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PubMed1997

Genomic organization of the 3' region of the human mucin gene MUC5B.

MUC5B, mapped clustered with MUC6, MUC2, and MUC5AC to chromosome 11p15.5, is a human mucin gene of which the genomic organization is being elucidated. We have recently published the sequence and the peptide organization of its huge central exon, 10,713 base pairs (bp) in length. We present here the genomic organization of its 3' region, which encompasses 10,690 bp. The genomic sequence has been completely determined. The 3' region of MUC5B is composed of 18 exons ranging in size from 32 to 781 bp, contrasting thus with the very large central exon. The sizes of the 18 introns range from 114 to 1118 bp. Some repetitive sequences were identified in four introns. The peptide deduced from the sequence of the 18 exons consists of an 808-amino acid peptide. This carboxyl-terminal region exhibits extensive sequence similarity to MUC2, MUC5AC, and von Willebrand factor, particularly the number and the positions of the cysteine residues, suggesting that this domain may be derived from a common ancestral gene. The presence in these components of a cystine knot also found in growth factors such as transforming growth factor-beta is of particular interest. Moreover, one part of this peptide is identical to the 196-amino acid sequence deduced from the cDNA clone pSM2-1, which codes for a part of the high molecular weight mucin MG1 isolated from human sublingual gland. Considering the expression pattern of MUC5B and the origin of MG1, we can thus conclude that MUC5B encodes MG1.

Amino Acid Sequence↗

PubMed2005

Genomic organization of zebrafish cone-rod homeobox gene and exclusion as a candidate gene for retinal degeneration in niezerka and mikre oko.

PURPOSE: To determine the genomic organization of the zebrafish crx gene and to evaluate if mutations in crx are responsible for the retinal degeneration phenotype in the zebrafish (Danio rerio) mutants niezerka (nie(m743)) and mikre oko (mok(m632)). METHODS: Overlapping fragments were PCR amplified from genomic DNA isolated from homozygous mutant embryos and wild-type siblings (sibs). Amplicons were sequenced and sequence data assembled into contigs. Genomic organization was determined by alignment of contigs with published cDNA sequences and zebrafish genomic sequence from Sanger and Ensembl databases. Linkage analysis used DNA from mapping panels of single homozygous mutant animals with mixed genetic backgrounds. RESULTS: The analysis indicated that the zebrafish crx gene consisted of three exons and 2 introns, and spans 3.8 kb of genomic DNA. The splice junctions were all located within the coding region. Highly repetitive sequences present in non-coding regions of crx and extended tetra-nucleotide repeats in intronic regions were associated with sequence variation between different strains. Homozygous mok(m632) or nie(m743) mutants and their respective wild-type sibs, showed identical patterns of heterozygosity and sequence variations within each line. No mutation in crx were identified in homozygous mok(m632) or nie(m743). Consistent with the absence of identified mutations, linkage analysis excluded linkage of the mutant phenotypes to crx. CONCLUSIONS: Despite the presence of sequence variations in their respective genetic backgrounds, within each line the sequence of crx was identical. Consistent with the absence of mutations, further analysis excluded linkage of the mutant phenotypes to crx. Analysis is in progress to map these loci and identify the genes responsible for the retinal degeneration phenotype in these mutant lines.

Animals↗

PubMed1999

Genomic organization, transcription, splicing and gene regulation in Leishmania.

The parasitic protozoan Leishmania is the aetiological agent of a spectrum of clinical diseases, ranging from disfiguring skin lesions to life-threatening visceral infection, and is a serious health problem in tropical and subtropical areas world-wide. Leishmania parasites undergo a dramatic transformation as they move between the different environments of an extracellular insect stage and an intracellular form in the vertebrate host. In an attempt to develop new strategies for the treatment of leishmaniasis, the techniques of molecular genetics have been utilised to elucidate the mechanisms which direct and control this cyclical differentiation. This review discusses current knowledge concerning the organization and regulation of the Leishmania nuclear genome and includes a discussion of chromosomal organization, genomic arrangement, transcription, transcript processing by trans-splicing and polyadenylation, and post-transcriptional regulation. The salient features as well as the supporting evidence for each topic are briefly reviewed.

