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PubMed2026

Transcriptome Analysis and Experimental Validation of Palmitoylation- Related Biomarkers in Atherosclerosis.

INTRODUCTION: Protein palmitoylation contributes to membrane localisation, signal transduction, and cell-fate regulation. It is closely associated with lipid metabolic dysfunction, immune inflammation, and vascular remodelling in atherosclerosis (AS). However, key palmitoylation-related transcriptomic markers and their potential causal associations with AS remain incompletely defined. METHODS: The Gene Expression Omnibus (GEO) dataset GSE100927 was used as the training cohort, and GSE43292 was used as an external validation cohort. Differentially expressed genes were identified using limma and intersected with palmitoylation-related genes to obtain palmitoylation-related differentially expressed genes (PRDEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were then performed using clusterProfiler. Two-sample Mendelian randomisation was used to evaluate potential causal relationships between characteristic genes and AS. Feature selection was conducted using random forest and support vector machine recursive feature elimination (SVM-RFE), and the overlapping genes selected by both methods were retained. Receiver operating characteristic (ROC) curves were used to assess diagnostic performance. A five-gene nomogram was constructed, and its clinical utility was evaluated using calibration curves and decision curve analysis (DCA). Gene set variation analysis (GSVA) was applied to compare pathway activity between high- and low-expression groups for each core gene. Single-cell analysis using Seurat and expression-based cell-cell communication analysis using CellChat were conducted with GSE159677, and upstream transcription factors were predicted using NetworkAnalyst. For in vivo validation, an AS model was established in ApoE⁸/⁸ mice fed a high-fat diet, and aortic gene and protein expression were assessed by RT-qPCR and western blotting. RESULTS: In GSE100927, 51 PRDEGs were identified. GO and KEGG enrichment analyses highlighted pathways associated with regulation of monoatomic ion transport, sarcomere and myofibril organisation, and immune inflammation. Mendelian randomisation suggested a potential protective causal association between SLC7A7 and AS. By integrating MR with random forest and SVM-RFE feature selection, we prioritised five core genes: PLCB2, GMIP, NEXN, PLN, and SLC7A7. These genes showed good diagnostic performance in GSE43292. The resulting nomogram was well calibrated and demonstrated stable net benefit in decision curve and clinical impact curve analyses. Single-gene GSVA identified consistently activated pathways across multiple genes, including innate and adaptive immune recognition, calcium signalling and myocardial contraction/cardiomyopathy, extracellular matrix-receptor interaction, cell junction pathways, autophagy-lysosome pathways, and several metabolic programmes. At the single-cell level, PLCB2 and GMIP were predominantly expressed in T cells and macrophages, NEXN and PLN were enriched in vascular smooth muscle cells, and SLC7A7 was mainly expressed in macrophages. CellChat analysis indicated increased signals for immune-related ligand-receptor interactions. In ApoE⁸/⁸ mice fed a high-fat diet, PLCB2, GMIP, and SLC7A7 were upregulated, whereas NEXN and PLN were downregulated; protein-level changes were concordant with the transcriptomic trends. DISCUSSION: These findings indicate that palmitoylation-related dysregulation in AS converges on immune inflammation, calcium signalling/contractile programmes, ECM remodelling, and autophagy-linked metabolism. The five-gene panel is supported by external validation, single-cell localisation to immune and vascular compartments, and concordant results in ApoE⁸/⁸ mice. CONCLUSION: This study identified and validated five palmitoylation-related genes associated with AS. SLC7A7 showed a potential protective causal signal in MR analysis. The enriched pathway patterns linked these genes to immune inflammation, calcium signalling-contraction coupling, ECM remodelling, cell adhesion, and autophagy- associated metabolic reprogramming. The five-gene nomogram showed potential utility for diagnostic classification and decision support, nominating candidate biomarkers and pathway targets for AS molecular subtyping, diagnosis, and mechanistic investigation.

