Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression (Biochim Biophys Acta Gene Struct Expr )

Publisher: Elsevier


BBA's Gene Structure and Expression covers DNA and RNA structure, DNA replication, damage and repair, gene re-arrangements and recombination, control of gene expression, transcription and translation mechanisms, RNA processing, cell-cycle control, nucleic acid-ligand interactions, DNA-modifying enzymes, viral systems and molecular genetics. This section also includes Short functional sequence-papers describing DNA and RNA sequences for protein coding, regulatory or structural elements combined with significant functional studies, and Promoter papers describing sequence and functional analysis of promoter and enhancer regions. Short functional sequence-papers are also published in other sections of BBA when this is more appropriate. This section welcomes papers on functional genomics that provide significant experiments that address the function of genes whose sequences and not function are already established. Types of papers:Regular papers, short sequence-papers, promoter papers, and rapid reports.

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    Biochimica et biophysica acta., Gene structure and expression, BBA
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Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Stathmin (STMN1) is a microtubule destabilizing protein with a key role in cell cycle progression and cell migration that is up-regulated in several cancers and may contribute to the malignant phenotype. However, the factors that regulate its expression are not well understood. Loss as well as gain-of-function p53 mutations up-regulate STMN1 and in acute myelogenous leukemia where p53 is predominantly wild‐type, STMN1 is also over-expressed. Here we show regulatory control of STMN1 expression by the leucine zipper transcription factor (TF) CREB1 and the basic helix–loop–helix TF LYL1. By ChIP-chip experiments we demonstrate in vivo the presence of LYL1 and CREB1 in close proximity on the STMN1 promoter and using promoter assays we reveal co-regulation of STMN1 by CREB1 and LYL1. By contrast, TAL1, another suspected oncoprotein in leukemia and close relative of LYL1, exerts no regulatory effect on the STMN1 promoter. NLI, LMO2 and GATA2 are previously described co-activators of Tal1/Lyl1-E47 transcriptional complexes and potentiate Lyl1 activation of the STMN1 promoter while having no effect on TAL1 transactivation. Promoter mutations that abrogate CREB1 proximal binding or mutations of the DNA-binding domain of CREB1 abolish LYL1 transcriptional activation. These results show that CRE and Ebox sites function as coordinated units and support previous evidence of joint CREB1-and LYL1 transcription events activating an aberrant subset of promoters in leukemia. CREB1 or LYL1 shRNA knock-down down-regulate STMN1 expression. Because down-regulation of STMN1 has been shown to have anti-proliferative effects, while CREB1 and LYL1 are suspected oncoproteins, interference with CREB1–LYL1 interactions may complement standard chemotherapy and yield additional beneficial effects.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 09/2012;
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    ABSTRACT: In Bacillus subtilis, four codons, CCU, CCC, CCA, and CCG, are used for proline. There exists, however, only one proline-specific tRNA having the anticodon mo5UGG. Here, we found that this tRNAPro(mo5UGG) can read not only the codons CCA, CCG and CCU but also CCC, using an in vitro assay system. This means that the first nucleoside of its anticodon, 5-methoxyuridine (mo5U), recognizes A, G, U and C. On the other hand, it was reported that mo5U at the first position of the anticodon of tRNAVal(mo5UAC) can recognize A, G, and U but not C. A comparison of the structure of the anticodon stem and loop of tRNAPro(mo5UGG) with those of other tRNAs containing mo5U at the first positions of the anticodons suggests that a modification of nucleoside 32 to pseudouridine (Ψ) enables tRNAPro(mo5UGG) to read the CCC codon.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 05/2005; 1728(3):143–149.
