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At least 343 records · Page 19Linked to original sources

The map-based sequence of the rice genome.

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

Cell Nucleus↗

Complete nucleotide sequence of the cotton (Gossypium barbadense L.) chloroplast genome with a comparative analysis of sequences among 9 dicot plants.

Recently, the complete chloroplast genome sequences of many important crop plants were determined, and this can be considered a major step forward toward exploiting the usefulness of chloroplast genetic engineering technology. Economically, cotton is one of the most important crop plants for many countries. To further our understanding of this important crop, we determined the complete nucleotide sequence of the chloroplast genome from cotton (Gossypium barbadense L.). The chloroplast genome of cotton is 160,317 base pairs (bp) in length, and is composed of a large single copy (LSC) of 88,841 bp, a small single copy (SSC) of 20,294 bp, and two identical inverted repeat (IR) regions of 25,591 bp each. The genome contains 114 unique genes, of which 17 genes are duplicated in the IRs. In addition, many open reading frames (ORFs) and hypothetical chloroplast reading frames (ycfs) with unknown functions were deduced. Compared to the chloroplast genomes from 8 other dicot plants, the cotton chloroplast genome showed a high degree of similarity of the overall structure, gene organization, and gene content. Furthermore, the sequences of the genes showed high degrees of identity at the DNA and amino acid levels. The cotton chloroplast genome was somewhat longer than the chloroplast genomes of most of the other dicot plants compared here. However, this elongation of the cotton chloroplast genome was found to be due mainly to expansions of the intergenic regions and introns (non-coding DNA). Moreover, these expansions occurred predominantly in the LSC and SSC regions.

Base Sequence↗

Molecular characterization of the C-3 DNA puff gene of Rhynchosciara americana.

We have mapped a region of about 33 kb which includes the transcription unit of the C-3 DNA puff gene of Rhynchosciara americana. The C-3 TU and a region extending approximately 800 bp upstream of the C-3 promoter were characterized. The TU is composed of three exons and produces a 1.1-kb mRNA whose level in salivary glands increases with the expansion of the C-3 puff. The C-3 messenger appears to undergo rapid deadenylation resulting in an RNA of about 0.95 kb which can still be observed in gland cells 15 h after the puff has regressed. The 1.1-kb mRNA codes for a 32.4-kDa, predominantly alpha-helical polypeptide with three conserved parallel coiled-coil stretches. The aa composition and structure of this polypeptide suggests that it is secreted and contributes to the formation of the cocoon in which the larvae pupate. The region upstream of the promoter contains several A-rich sequences with similarity to the ACS of yeast which might have a role in the initiation of replication/amplification.

Amino Acid Sequence↗

Structure of the goat psi beta y beta-globin pseudogene. Analysis of goat pseudogene evolutionary patterns.

The 12-member beta-globin gene locus of the goat contains three beta(adult)-type pseudogenes, one in each of three four-gene subsets of the locus. We have determined the complete nucleotide sequence of psi beta y, the pseudogene present in the most downstream four-gene subset, which also contains the functional fetal gene, beta F. psi beta y contains, throughout its length, numerous incapacitating mutations in common with the previously sequenced goat psi beta x and psi beta z pseudogenes consistent with the model that all were descended from a common pseudogene ancestor which became defective prior to the expansion of the beta-globin locus in the goat lineage. Evolutionary analysis of the psi beta y sequence in comparison to psi beta x and psi beta z provides evidence that nucleotide substitutions were fixed in a random manner within these pseudogenes with respect to polarity, coding versus non-coding regions, and replacement sites versus silent sites. However, substitutions appear to have accumulated asymmetrically between different pseudogenes in a manner that provides evidence for partial gene conversion. Moreover, the presence of deletions in goat psi beta y, which are also observed in the cow pseudogene psi 2, but not in the cow psi 1 pseudogene, indicate that goat psi beta y and cow psi 2 are orthologous but cow psi 1 actually arose prior to the goat/cow divergence. The authentic goat orthologue to cow psi 1 temporarily existed in the goat lineage but was deleted, probably prior to the divergence of goats and sheep.