Atherosclerosis (AS)↗

PubMed1985

Relationship between the proteins encoded by the exclusion determining locus of the IncI plasmid R144 and the cellular localization of these proteins in Escherichia coli K-12.

A region of the IncI plasmid R144, determining and controlling exclusion (exc), codes for two proteins, designated 13K and 19K after their apparent molecular weights (respectively 13,000 and 19,000). Both proteins were simultaneously affected by various mutations that resulted in exclusion deficiency. In this paper the relationship between these proteins as well as their cellular location is reported. We found no indications that the 19K protein is a precursor form of the 13K protein. Analysis of gene products of recombinant plasmids carrying exc as well as of several derivatives, however, provided a strong indication that the proteins result from overlapping genes. Besides, evidence was obtained that the 19K protein is essential for exclusion. Localization studies revealed that this protein exists in a membrane-bound form, associated at the periplasmic side of the inner membrane, and in a soluble form residing in the cytoplasm.

Bacterial Proteins↗

PubMed1996

Genetic organization of a DNA-processing region required for mobilization of a non-self-transmissible plasmid, pEC3, isolated from Erwinia carotovora subsp. carotovora.

A non-self-transmissible multiple-copy plasmid, pEC3, isolated from the phytopathogenic bacterium, Erwinia carotovora subsp. carotovora, can be mobilized by an IncP-type plasmid. The hybrid plasmid vector, pETC3, constructed from pEC3 by fusion to markers conferring TcR and CmR, was transferred by conjugation from Escherichia coli (Ec) to various genera of Enterobacteriaceae and to other genera of Gram(-) bacteria which included Xanthomonas, Agrobacterium and Rhizobium. Deletion analysis and successive subcloning of pEC3 revealed that a cis-acting locus, oriT and a trans-acting locus, mob, were involved in mobilization of pEC3. Five open reading frames (ORFs) were found in the mob region, of which four were identified as mobA, B, C and D. The mobA gene overlapped with mobC, B, D and ORF1 that were transcribed polycistronically from upstream from mobC. The nature of the four products of mob genes, MobA, B, C and D, was verified by use of the T7 promoter system in Ec.

Amino Acid Sequence↗

PubMed2003

Characterization of the bidirectional promoter region between the human genes encoding VLCAD and PSD-95.

Bidirectional promoters are widely known among lower organisms but rare in mammals. A shared promoter between the two human genes encoding very long chain acyl-CoA dehydrogenase (VLCAD) and postsynaptic density protein 95 (PSD-95) is an ideal model to investigate bidirectional transcription in mammals. VLCAD associates with the inner mitochondrial membrane and catalyzes the initial step in mitochondrial long-chain fatty acid beta-oxidation. PSD-95, a component protein of the PSD, plays an essential role in clustering the transmembrane proteins in synaptic membranes. Interestingly, the human genes encoding VLCAD (ACADVL) and PSD-95 (DLG4) are adjacently located in the head-to-head orientation on chromosome 17p. The transcribed regions of the two genes overlap, while the two transcription start sites stand approximately 220 bp apart. To analyze the common transcriptional control region shared by the two genes, we generated serial promoter partial deletion constructs using firefly luciferase as the reporter gene. Our results showed that the essential promoter activity of PSD-95 is carried within an approximately 400-bp region, which covers the entire approximately 270-bp minimal promoter of VLCAD. The results from di-(2-ethylhexyl) phthalate (DEHP)-treated HepG2 cells revealed that the minimal VLCAD promoter is able to up-regulate VLCAD expression in response to DEHP treatment. Site-directed mutagenesis experiments showed that a mutated activator protein 2-binding site markedly reduced the transcriptional activity of both promoters and abolished the minimal VLCAD promoter's response to DEHP treatment.

Acyl-CoA Dehydrogenase, Long-Chain↗

PubMed1994

The E subunit of vacuolar H(+)-ATPase localizes close to the centromere on human chromosome 22.