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    ABSTRACT: Neuronal expression of the mouse glutamate decarboxylase 67 (mGAD67) gene occurs exclusively in neurons that synthesize and release GABA (GABAergic neurons). This gene is also expressed in pancreatic islet cells and testicular spermatocytes. In order to elucidate the molecular mechanisms underlying the regulation of mGAD67 gene expression, we isolated and characterized the 5′-flanking region of this gene. Sequence analysis of a 10.2-kb DNA fragment of this gene containing a promoter region (8.4 kb) and noncoding exons 0A and 0B revealed the presence of numerous potential neuron-specific cis-regulatory elements.Functional analysis of the 5′-flanking region of exons 0A and 0B by transient transfection into cultured cells revealed that the region −98 to −52 close to exon 0A is important for the transcriptional activity of both exons 0A and 0B. In addition, we used transgenic mice to examine the expression pattern conferred by the 10.2 kb DNA fragment of the mGAD67 gene fused to the bacterial lacZ reporter gene. Transgene expression was observed in neurons of particular brain regions containing abundant GABAergic neurons such as the basal ganglia, in pancreatic islet cells and in testicular spermatocytes and spermatogonia. These results suggest that the 10.2 kb DNA fragment of the mGAD67 gene contains regulatory elements essential for its targeted expression in GABAergic neurons, islet cells and spermatocytes.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 08/2003; 1628(3):156-168.
  • Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 05/2003; 1627(1):56-61.
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    ABSTRACT: Recent studies have identified two novel biofunctional proteins, termed prokineticin 1/EG-VEGF and prokineticin 2, which were mammalian homologues of mamba MIT1 and frog Bv8. Prokineticins have been demonstrated to exert their physiological functions through G-protein coupled receptors (GPCRs). In this study, we report the molecular identification of two endogenous prokineticin receptors, designated PK-R1 and PK-R2, through a search of the human genomic DNA database. PK-R1, locating in chromosome 2, and PK-R2, locating in chromosome 20p13, shared 87% homology, which was an extremely high value among known GPCRs. In functional assays, mammalian cells expressing PK-Rs responded to prokineticins in a concentration-dependent manner. Tissue distribution analysis revealed that expression of PK-R1 was observed in the testis, medulla oblongata, skeletal muscle and skin, while that of PK-R2 showed preferential expression in the central nervous system. The tissue distribution of PK-Rs reported in this paper suggests that the prokineticins play multifunctional roles in vivo.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 12/2002; 1579:173-179.
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    ABSTRACT: Glutathione (γ-l-glutamyl-l-cysteinylglycine) is an important antioxidant molecule, helping to protect the cell against oxidative stress. Expression of the Saccharomyces cerevisiaeGSH1 gene, coding for the first enzyme involved in glutathione biosynthesis, is regulated at the level of transcription by oxidants and heavy metals. We have characterised the sequences of the GSH1 promoter responsible for the amino acid-dependent H2O2 regulation of transcription. We show that there are at least two H2O2-responsive elements in the promoter, neither of which map to the putative Yap1 binding site. Our results suggest that the Yap1 protein plays an important, but indirect role in the H2O2-dependent regulation of GSH1 transcription.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 06/2002; 1576:23-29.
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    ABSTRACT: Neuronal apoptosis inhibitory protein (NAIP) has been shown to inhibit apoptosis in vitro and in vivo with an expression which is regulated in a variety of cells and tissues and may be modulated by a variety of external stimuli. To understand the molecular basis of the transcriptional regulation of the NAIP gene, we have analyzed the 5′-flanking region and transcription of the human NAIP gene. The functional promoter and silencer elements were identified by luciferase reporter constructs in transient transfection experiments using four different human cells. Although the location of the functional elements were shared among the different cells used, the activities for the NAIP promoter varied. Further, cell type-specific protein binding activities were observed by an electrophoretic mobility shift assay (EMSA). EMSA analysis with specific antibodies and DNA sequence analysis identified the POU domain transcription factor Brn-2 as a candidate transcriptional regulator of the NAIP gene. The DNA sequence of the promoter region of the ΨNAIP gene, a copy gene for NAIP, was nearly identical to that of the NAIP gene, indicating a common regulatory mechanism for transcription of the NAIP and ΨNAIP genes. Indeed, the transcript of the ΨNAIP gene was identified. These results provided the first evidence for the functional promoter and candidate transcriptional factor for the NAIP gene and transcription of the ΨNAIP gene.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 02/2002; 1574(1):35–50.
