several regulatory elements, including a putative androgen receptor binding site, "CACCC-boxes," NF-1, Oct-1, and SP-1 recognition sites, are conserved in the proximal promoter. Analysis of the nucleotide sequence of the mE-RABP gene revealed the presence of seven exons and showed that the genomic organization is highly related to other genes encoding lipocalins. The mE-RABP gene was mapped by fluorescent in situ hybridization to the [A3-B] region of the murine chromosome 2. Our data, combined with that of others, suggest that the proximal segment of the mouse chromosome 2 may be a rich region for genes encoding lipocalins with a genomic organization highly related to the mE-RABP gene.

Amino Acid Sequence↗

PubMed1996

Genomic organization of human papillomavirus type 18 in cervical cancer specimens.

It has been reported that cervical cancers positive for human papillomavirus (HPV) 18 have a poorer prognosis than those with other HPV types. To gain a better understanding of the aggressive character of HPV 18-positive cancers, we examined the difference in genomic organization between HPV 18 and HPV 16 harbored in cervical cancers. We amplified E1 and E2 genes from 9 HPV 18-positive and 31 HPV 16-positive cervical cancers by polymerase chain reaction (PCR). At least one of the two early genes was missing in 3 out of 9 HPV 18-positive cancers, while both PCRs were positive in all 31 HPV 16-positive cancers (P < 0.05). We then analyzed the 9 HPV 18-positive cancers by 15 contiguous polymerase chain reactions covering collectively the whole HPV 18 genome. In addition to the three with a deletion of the E1 or E2 gene, one had a deletion in the E5 and L2 genes and one had an insertion in the long control region. The frequent alterations in genomic organization, especially preferential deletion of the E1 or E2 gene, may be related to the more aggressive properties of HPV 18-positive cervical cancers.

Adenocarcinoma↗

PubMed1999

Genomic organization of the 3' region of the human thyroglobulin gene.

The genomic organization of the 3' end of the human Thyroglobulin (Tg) gene has not previously been characterized. We isolated and characterized seventeen lambda phage clones from a human genomic library that included nucleotides 6263 to 8410 of the Tg mRNA, encompassing the last thirteen 3' exons of the Tg gene. The region contained exons ranging in size from 94 to 222 nucleotides, split by introns of 1 to 64 kb. We estimate a total of 48 exons in the Tg gene. All the intron-exon boundaries were sequenced. We found that the splicing sequences diverged considerably from the 3' and 5' consensus. However, the GT-AG rule was perfectly respected in all the exons. A total of 5788 intronic bases and most of the sequences contained in the 13 exons were analyzed (1846 bases). One sequence variation, TT to CC at positions 8377-8378, was found in the 3' untranslated segment. The three tyrosine residues involved in thyroid hormones synthesis (amino acids 2554, 2568, and 2747) at the carbosyl termini of Tg, are encoded by exons 44, 45, and 48. The knowledge of the precise organization of the Tg gene should help to direct studies of Tg gene mutations in families in which a defect in the synthesis of Tg occurs.

Bacteriophage lambda↗