Amino Acid Sequence↗

Analysis of polyglutamine-coding repeats in the TATA-binding protein in different neurodegenerative diseases.

Trinucleotide repeat (TNR) expansion in the gene for TATA binding protein (TBP) has recently been described as causal for spinocerebellar ataxia type 17. The normal number of repeats has been considered to be 42 or less. An intermediate range with reduced penetrance has been assumed to be 43-47 CAA/CAG repeats. We examined this gene in 30 patients with autosomal-dominant cerebellar ataxia (ADCA), 35 patients with sporadic ataxia, 11 patients with Huntington's disease (HD), 351 patients with idiopathic Parkinson's disease (PD), 105 patients with Alzheimer's disease (AD), and 291 controls with no history of neurodegenerative disease. Three patients (one with sporadic PD and two with AD) carrying more than 42 TNRs in the TBP gene were identified. This reveals that the phenotype associated with CAG/CAA expansion in the TBP gene may be heterogeneous.

Aged↗

The human FK506-binding proteins: characterization of human FKBP19.

Analysis of the human repertoire of the FK506-binding protein (FKBP) family of peptidyl-prolyl cis/trans isomerases has identified an expansion of genes that code for human FKBPs in the secretory pathway. There are distinct differences in tissue distribution and expression levels of each variant. In this article we describe the characterization of human FKBP19 (Entrez Gene ID: FKBP11), an FK506-binding protein predominantly expressed in vertebrate secretory tissues. The FKBP19 sequence comprises a cleavable N-terminal signal sequence followed by a putative peptidyl-prolyl cis/trans isomerase domain with homology to FKBP12. This domain binds FK506 weakly in vitro. FKBP19 mRNA is abundant in human pancreas and other secretory tissues and high levels of FKBP19 protein are detected in the acinar cells of mouse pancreas.

Amino Acid Sequence↗

Evaluation of FOXP2 as an autism susceptibility gene.

A mutation in the gene FOXP2 was recently identified as being responsible for a complicated speech and language phenotype in a single large extended pedigree. This gene is of interest to autism because it lies in one of the most consistently linked autism chromosomal regions of interest. We therefore tested this gene for its involvement in autism in a large sample of autism families. We completely sequenced the exon containing the mutation, screened the remaining coding sequence using SSCP technology, and identified and genotyped two novel intronic tetranucleotide repeat polymorphisms that were then analyzed for evidence of linkage and linkage disequilibrium (LD). We identified two families in which heterozygous deletions of a small number of glutamines in a long poly-glutamine stretch were found in one parent and the autistic probands; no other non-conservative coding sequence changes were identified. Linkage and LD analyses were performed in 75 affected sibling pair families and in two subgroups of this sample defined by the presence/absence of severe language impairment. One allele appeared to have an opposite pattern of transmission in the language based subgroups, but otherwise the linkage and LD analyses were negative. We conclude that FOXP2 is unlikely to contribute significantly to autism susceptibility.

Alleles↗

Molecular mechanisms of TRS instability.