As part of a general effort to identify new genes mapping to disease-associated regions of human chromosome 22, we have isolated heterogeneous nuclear RNA from somatic cell hybrids selected for their chromosome 22 content. Inter-Alu PCR amplification yielded a series of human DNA fragments which all detected evolutionarily-conserved sequences. The centromere-most gene fragment candidate, XEN61, was shown to lie centromeric to the chromosome 22 breakpoint in the X/22-33-11TG somatic cell hybrid. This region, which is still devoid of characterized genes, overlaps with the critical region for the cat eye syndrome (CES), a developmental disorder associated with chromosomal duplication within 22pter-q11.2. Gene dosage analysis performed on DNA from six CES patients consistently revealed the presence of four copies of XEN61. A fetal brain cDNA clone, 61EW, was identified with XEN61 and entirely sequenced. The deduced protein is the E subunit of vacuolar H(+)-ATPase. This 31 KDa component of a proton pump is essential in eukaryotic cells as it both controls acidification of the vacuolar system and provides it with its main protonmotive force. RT-PCR experiments using oligonucleotides designed from the 61EW cDNA sequence indicated that the corresponding messenger is widely transcribed.

Base Sequence↗

PubMed2006

Diabetic nephropathy is associated with gene expression levels of oxidative phosphorylation and related pathways.

The in vitro behavior of skin fibroblasts from patients with or without diabetic nephropathy is associated with diabetic nephropathy risk. Here we compared skin fibroblast gene expression profiles from two groups of type 1 diabetic patients: 20 with very fast ("fast-track") versus 20 with very slow ("slow-track") rates of development of diabetic nephropathy lesions. Gene expression profiles of skin fibroblasts grown in 25 mmol/l glucose for 36 h were assessed by Affymetrix HG-U133A GeneChips to determine the proportion of genes in a given biological pathway that were directionally consistent in their group differences. Five pathways reached statistical significance. All had significantly greater proportions of genes with higher expression levels in the fast-track group. These pathways, the first four of which are closely related and have overlapping genes, included oxidative phosphorylation (P<0.001), electron transport system complex III (P=0.017), citrate cycle (P=0.037), propanoate metabolism (P=0.044), and transcription factors (P=0.046). These results support the concept that oxidative phosphorylation and related upstream pathways may be important in the pathogenesis of diabetic nephropathy. Whether these findings reflect inherent genetic cellular characteristics, "cell memory," or both requires further study.

Adult↗

PubMed1986

Tetanus toxin: primary structure, expression in E. coli, and homology with botulinum toxins.

A pool of synthetic oligonucleotides was used to identify the gene encoding tetanus toxin on a 75-kbp plasmid from a toxigenic non-sporulating strain of Clostridium tetani. The nucleotide sequence contained a single open reading frame coding for 1315 amino acids corresponding to a polypeptide with a mol. wt of 150,700. In the mature toxin molecule, proline (2) and serine (458) formed the N termini of the 52,288 mol. wt light chain and the 98,300 mol. wt heavy chain, respectively. Cysteine (467) was involved in the disulfide linkage between the two subchains. The amino acid sequences of the tetanus toxin revealed striking homologies with the partial amino acid sequences of botulinum toxins A, B, and E, indicating that the neurotoxins from C. tetani and C. botulinum are derived from a common ancestral gene. Overlapping peptides together covering the entire tetanus toxin molecule were synthesized in Escherichia coli and identified by monoclonal antibodies. The promoter of the toxin gene was localized in a region extending 322 bp upstream from the ATG codon and was shown to be functional in E. coli.

Amino Acid Sequence↗

PubMed1996

The product of a 1.9-kb mRNA which overlaps the HSV-1 alkaline nuclease gene (UL12) cannot relieve the growth defects of a null mutant.