Animals↗

PubMed1999

Rat endozepine-like peptide (ELP): cDNA cloning, genomic organization and tissue-specific expression.

A cDNA encoding the rat homolog of the previously characterized murine endozepine-like peptide (ELP) was isolated by a PCR cloning strategy. Sequence comparison with the murine cDNA sequence revealed a conservation of the ELP primary structure between both rodent species with minor amino acid exchanges. We investigated the genomic organization of the rat ELP gene by genomic PCR. This indicated the presence of a single short intron of 451bp interrupting the 5' untranslated region. Tissue-dependent ELP expression was determined by Northern hybridization and semiquantitative RT-PCR. Northern hybridization showed an ELP specific transcript in both the male and the female gonad, but the level of ovarian ELP transcription was considerably lower than in the testis. RT-PCR analysis demonstrated a low and varying level of ELP background expression in all examined tissues. In contrast to the closely related ACBP gene, ELP shows a different genomic organization and a more regulated expression pattern, and may exert a specific function as a gonadal acyl-CoA pool former and transporter.

5' Untranslated Regions↗

PubMed1998

The novel genome organization of the insect picorna-like virus Drosophila C virus suggests this virus belongs to a previously undescribed virus family.

The complete nucleotide sequence of the genomic RNA from the insect picorna-like virus Drosophila C virus (DCV) was determined. The DCV sequence predicts a genome organization different to that of other RNA virus families whose sequences are known. The single-stranded positive-sense genomic RNA is 9264 nucleotides in length and contains two large open reading frames (ORFs) which are separated by 191 nucleotides. The 5' ORF contains regions of similarities with the RNA-dependent RNA polymerase, helicase and protease domains of viruses from the picornavirus, comovirus and sequivirus families. The 3' ORF encodes the capsid proteins as confirmed by N-terminal sequence analysis of these proteins. The capsid protein coding region is unusual in two ways: firstly the cistron appears to lack an initiating methionine and secondly no subgenomic RNA is produced, suggesting that the proteins may be translated through internal initiation of translation from the genomic length RNA. The finding of this novel genome organization for DCV shows that this virus is not a member of the Picornaviridae as previously thought, but belongs to a distinct and hitherto unrecognized virus family.

Amino Acid Sequence↗

PubMed1997

Oat blue dwarf marafivirus resembles the tymoviruses in sequence, genome organization, and expression strategy.

The complete nucleotide sequence and genome organization of oat blue dwarf marafivirus (OBDV) were determined. The 6509 nucleotide RNA genome encodes a putative 227-kDa polyprotein (p227) with sequence motifs similar to the methyltransferase, papain-like protease, helicase, and polymerase motifs present in the nonstructural proteins of other positive strand RNA viruses. The 3' end of the open reading frame (ORF) that encodes p227 (ORF 227) also encodes the two capsid proteins: a 24-kDa capsid protein is presumably cleaved from the p227 polyprotein, whereas the 21-kDa capsid protein appears to be translated from a subgenomic RNA (sgRNA). Encoded amino acid and nucleotide sequence comparisons, as well as the OBDV genome expression strategy, show that OBDV closely resembles the tymoviruses. OBDV differs from the tymoviruses in its general biology, in its lack of a putative movement gene that overlaps the replication-associated genes, and in its fusion of the capsid gene sequences to the major ORF. OBDV also possesses a 3' poly(A) tail, as compared to the tRNA-like structures found in most tymoviral genomes. Due to the strong similarities in genome sequence and expression strategy, OBDV, and presumably the other marafiviruses, should be considered a member of the tymovirus lineage of the alpha-like plant viruses.

Amino Acid Sequence↗

PubMed1993

Sequence and genomic organization of Norwalk virus.