To date several neurodegenerative disorders including myotonic dystrophy, Huntington's disease, Kennedy's disease, fragile X syndrome, spinocerebellar ataxias or Friedreich's ataxia have been linked to the expanding trinucleotide sequences. Although phenotypic features vary among these debilitating diseases, the structural abnormalities of the triplet repeat containing DNA sequences is the primary cause for all of these disorders. Expansions of the CAG repeat within coding regions of miscellaneous genes result in the synthesis of aberrant proteins containing enormously long polyglutamine stretches. Such proteins acquire toxic functions and/or may direct cells into the apoptotic cycle. On the other hand, massive expansions of various triplet repeats (i.e., CTG/CAG, CGG/CCG/, GAA/TTC) inside the noncoding regions lead to the silencing of transcription and therefore affect expression of the adjacent genes. The repetitive character of TRS allows stretches of such tracts to form slipped-stranded structures, self-complementary hairpins, triplexes or more complex configurations called "sticky DNA", which are not equally processed by some cellular mechanisms, as compared to random DNA. It is likely that the instability of the short TRS (below the threshold level) occurs due to the SILC pathway, which is driven by the DNA slippage. Accumulation of the short expansions leads to the disease premutation state where the MLC pathway becomes predominant. Independent of which mechanism is involved in the MLC pathway (replication, transcription, repair or recombination) the process of complementary strand synthesis is crucial for the TRS instability. Generally, dependent on the location of the tract which has higher potential to form secondary DNA structure, further processing of such tract may result in expansions (secondary structure formed at the newly synthesized strand) or deletions (structure present on the template strand). Analyses of molecular mechanisms of the TRS genetic instability using bacteria, yeast, cell lines and transgenic animals as models allowed the scientists to better understand the role of some major cellular processes in the development of neurodegenerative disorders in humans. However, it is necessary to remember that most of these investigations were focused on the involvement of each particular process separately. Much less of this work though was dedicated to the search for the interactions between such cellular systems that in effect could result in different rate of TRS expansions. Thus, more intensive studies are necessary in order to fully understand the phenomenon ofthe dynamic mutations leading to the human hereditary neurodegenerative diseases.

Animals↗

An increase in the number of recombinant molecules and other effects of the simultaneous allotype suppression of trans-chromosomal a VH and n Cmu Ig gene products.

The concomitant effects of trans-chromosomal allotype suppression of both an a VH and an n Cmu locus allotype in multiheterozygous rabbits were investigated. For example of the expression of the a2 VH and n81 Cmu allotypes were suppressed in a multiheterozygous rabbit having the a1 chi-y-n81de12,15f73g74/a2 chi 32y33n80de12.14f69g77 genotype. This trans-chromosomal allotype suppression led to the concomitant suppression of other CH allotypes in the same parental haplotype as the suppressed-n81 allotype (i.e. the e15, f73 and g74 allotype) and the partial suppression of the a1 VH allotype (from the normal level of 70% of the total Ig to 10%), and also led to compensation by other VH allotypes from the same parental haplotype as the suppressed-a2 allotype (i.e. the x32 and y33 allotypes). The x32 and y33 allotypes were expressed on Ig molecules with the CH allotypes coded by the same haplotype (i.e. the cis molecules). In a further analysis of the IgG molecules having the partially-suppressed-a1 allotype, one-half (5%) of these molecules were trans-chromosomal recombinant molecules (i.e. a1e14 IgG) and the other half (5%) were cis-chromosomal molecules (i.e. a1e15 IgG). The trans-chromosomal a1e14 IgG molecules probably were derived from the expansion of a limited number of lymphoid clones that normally produce only 1.5% trans-chromosomal recombinant molecules. The cis-chromosomal a1e15 IgG molecules were probably derived either from lymphoid clones that survived the suppression by the anti-n81 Ab, or from lymphoid clones that bore a different subclass of IgM (i.e. n-negative IgM).

Animals↗

Anonymous marker loci within 400 kb of HLA-A generate haplotypes in linkage disequilibrium with the hemochromatosis gene (HFE)