Alkaline nuclease, a relatively abundant viral phosphoprotein in herpes simplex virus type 1 (HSV-1)- or HSV-2-infected cells, is encoded by a 2.3-kb mRNA (R. H. Costa, K. G. Draper, L. Banks, K. L. Powell, G. Cohen, R. Eisenberg, and E. K. Wagner, 1983. J. Virol. 48, 591-603). This mRNA is a member of a family of five unspliced 3'-coterminal messages. Costa et al. proposed that another member of this family of mRNAs (1.9-kb) may encode an N-terminally truncated protein which shares its carboxy-terminus with the alkaline nuclease protein. We previously described the isolation of AN-1, a deletion/insertion mutant of the alkaline nuclease gene (S. K. Weller, R. M. Seghatoleslami, L. Shao, D. Rowse, and E. P. Carmichael, 1990. J. Gen. Virol. 71, 2941-2952). The deletion in AN-1 would be predicted to abolish gene products of both the 2.3- and the 1.9-kb mRNAs. To investigate whether the putative truncated version of alkaline nuclease encoded by the 1.9-kb mRNA has enzymatic activity and plays a role in the viral life cycle, a viral mutant (AN-F1) was constructed which is predicted to abolish the gene product of the 2.3-kb mRNA (full-length alkaline nuclease) but leave intact the putative product of the 1.9-kb mRNA. Using a highly sensitive polyclonal antiserum raised against a bacterially expressed full-length alkaline nuclease, we observed a 60-kDa protein in KOS- and AN-F1-infected cells but not in AN-1-infected cells. This suggests that the 60-kDa protein is likely to be expressed from the 1.9-kb mRNA; the open reading frame is now designated UL12.5. Despite the presence of the 60-kDa band, AN-F1 failed to exhibit any alkaline exonuclease activity. This result suggests that the truncated polypeptide (UL12.5) is not enzymatically active, has low levels of activity, or possesses enzymatic activity which is not detected because of the low abundance of the polypeptide. AN-1 and AN-F1 are both severely restricted with respect to growth in Vero cells, as viral yields are 100- to 1000-fold lower than those of wild-type virus. We previously reported that the major defect in AN-1 is in the ability of DNA-containing capsids which form in the nucleus to mature into the cytoplasm (L. Shao, L. M. Rapp, and S. K. Weller, 1993. Virology 196, 146-162); AN-F1 exhibits the same defect. These results indicate that although the 1.9-kb mRNA encodes a 60-kDa protein presumably from the UL12.5 open reading frame, this polypeptide cannot substitute for the full-length UL12 product.

Animals↗

PubMed2005

Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors.

Histone deacetylase inhibitors (HDACis) inhibit tumor cell growth and survival, possibly through their ability to regulate the expression of specific proliferative and/or apoptotic genes. However, the HDACi-regulated genes necessary and/or sufficient for their biological effects remain undefined. We demonstrate that the HDACis suberoylanilide hydroxamic acid (SAHA) and depsipeptide regulate a highly overlapping gene set with at least 22% of genes showing altered expression over a 16-h culture period. SAHA and depsipeptide coordinately regulated the expression of several genes within distinct apoptosis and cell cycle pathways. Multiple genes within the Myc, type beta TGF, cyclin/cyclin-dependent kinase, TNF, Bcl-2, and caspase pathways were regulated in a manner that favored induction of apoptosis and decreased cellular proliferation. APAF-1, a gene central to the intrinsic apoptotic pathway, was induced by SAHA and depsipeptide and shown to be important, but not essential, for HDACi-induced cell death. Overexpression of p16(INK4A) and arrest of cells in G(1) can suppress HDACi-mediated apoptosis. Although p16(INK4A) did not affect the genome-wide transcription changes mediated by SAHA, a small number of apoptotic genes, including BCLXL and B-MYB, were differentially regulated in a manner consistent with attenuated HDACi-mediated apoptosis in arrested cells. We demonstrate that different HDACi alter transcription of a large and common set of genes that control diverse molecular pathways important for cell survival and proliferation. The ability of HDACi to target multiple apoptotic and cell proliferation pathways may provide a competitive advantage over other chemotherapeutic agents because suppression/loss of a single pathway may not confer resistance to these agents.