A library of overlapping cDNAs obtained from Norwalk virus purified from stools of human volunteers (Jiang et al., 1990, Science 250, 1580-1583) was used to obtain the nucleotide sequence of the viral genome. The sequence has a total of 7642 nucleotides, excluding the 3' poly(A) tail, and has a base composition of 48% G + C. Three open reading frames (ORF) are predicted in the sequence. The longest ORF (ORF1, nucleotides (nt) 146 to 5359) is predicted to encode a polyprotein precursor to nonstructural proteins based on identification of sequences similar to the picornavirus 2C protein, 3C protease, and 3D RNA-dependent RNA polymerase. ORF2 (nt 5346 to 6935) is predicted to encode a polypeptide with a predicted molecular weight of 56,571 (56.6K, close to the expected size of the viral capsid protein), and it contains a short region of sequence similarity to the picornavirus structural protein VP3. A third potential ORF (nt 6938 to 7573) could encode a small polypeptide of 22.5K. The genomic organization found in Norwalk virus shares striking similarities with the genome of two caliciviruses, the feline calicivirus and the rabbit hemorrhagic disease virus. The morphology, size, polarity, and genomic organization of the Norwalk virus indicate it is a member of the Caliciviridae family.

Base Sequence↗

PubMed1996

Base composition and gene distribution: critical patterns in mammalian genome organization.

Recent success in developing transcriptional maps of large genomic regions provide excellent opportunities for the investigation of mammalian genome organization. Detailed definition of organizational features will, in the short term, aid in prioritizing genomic sequencing efforts and in interpreting sequencing results and, in the long term, will surely provide insights into the structural, functional and evolutionary basis for the mammalian chromosome and chromosomal banding patterns. For such efforts, human chromosome 21 provides an excellent model system because the physical and clone maps are detailed, and several transcriptional mapping projects have provided large numbers of novel genes. It is, therefore, valuable at this point to examine these transcriptional mapping data and to compare them with the isochore model of the mammalian genome, which describes patterns in base composition and predicts gene distributions. Not only do compelling organizational patterns appear, but new questions about additional possible patterns in gene size, structure, conservation and transcription can be asked.

Animals↗

PubMed1998

Variation in genome organization of the plant pathogenic fungus Colletotrichum lindemuthianum.

The genome structure of Colletotrichum lindemuthianum in a set of diverse isolates was investigated using a combination of physical and molecular approaches. Flow cytometric measurement of genome size revealed significant variation between strains, with the smallest genome representing 59% of the largest. Southern-blot profiles of a cloned fungal telomere revealed a total chromosome number varying from 9 to 12. Chromosome separations using pulsed-field gel electrophoresis (PFGE) showed that these chromosomes belong to two distinct size classes: a variable number of small (< 2.5 Mb) polymorphic chromosomes and a set of unresolved chromosomes larger than 7 Mb. Two dispersed repeat elements were shown to cluster on distinct polymorphic minichromosomes. Single-copy flanking sequences from these repeat-containing clones specifically marked distinct small chromosomes. These markers were absent in some strains, indicating that part of the observed variability in genome organization may be explained by the presence or absence, in a given strain, of dispensable genomic regions and/or chromosomes.

Ascomycota↗

PubMed1998

The genomic organization of the human GLP-1 receptor gene.

The genomic organization of the human gene encoding the receptor for glucagon-like peptide-1 (GLP-1 (7-37)/(7-36) amide) was analyzed to reveal the relationship to other G-protein-coupled receptors. The coding sequence of the GLP-1 receptor is interrupted by 12 introns. These introns are uniformly distributed within the open reading frame. The length of the introns varies between 6.6 kb and 100 bp, in contrast to the relative constant length of 100 bp of the exons. All of the exon/intron splice junctions characterized followed the consensus GT-AG rule. A comparison of the genomic structure with other related receptor genes indicates that the exon/intron organization is well-conserved among the VIP/ glucagon/secretin receptor family.

3' Untranslated Regions↗

PubMed2006

Genomic organization of the sex-determining and adjacent regions of the sex chromosomes of medaka.