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    ABSTRACT: A genomic DNA encoding a second thioredoxin (TRX2) was isolated from the chromosomal DNA of the fission yeast Schizosaccharomyces pombe. The cloned sequence contains 1823 bp and encodes a protein of 121 amino acids. It has extra N-terminal 17 amino acid residues compared to previously identified thioredoxin (TRX1), which are positively charged and hydrophobic amino acids. The additional N-terminal region contains a plausible prepeptidase cleavage site, indicating that the TRX2 protein exists in mitochondria. The cloned TRX2 gene produced functional TRX estimated with insulin reduction assay. The upstream region of the TRX2 gene was fused into the promoterless β-galactosidase gene of the shuttle vector YEp357R. The 782 bp sequence in the region further upstream of the TRX2 gene was found to be inhibitory in its expression. Synthesis of β-galactosidase from the fusion plasmid pYFX135-HRL was enhanced by the addition of aluminum chloride and ferrous chloride, indicating that the TRX2 protein is involved in stress response.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 01/2002; 1575:143-147.
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    ABSTRACT: Cox17p, essential for the assembly of functional cytochrome c oxidase (CCO) in Saccharomyces cerevisiae, has been believed to deliver copper ions to the mitochondrion for insertion into the enzyme. We have recently isolated an ∼20 kb genomic fragment of the mouse COX17. Reporter assay experiments have shown that most of the promoter activity was restricted to a 0.85 kb fragment flanking the first exon. Further intensive deletion and detailed mutation analysis suggested that the minimal essential region for transactivation was located at bases −155 to −70. This 5′-flanking region did not possess a TATA box, but contained putative Sp1, NRF-1 and NRF-2 binding sites. COX17 basal promoter activity was abrogated by site-directed mutagenesis of Sp1, NRF-1 and NRF-2 binding sites. Electrophoretic mobility shift assays with AtT-20 and NIH3T3 cell nuclear extract revealed that this region binds both a Sp1-like protein and NRF-1 transcription factors. These results indicated that Sp1, NRF-1 and NRF-2 are involved in basal transcription of the COX17 gene, similar to the transcription mechanism of other CCO-related genes.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 01/2002; 1574(3):359-364.
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    ABSTRACT: Microphthalmia-associated transcription factor (Mitf) regulates the differentiation of melanocytes, optic cup-derived retinal pigment epithelium (RPE), and some types of bone marrow-derived cells. Mitf consists of at least five isoforms with different N-termini, each of which is encoded by a separate exon 1. Here we identified a novel isoform, termed mouse Mitf-D/human MITF-D, that is expressed in RPE, macrophages, and osteoclasts affected by the Mitf mutations, but not expressed in other Mitf target cells, including melanocyte-lineage cells and natural killer cells. The initiation Met of MITF-D is located in the downstream domain (B1b domain) that is shared by other MITF isoforms. The 5′-untranslated region of MITF-D mRNA is encoded by the newly identified first exon of the MITF gene, termed exon 1D, which is located 3 kb upstream of the exon encoding the B1b domain. Thus, the MITF gene generates multiple isoforms with different expression patterns by using the alternative promoters in a cell-dependent manner, thereby providing the molecular basis for the phenotypic variability seen in the MITF/Mitf mutants.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 01/2002; 1574(1):15-23.
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    ABSTRACT: Klp1 (K562 cells-derived leucine zipper-like protein 1) is a transcription factor which binds to the coproporphyrinogen oxidase promoter regulatory element (GGACTACAG). In order to clarify the function of Klp1, we determined the complete human Klp1 genomic structure and regulatory element in the promoter region. The gene spans about 2.4 kb and has three exons. Its promoter region has multiple GC boxes, E2F binding site, one cAMP response element (CRE), and no TATA box with multiple transcription initiation sites, which is characteristic of housekeeping and growth regulating genes. Promoter analysis showed that the promoter was more active in K562 cells entered into the cell cycle by serum stimulation than quiescent cells. Further promoter analysis revealed that CRE at −42 is essential for full promoter activity, and c-Jun and activation transcription factor 1/cAMP response element binding protein 1 proteins bind to this element. These structural characteristics and the promoter function suggest that Klp1 may play a role in cell cycle regulation.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 12/2001; 1522(3):207-211.