Apoptosis↗

PubMed2002

Gene profiling in anaplastic large-cell lymphoma-derived cell lines with cDNA expression arrays.

Comparative hybridization of cDNA arrays is a powerful high-throughput tool for the measurement of gene expression between two or more tissues. Moreover, cDNA array technology permits detection of genes involved in carcinogenesis and prospective targets for diagnosis or therapy in the future. We used this technique in cell lines to discover genes possibly involved in the pathogenesis of the large-cell anaplastic lymphoma (ALCL). CD30(+) lymphoma cells are characteristic for this lymphoma entity and were first described 16 years ago. Still, little is known about the biology of this aggressive lymphoma. Identical arrays covering 1176 genes (Clontech Human Cancer 1.2) were hybridized with labeled first-strand cDNA from five ALCL cell lines and stimulated T cells. We found overlapping gene expression patterns in the five cell lines. Three genes, tissue inhibitor of metalloproteinases 1 (TIMP-1), nm23-H4, and interferon-induced 56K protein (IFI-56K) were strongly overexpressed in all ALCL cell lines compared with stimulated T cells. Whereas interleukin-2 precursor, interleukin-9 precursor, interferon-gamma precursor, T cell surface glycoprotein CD3 epsilon subunit, 40S ribosomal protein SA, and protein-tyrosine phosphate 1C were underexpressed, Reverse transcription polymerase chain reaction and Northern blot analysis were employed to confirm the expression patterns of the genes identified by Atlas hybridization.

DNA Fingerprinting↗

PubMed1991

Molecular analysis of Bacillus subtilis ada mutants deficient in the adaptive response to simple alkylating agents.

Previously, we isolated and characterized six Bacillus subtilis ada mutants that were hypersensitive to methylnitroso compounds and deficient in the adaptive response to alkylation. Cloning of the DNA complementing the defects revealed the presence of an ada operon consisting of two tandem and partially overlapping genes, adaA and adaB. The two genes encoded proteins with methylphosphotriester-DNA methyltransferase and O6-methylguanine-DNA methyltransferase activities, respectively. To locate the six mutations, the ada operon was divided into five overlapping regions of about 350 bp. The fragments of each region were amplified by polymerase chain reaction and analyzed by gel electrophoresis to detect single-strand conformation polymorphism. Nucleotide sequences of the fragments exhibiting mobility shifts were determined. Three of the mutants carried sequence alterations in the adaA gene: the adaA1 and adaA2 mutants had a one-base deletion and insertion, respectively, and the adaA5 mutant had a substitution of two consecutive bases causing changes of two amino acid residues next to the presumptive alkyl-accepting Cys-85 residue. Three mutants carried sequence alterations in the adaB gene: the adaB3 mutant contained a rearrangement, the adaB6 mutant contained a base substitution causing a change of the presumptive alkyl-accepting Cys-141 to Tyr, and the adaB4 mutant contained a base substitution changing Leu-167 to Pro. The adaB mutants produced ada transcripts upon treatment with low doses of alkylating agents, whereas the adaA mutant did not. We conclude that the AdaA protein functions as the transcriptional activator of this operon, while the AdaB protein specializes in repair of alkylated residues in DNA.

Adaptation, Physiological↗

PubMed1988

Regulation of varicella zoster virus gene 27 translation in vitro by upstream sequences.

Northern blot analysis revealed the presence of varicella-zoster virus (VZV) gene 27 transcripts in infected cells. The Sal I-G DNA fragment, located in the unique long segment of the VZV genome and containing overlapping genes 26 and 27, was analyzed in an in vitro transcription-translation system. Translation of RNA transcribed from these open reading frames showed prominent expression of gene 27. Four different subclones were constructed to contain gene 27 with and without 100 base pairs (bp) of upstream sequences. Translation of RNA from these constructs using wheat germ extract or rabbit reticulocyte lysate indicated that the sequences upstream from the predicted initiation codon (AUG) of gene 27 downregulated the expression of this gene at the level of translation and that the predicted AUG within gene 27 was preferentially used.