Sequencing of the human Y chromosome has uncovered the peculiarities of the genomic organization of a heterogametic sex chromosome of old evolutionary age, and has led to many insights into the evolutionary changes that occurred during its long history. We have studied the genomic organization of the medaka fish Y chromosome, which is one of the youngest heterogametic sex chromosomes on which molecular data are available. The Y specific and adjacent regions were sequenced and compared to the X. The male sex-determining gene, dmrt1bY, appears to be the only functional gene in the Y-specific region. The Y-specific region itself is derived from the duplication of a 43-kb fragment from linkage group 9. All other coduplicated genes except dmrt1bY degenerated. The Y-specific region has accumulated large stretches of repetitive sequences and duplicated pieces of DNA from elsewhere in the genome, thereby growing to 258 kb. Interestingly the non-recombining part of the Y did not spread out considerably from the original duplicated fragment, possibly because of a large sequence duplication bordering the Y-specific fragment. This may have conserved the more ancestral structure of the medaka Y and provides insights into some of the initial processes of Y chromosome evolution.

Animals↗

PubMed1999

Elucidation of the genome organization of tobacco mosaic virus.

Proteins unique to tobacco mosaic virus (TMV)-infected plants were detected in the 1970s by electrophoretic analyses of extracts of virus-infected tissues, comparing their proteins to those generated in extracts of uninfected tissues. The genome organization of TMV was deduced principally from studies involving in vitro translation of proteins from the genomic and subgenomic messenger RNAs. The ultimate analysis of the TMV genome came in 1982 when P. Goelet and colleagues sequenced the entire genome. Studies leading to the elucidation of the TMV genome organization are described below.

Capsid Proteins↗

PubMed2003

[Analysis of the genomic organization of a novel scorpion toxin BmTXK beta].

Scorpion venoms contain different types of low molecular mass toxic peptides acting on ion channels. Many cDNAs and genomic genes encoding these toxins have been isolated and sequenced while the mechanisms of expression and regulation of scorpion toxins is not well studied yet. BmTXK beta, one of the four putative long-chain potassium channel toxins, is isolated from the cDNA library of the venom gland of Chinese scorpion BmK (Buthus martensii Karsch). It has an 886 bp intron located in the mature peptide while other scorpion toxins' introns are located in the signal peptide. The special genomic organization of BmTXK beta makes it a good object to study the mechanism of expression and regulation of scorpion toxins. With primers designed according to the already known sequence of BmTXK beta, its 5' and 3' flanking regions are cloned by the Vecttorette II Staorette Pack method and sequenced. Analysis of the sequence shows that another intron longer than 997 bp is located in the signal peptide region of BmTXK beta, which makes BmTXK beta different from all the other scorpion toxins that have no intron or only one intron in the signal peptide. The special genomic organization of BmTXK beta indicates that BmTXK beta is a new membership of long-chain potassium channel toxin.

Amino Acid Sequence↗

PubMed2000

Genomic organization and tissue-specific expression of rat urocortin.

The genomic organization of rat urocortin was determined using both cDNA and liver genomic DNA as templates for polymerase chain reactions. A single intron of 261 bp was found upstream to the ATG start codon, and the whole urocortin coding sequence was shown to be contained in a single exon. Relying on these results, oligonucleotide primers were designed, which can differentiate genomic DNA contamination from cDNA-derived signals in a reverse transcription-polymerase chain reaction. Tissue screening for urocortin expression revealed that the mid-brain is the major site of urocortin mRNA expression, and that other peripheral organs, including lymphoid tissues and peripheral blood lymphocytes, do not produce urocortin.

Animals↗

PubMed1993

Genomic organization of the porcine skeletal muscle ryanodine receptor (RYR1) gene coding region 4624 to 7929.

Excitation-contraction coupling in skeletal muscle is mediated by two calcium channels located in the membranes of the transverse tubule and the sarcoplasmic reticulum. Calcium is released from the terminal cisternae of the sarcoplasmic reticulum via the ryanodine receptor. Abnormal increases in myoplasmic free calcium caused by a defect in the ryanodine receptor have been reported in malignant hyperthermia. Malignant hyperthermia is a life-threatening pharmacogenetic disorder in a variety of species and is triggered by volatile anesthetics and depolarizing muscle relaxants. To study the genomic organization of the porcine skeletal muscle ryanodine receptor gene, we have isolated six genomic fragments spanning approximately 80 kb of chromosomal DNA. In this report, we describe the genomic organization of a 15.5-kb genomic fragment comprising 18 exons coding for region 4624 to 7929 of the porcine skeletal muscle ryanodine receptor gene.