The hemochromatosis gene (HFE) maps to 6p21.3 and is less than 1 cM from the HLA class I genes; however, the precise physical location of the gene has remained elusive and controversial. The unambiguous identification of a crossover event within hemochromatosis families is very difficult; it is particularly hampered by the variability of the phenotypic expression as well as by the sex- and age-related penetrance of the disease. For these practical considerations, traditional linkage analysis could prove of limited value in further refining the extrapolated physical position of HFE. We therefore embarked upon a linkage-disequilibrium analysis of HFE and normal chromosomes from the Brittany population. In the present report, 66 hemochromatosis families yielding 151 hemochromatosis chromosomes and 182 normal chromosomes were RFLP-typed with a battery of probes, including two newly derived polymorphic markers from the 6.7 and HLA-F loci located 150 and 250 kb telomeric to HLA-A, respectively. The results suggest a strong peak of existing linkage disequilibrium focused within the i82-to-6.7 interval (approximately 250 kb). The zone of linkage disequilibrium is flanked by the i97 locus, positioned 30 kb proximal to i82, and the HLA-F gene, found 250 kb distal to HLA-A, markers of which display no significant association with HFE. These data support the possibility that HFE resides within the 400-kb expanse of DNA between i97 and HLA-F. Alternatively, the very tight association of HLA-A3 and allele 1 of the 6.7 locus, both of which are comprised by the major ancestral or founder HFE haplotype in Brittany, supports the possibility that the disease gene may reside immediately telomeric to the 6.7 locus within the linkage-disequilibrium zone. Additionally, hemochromatosis haplotypes possessing HLA-A11 and the low-frequency HLA-F polymorphism (allele 2) are supportive of a separate founder chromosome containing a second, independently arising mutant allele. Overall, the establishment of a likely "hemochromatosis critical region" centromeric boundary and the identification of a linkage-disequilibrium zone both significantly contribute to a reduction in the amount of DNA required to be searched for novel coding sequences constituting the HFE defect.

Alleles↗

Analysis of the mouse CD30 gene: a candidate for the NOD mouse type 1 diabetes locus Idd9.2.

Members of the tumor necrosis factor receptor superfamily play an important role in the initiation, expansion, and termination of an immune response. It has recently been demonstrated that one member of this family, CD30, plays a central role in maintaining peripheral tolerance by controlling the expansion of autoreactive CD8+ T-cells. In the present study, Cd30 was mapped to a 5.6-cM interval on chromosome 4 containing the type 1 diabetes susceptibility locus Idd9.2. We determined the intron/exon structure of Cd30 and sequenced the exons, as well as 1.8 kb of the 5' putative promoter region, from 6 different mouse strains. Remarkably, 63 sequence variants, both coding and noncoding, were found. A total of 27 sequence variants, 4 of which were nonsynonymous, were found between the diabetes susceptible NOD strain and the resistant B10 strain. Of these sequence variants, 19 are within the promoter region. However, no difference between NOD and the congenic strain NOD.B10 Idd9R1, which has the B10 allele of Cd30, was observed in CD30 expression at either the mRNA or protein level. Given its role in protecting against autoimmunity, one or more of the coding variants within CD30 is a good candidate for the Idd9.2 etiological variant.

Animals↗

Delta, a Drosophila neurogenic gene, is transcriptionally complex and encodes a protein related to blood coagulation factors and epidermal growth factor of vertebrates.

Delta (D1) is required for normal segregation of the embryonic ectoderm into neural and epidermal cell lineages in Drosophila melanogaster. Loss-of-function mutations in D1 and other zygotic neurogenic loci lead to expansion of the neuroblast population at the expense of the dermoblast population within the ectoderm. Characterization of the transcriptional organization and maternal/embryonic expression within the chromosomal interval corresponding to D1 reveals that the locus encodes multiple transcripts: a minimum of two maternal transcripts, approximately 4.5 and 3.6 kb in length, and four zygotic transcripts, approximately 5.4 (two distinct species), 3.5, and 2.8 kb in length. These transcripts differ on the bases of differential splicing and differential polyadenylation site choice. The DNA sequence of a cDNA clone representing the predominant transcripts of the locus indicates that D1 encodes a transmembrane protein homologous to blood coagulation factors and epidermal growth factor. The relationship between coding sequences and transcript-specific exons within the locus suggests that D1 encodes multiple translational products.