Animals↗

PubMed1993

Molecular cloning and chromosomal assignment of the gene for human Zn-alpha 2-glycoprotein.

Genomic clones containing the human Zn-alpha 2-glycoprotein gene were isolated. Two of them were for the functional gene overlapped, and the other four were for two different pseudogenes (1 and 2) retaining exon-intron organization. The complete DNA sequence of the functional gene (9.3 kb) and its 5'- and 3'-flanking regions (5.3 and 0.1 kb, respectively) was determined. The gene is composed of four exons; the first exon is for the 5'-untranslated region, the signal sequence, and the first six amino acids; the second, for domain A; the third, for domain B; and the fourth, for domain C and the 3'-untranslated region. The 5'-flanking region contains a TATA box, a CAT box, an octamer sequence, and three possible Spl-binding sites. Ten and three copies of Alu repetitive DNA were identified within the gene and the 5'-flanking region, respectively, and they occupy 30% of the gene. The nucleotide sequences around the exons of pseudogene 1 were also determined; they had high homology (90-91%) with the corresponding region of the functional gene. Southern blot analysis suggested that there are only three genes, including nonfunctional ones, for Zn-alpha 2-glycoprotein in humans. The gene (ZA2G) was mapped to human chromosome band 7q22.1 by fluorescence in situ hybridization.

Amino Acid Sequence↗

PubMed1989

A Yersinia pestis-specific DNA fragment encodes temperature-dependent coagulase and fibrinolysin-associated phenotypes.

The effect of temperature on coagulase and fibrinolysin expression (Pla) by Yersinia pestis has been implicated in the transmission of plague by fleas. In an attempt to improve our understanding of this process, we have cloned, sequenced and characterized the gene encoding the Pla phenotypes in Y. pestis, and examined its temperature-dependent regulation. The coding region for this gene overlaps a 900bp Y. pestis-specific DNA fragment that we have previously shown to be capable of detecting plague bacilli in fleas. The pla gene contains a single open reading frame encoding 312 amino acids with a predicted molecular weight of 34.7 kD and a putative signal sequence of 20 amino acids. This coding region appears to be sufficient for both coagulase and fibrinolytic activities. In Y. pestis, modulation between coagulase and fibrinolytic activities is temperature-dependent: coagulase activity is most evident at temperatures below 30 degrees C but fibrinolytic activity increases with higher temperatures (greater than 30 degrees C), regardless of the temperature at which the bacteria are grown. Our results lead us to believe that this regulation occurs post-translationally. It is possible that the alternative forms of the Pla protein are essential to 'flea blockage' and subsequent transmission of the plague bacillus to animals.

Amino Acid Sequence↗

PubMedDate not supplied

Expression of Dlx genes during the development of the zebrafish pharyngeal dentition: evolutionary implications.

In order to investigate similarities and differences in genetic control of development among teeth within and between species, we determined the expression pattern of all eight Dlx genes of the zebrafish during development of the pharyngeal dentition and compared these data with that reported for mouse molar tooth development. We found that (i) dlx1a and dlx6a are not expressed in teeth, in contrast to their murine orthologs, Dlx1 and Dlx6; (ii) the expression of the six other zebrafish Dlx genes overlaps in time and space, particularly during early morphogenesis; (iii) teeth in different locations and generations within the zebrafish dentition differ in the number of genes expressed; (iv) expression similarities and differences between zebrafish Dlx genes do not clearly follow phylogenetic and linkage relationships; and (v) similarities and differences exist in the expression of zebrafish and mouse Dlx orthologs. Taken together, these results indicate that the Dlx gene family, despite having been involved in vertebrate tooth development for over 400 million years, has undergone extensive diversification of expression of individual genes both within and between dentitions. The latter type of difference may reflect the highly specialized dentition of the mouse relative to that of the zebrafish, and/or genome duplication in the zebrafish lineage facilitating a redistribution of Dlx gene function during odontogenesis.