Animals↗

PubMed1991

Genomic organization of the human erythropoietin receptor gene.

Erythropoietin (EPO) mediates the growth and differentiation of erythroid progenitors through its interaction with a specific receptor. Using a partial cDNA clone for the murine erythropoietin receptor, we isolated a human genomic clone containing the erythropoietin receptor gene. The coding region of the human EPO receptor gene is contained within eight exons spanning approximately 6 kb. The human gene has a great deal of structural similarity and sequence homology with the murine gene. The murine gene also has eight exons, although the size of each intron is somewhat different. The locations at which the introns interrupt the coding sequence are conserved precisely. The genomic organization of the EPO receptor gene is also shown to be homologous to the genomic organization of the IL-2 receptor beta chain gene. The sequence of 1.1 kb of 5' flanking DNA was characterized and contains consensus sequences for both Sp1 and GATA-1 binding sites and an initiator (Inr)-like element, but lacks both a canonical TATA box and the CACCC consensus sequence found in the murine gene.

Amino Acid Sequence↗

PubMed2004

Little cherry virus-2: sequence and genomic organization of an unusual member of the Closteroviridae.

The complete genomic sequence of variant USA6b of Little cherry virus-2 (LChV-2), has been determined and is 15045 nucleotides in length, coding for 11 open reading frames (ORFs). The sequence shares 77.2% identity with a previously published, ca. 6 kb partial replicase sequence of LChV-2 (variant USA6a). Both LChV-2/USA6a and LChV-2/USA6b were obtained from the same tree infected with little cherry disease, and would suggest a mixed infection. LChV-2/USA6b is more closely related to the partially determined genomic sequence of a Canadian isolate of LChV-2, strain LC5 (92.9% identity). LChV-2/USA6b has an unusual genomic organization compared to other members of the Closteroviridae. The LChV-2/USA6b genome is potentially ambi-sense, with a negative sense ORF0 at the 5' terminus, from which an 18.1 kDa protein of unknown function can be expressed in vitro. The N-terminal region of the LChV-2/USA6 ORF1a translation product does not code for a papain-like protease motif. ORF1 codes for a novel motif, of unknown function, also present in isolates of the Grapevine leafroll associated virus-3, (genus Ampelovirus) as well as viruses of the family Flexiviridae. ORF3 lacks an AUG start codon, but could potentially be expressed via read-through of the ORF2 stop codon. At the 3' end, there is a re-organization of encoded genes compared with other members of the Closteroviridae including separation of the coat protein and coat protein duplicate genes by 4 other genes as found for LChV-2/LC5.

Amino Acid Sequence↗

PubMed1987

Genomic organization of low copy number sequences that are associated with deca-satellite DNA in the monkey genome.

A previously described segment of African green monkey DNA (cloned in phage lambda MkA) contains deca-satellite linked to DNA sequences that are estimated to occur once per genome. Sequences homologous to the low copy number sequences in lambda MkA are also associated with species-specific satellite DNAs in the human and mouse genomes. A second clone, lambda Mk8, contains a monkey DNA region that is colinear and homologous to a portion of the low copy number sequences in lambda MkA, but no satellite sequences. The two cloned segments are markedly different starting at a point proximal to the satellite DNA region in lambda MkA. DNA-blotting experiments indicate that lambda Mk8 but not lambda MkA represents the typical genomic organization and that the low copy number segments occur only once per haploid genome. The data suggest that rearrangements such as deletions or inversions occurring in monkey cells account in part for the structure of lambda MkA. Additional rearrangements may have occurred during cloning in E. coli. This unique chromosomal region may be particularly susceptible to recombination.

Animals↗