Amino Acid Sequence↗

High-resolution mtDNA evidence for the late-glacial resettlement of Europe from an Iberian refugium.

The advent of complete mitochondrial DNA (mtDNA) sequence data has ushered in a new phase of human evolutionary studies. Even quite limited volumes of complete mtDNA sequence data can now be used to identify the critical polymorphisms that define sub-clades within an mtDNA haplogroup, providing a springboard for large-scale high-resolution screening of human mtDNAs. This strategy has in the past been applied to mtDNA haplogroup V, which represents <5% of European mtDNAs. Here we adopted a similar approach to haplogroup H, by far the most common European haplogroup, which at lower resolution displayed a rather uninformative frequency distribution within Europe. Using polymorphism information derived from the growing complete mtDNA sequence database, we sequenced 1580 base pairs of targeted coding-region segments of the mtDNA genome in 649 individuals harboring mtDNA haplogroup H from populations throughout Europe, the Caucasus, and the Near East. The enhanced genealogical resolution clearly shows that sub-clades of haplogroup H have highly distinctive geographical distributions. The patterns of frequency and diversity suggest that haplogroup H entered Europe from the Near East approximately 20,000-25,000 years ago, around the time of the Last Glacial Maximum (LGM), and some sub-clades re-expanded from an Iberian refugium when the glaciers retreated approximately 15,000 years ago. This shows that a large fraction of the maternal ancestry of modern Europeans traces back to the expansion of hunter-gatherer populations at the end of the last Ice Age.

DNA, Mitochondrial↗

Huntingtin gene evolution in Chordata and its peculiar features in the ascidian Ciona genus.

BACKGROUND: To gain insight into the evolutionary features of the huntingtin (htt) gene in Chordata, we have sequenced and characterized the full-length htt mRNA in the ascidian Ciona intestinalis, a basal chordate emerging as new invertebrate model organism. Moreover, taking advantage of the availability of genomic and EST sequences, the htt gene structure of a number of chordate species, including the cogeneric ascidian Ciona savignyi, and the vertebrates Xenopus and Gallus was reconstructed. RESULTS: The C. intestinalis htt transcript exhibits some peculiar features, such as spliced leader trans-splicing in the 98 nt-long 5' untranslated region (UTR), an alternative splicing in the coding region, eight alternative polyadenylation sites, and no similarities of both 5' and 3'UTRs compared to homologs of the cogeneric C. savignyi. The predicted protein is 2946 amino acids long, shorter than its vertebrate homologs, and lacks the polyQ and the polyP stretches found in the the N-terminal regions of mammalian homologs. The exon-intron organization of the htt gene is almost identical among vertebrates, and significantly conserved between Ciona and vertebrates, allowing us to hypothesize an ancestral chordate gene consisting of at least 40 coding exons. CONCLUSION: During chordate diversification, events of gain/loss, sliding, phase changes, and expansion of introns occurred in both vertebrate and ascidian lineages predominantly in the 5'-half of the htt gene, where there is also evidence of lineage-specific evolutionary dynamics in vertebrates. On the contrary, the 3'-half of the gene is highly conserved in all chordates at the level of both gene structure and protein sequence. Between the two Ciona species, a fast evolutionary rate and/or an early divergence time is suggested by the absence of significant similarity between UTRs, protein divergence comparable to that observed between mammals and fishes, and different distribution of repetitive elements.

3' Untranslated Regions↗

Huntington toxicity in yeast model depends on polyglutamine aggregation mediated by a prion-like protein Rnq1.