Animals↗

PubMed1991

Gene organization and nucleotide sequence of the primase region of IncP plasmids RP4 and R751.

The primase genes of RP4 are part of the primase operon located within the Tra1 region of this conjugative plasmid. The operon contains a total of seven transfer genes four of which (traA, B, C, D) are described here. Determination of the nucleotide sequence of the primase region confirmed the existence of an overlapping gene arrangement at the DNA primase locus (traC) with in-phase translational initiation signals. The traC gene encodes two acidic and hydrophilic polypeptide chains of 1061 (TraC1) and 746 (TraC2) amino acids corresponding to molecular masses of 116,721 and 81,647 Da. In contrast to RP4 the IncP beta plasmid R751 specifies four large primase gene products (192, 152, 135 and 83 kDa) crossreacting with anti-RP4 DNA primase serum. As shown by deletion analysis at least the 135 and 83 kDa polypeptides are two separate translational products that by analogy with the RP4 primases, arise from in-phase translational initiation sites. Even the smallest primase gene products TraC2 (RP4) and TraC4 (R751) exhibit primase activity. Nucleotide sequencing of the R751 primase region revealed the existence of three in-phase traC translational initiation signals leading to the expression of gene products with molecular masses of 158,950 Da, 134,476 Da, and 80,759 Da. The 192 kDa primase polypeptide is suggested to be a fusion protein resulting from an in frame translational readthrough of the traD UGA stopcodon. Distinct sequence similarities can be detected between the TraC proteins of RP4 and R751 gene products TraC3 and TraC4 and in addition between the TraD proteins of both plasmids. The R751 traC3 gene contains a stretch of 507 bp which is unrelated to RP4 traC or any other RP4 Tra1 gene.

Amino Acid Sequence↗

PubMed1998

Identical small subunit ribosomal RNA gene nucleotide sequence of bovine Theileria isolates (Korea and Japan) and Theileria buffeli (Marula, Kenya).

Small subunit ribosomal RNA (SSU rRNA) gene nucleotide sequences of bovine Theileria isolates from Korea (KLS and KCB) and Japan (JHS) were determined. The genes from each isolate were amplified by the polymerase chain reaction and the approximately 1.8 kb product cloned and sequenced by a modified dideoxynucleotide method. Overlapping gene segments produced with a series of primers were sequenced, resulting in a complete DNA sequence for both forward and reverse strands of the SSU rRNA genes of each isolate. SSU rRNA gene sequences (termed Type A) were identical among the bovine Theileria isolates from Korea and the isolate from Japan. A GenBank data library homology search showed the sequence to be the same as that listed as Theileria buffeli isolated from cattle in Marula, Kenya.

Animals↗

PubMed1987

DNAase I sensitivities in chromatin of the Xenopus laevis somatic and oocyte 5 S DNAs.

The DNAase I sensitivities of the somatic-type 5 S DNA and oocyte-type 5 S DNA have been compared in nuclei from adult somatic tissues of Xenopus laevis. Neither of these Type III genes is expressed in mature erythrocytes and only somatic-type 5 S DNA is expressed in liver. We find that somatic-type 5 S DNA is DNAase-I-sensitive in liver nuclei and less sensitive in erythrocyte nuclei, while oocyte-type 5 S DNA is insensitive in both tissues. The DNAase I sensitivity appears to be uniform across each active somatic-type 5 S DNA repeat. Two regions slightly hypersensitive to DNAase I are found only in liver somatic-type 5 S DNA. One of these regions is within the gene, overlapping with the binding site of the transcription factor (TF III A) required for 5 S RNA synthesis. Thus, the correlation between DNAase I sensitivity and gene activity previously seen for protein-coding genes also holds for these Type III genes. Our data lead us to suggest that the fully DNAase-I-sensitive chromatin conformation on 5 S DNA requires the presence both of transcription factors and RNA polymerase.

Animals↗