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    ABSTRACT: A glutathione S-transferase (GST) gene has been cloned from Schizosaccharomyces pombe for the first time. The nucleotide sequence determined was found to contain 2030 base pairs including an open reading frame of 229 amino acids that would encode a protein of a molecular mass of 27 017 Da. The cloned GST gene was expressed and was found to function in S. pombe, Saccharomyces cerevisiae, and Escherichia coli. The plasmid pGT207 encoding the S. pombe GST gene appeared to be able to accelerate the growth of a wild type S. pombe culture. In a culture of S. pombe containing plasmid pGT207, the growth was inhibited less by mercuric chloride than in a culture with vector alone. The 1088 bp region upstream from the GST gene as well as the region encoding the N-terminal 14 amino acids was transferred into the promoterless β-galactosidase gene of plasmid YEp357R to yield the fusion plasmid pYSH2000. β-Galactosidase synthesis was induced by cadmium chloride, mercuric chloride, hydrogen peroxide, and menadione. It was also induced by high temperature. These results suggest that the cloned S. pombe GST gene is involved in the oxidative stress response.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 08/2001; 1520(2):179-185.
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    ABSTRACT: p57Kip2 and p21Cip1/Waf1 are members of cyclin-dependent kinase (Cdk) inhibitors which play critical roles in the terminal differentiation of skeletal muscle and lung. We investigated mRNA levels of p57Kip2 and p21Cip1/Waf1 in skeletal muscle and lung of mice during maturation and aging using Northern hybridization. The mRNA levels of p57Kip2 and p21Cip1/Waf1 decreased in skeletal muscle and lung of mice during maturation and aging except that the level of p21Cip1/Waf1 mRNA in skeletal muscle of mice showed an increase only during maturation. The decrease of the p57Kip2 mRNA level involved neither a change of DNA methylation at the promoter region nor an alteration of the imprinting status in aged mice. The decreases of p57Kip2 and p21Cip1/Waf1 mRNA levels during aging suggest that the process of tissue-specific terminal differentiation may be gradually downregulated with senescence in tissues where p57Kip2 and p21Cip1/Waf1 play key roles in differentiation. The downregulation of p57Kip2 and p21Cip1/Waf1 during aging is contrary to the upregulation of Cdk inhibitors during cellular replicative senescence, indicating that aging in an organismal level is mediated by mechanisms different from replicative senescence of cultured cells.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 08/2001; 1520(2):163–168.
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    ABSTRACT: The glyoxylate cycle occurs in the three domains of living organisms: Eukarya, Bacteria and Archaea. We have isolated and sequenced the ace (acetate assimilation) gene operon, comprising the glyoxylate cycle key enzymes isocitrate lyase and malate synthase genes (icl or aceA and ms or aceB), from the halophilic archaeon Haloferax volcanii. This is the first time that these genes are sequenced in an organism from the domain Archaea. Phylogenetic analysis of the sequenced genes revealed that isocitrate lyase shows a significant identity with isocitrate lyases from Eukarya and Bacteria, but it is not more closely related to eukaryal or bacterial enzymes, and that malate synthase from H. volcanii has very little identity with any other known protein. This enzyme forms a new class of malate synthases. Transcriptional analysis indicated that both genes are cotranscribed in a single 2.7 kb mRNA molecule. The genes were transcribed only when acetate was the carbon source, indicating transcriptional regulation. Two sets of palindromic sequences were found in the promoter region, possibly involved in binding of transcriptional regulators (repressors and/or activators).
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 08/2001; 1520(2):154–162.
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    ABSTRACT: By means of differential cDNA expression cloning, we earlier isolated a novel rat cDNA and its protein, named hepassocin, which is upregulated during liver regeneration. Using the rat cDNA as a probe, we have now isolated human hepassocin cDNA encoding a protein of 312 amino acids, which has 81.4% and 83.8% identity, respectively, to rat hepassocin before and after elimination of its signal peptide. Dot blot analysis revealed that hepassocin mRNA was strongly expressed in adult liver, fairly strongly in fetal liver, and weakly in pancreas, but not in other tissues. Recombinant human hepassocin produced in Chinese hamster ovary (CHO) cells by the dihydrofolate reductase–methotrexate (DHFR–MTX) gene amplification method is a homodimer (68 kDa) and has mitogenic activities in hepatocytes of various animal species including rat, mouse, rabbit and dog, and the activity was lost with 2-mercaptoethanol treatment. These results suggest that hepassocin is a potent regulator in liver cell growth not only in rats but also in humans. Computer searches revealed that human hepassocin as well as rat hepassocin has a characteristic disulfide structure close to that of fibrinogen-γ. We assume that this newly identified growth factor exerts functions in association with an extracellular matrix such as fibrinogen.
    Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression 07/2001; 1520(1):45-53.

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