The cause of Huntington's disease is expansion of polyglutamine (polyQ) domain in huntingtin, which makes this protein both neurotoxic and aggregation prone. Here we developed the first yeast model, which establishes a direct link between aggregation of expanded polyQ domain and its cytotoxicity. Our data indicated that deficiencies in molecular chaperones Sis1 and Hsp104 inhibited seeding of polyQ aggregates, whereas ssa1, ssa2, and ydj1-151 mutations inhibited expansion of aggregates. The latter three mutants strongly suppressed the polyQ toxicity. Spontaneous mutants with suppressed aggregation appeared with high frequency, and in all of them the toxicity was relieved. Aggregation defects in these mutants and in sis1-85 were not complemented in the cross to the hsp104 mutant, demonstrating an unusual type of inheritance. Since Hsp104 is required for prion maintenance in yeast, this suggested a role for prions in polyQ aggregation and toxicity. We screened a set of deletions of nonessential genes coding for known prions and related proteins and found that deletion of the RNQ1 gene specifically suppressed aggregation and toxicity of polyQ. Curing of the prion form of Rnq1 from wild-type cells dramatically suppressed both aggregation and toxicity of polyQ. We concluded that aggregation of polyQ is critical for its toxicity and that Rnq1 in its prion conformation plays an essential role in polyQ aggregation leading to the toxicity.

Crosses, Genetic↗

Moderate instability of the trinucleotide repeat in spino bulbar muscular atrophy.

Increased length of a protein-coding CAG repeat within the androgen receptor gene appears to be the only type of mutation responsible for spino-bulbal muscular atrophy (SBMA or Kennedy disease). We have analysed a large 4-generation SBMA family and found that the mutant allele was unstable upon transmission from parent to child, with a documented variation from 46 to 53 repeats and a tendency to increase in size (7 increases and a single decrease in 17 events), which appeared stronger upon transmission from a male than from a female. Our results suggest also limited somatic instability of the abnormal allele, with observable variation of up to 2-3 repeats. This indicates that the behavior of the CAG repeat is similar to that observed for small premutations in the fragile X syndrome, or small abnormal alleles in myotonic dystrophy, two diseases which are caused by expansion of an unstable trinucleotide repeat.

Alleles↗

[Disordered development of Drosophila melanogaster embryos mosaic for the Notch gene].

Gene Notch codes for a transmembrane protein, which is involved in cell interactions: mutations in Notch locus result in differentiation of all cells of the ventral and anterodorsal ectoderm into neuroblasts. In order to examine interrelations between cells of the normal and mutant phenotype, mosaic embryos were obtained. Procephalic regions of Drosophila trunk were most strongly affected in the experimental, as well as in the control, embryos. In control mosaics, the absence of anterodorsal ectoderm was accompanied by a decrease in the size of epipharyngeal ganglion, whereas Notch mosaics, in contrast, showed the expansion of epipharyngeal ganglion over dorsal ectoderm up to the posterior end of the embryo. Differentiation abnormalities of cells of the ventral ectoderm in Notch mosaics were rarer. Generally, the results of our experiments lead to a hypothesis about the presence of a certain threshold in the proportion between Notch cells and wild-type cells in ventral ectoderm. When this threshold value is exceeded, all cells of ventral ectoderm differentiate into neuroblasts.

Animals↗

Recent advances in understanding the pathogenesis of Huntington's disease.

Huntington's disease (HD) is an autosomal, dominantly inherited neurodegenerative disorder that is characterized by abnormal involuntary movements (chorea), intellectual impairment and selective neuronal loss. The expansion of a polymorphic trinucleotide repeat (the sequence CAG that codes for glutamine) to a length that exceeds 40 repeat units in exon 1 of the gene, HD, correlates with the onset and progression of the disease. The protein encoded by HD, huntingtin, is normally localized in the cytoplasm, whereas the mutant protein is also found in the nucleus, suggesting that its translocation to this site is important for the pathogenesis of HD. Although several proteins that interact with huntingtin have been identified in vitro, the significance of these interactions with the mutant protein in the pathogenesis of HD has yet to be determined. Recent progress in the development of cellular and animal models for the disease have provided invaluable insights and resources for studying the disease mechanisms underlying HD, and will be useful for screening and evaluating possible therapeutic strategies.

Animals↗