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

Publisher: Elsevier

Journal description

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.

Current impact factor: 1.70

Impact Factor Rankings

2016 Impact Factor Available summer 2017
2008 Impact Factor 1.704
2007 Impact Factor 1.704
2006 Impact Factor 2.293
2005 Impact Factor 2.506
2004 Impact Factor 2.045
2003 Impact Factor 2.137
2002 Impact Factor 1.713
2001 Impact Factor 1.782
2000 Impact Factor 1.75

Impact factor over time

Impact factor

Additional details

5-year impact 0.00
Cited half-life 7.10
Immediacy index 0.59
Eigenfactor 0.00
Article influence 0.00
Website Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression website
Other titles Biochimica et biophysica acta., Gene structure and expression, BBA
ISSN 0167-4781
OCLC 38491848
Material type Document, Periodical, Internet resource
Document type Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details


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    • Author can archive a pre-print version
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  • Conditions
    • Authors pre-print on any website, including arXiv and RePEC
    • Author's post-print on author's personal website immediately
    • Author's post-print on open access repository after an embargo period of between 12 months and 48 months
    • Permitted deposit due to Funding Body, Institutional and Governmental policy or mandate, may be required to comply with embargo periods of 12 months to 48 months
    • Author's post-print may be used to update arXiv and RepEC
    • Publisher's version/PDF cannot be used
    • Must link to publisher version with DOI
    • Author's post-print must be released with a Creative Commons Attribution Non-Commercial No Derivatives License
    • Publisher last reviewed on 03/06/2015
  • Classification

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.
    No preview · Article · Sep 2012 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    Preview · Article · Oct 2007 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression

  • No preview · Article · May 2007 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression

  • No preview · Article · Nov 2005 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
  • [Show abstract] [Hide abstract]
    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.
    No preview · Article · May 2005 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: In this report we describe the genomic organization of the mouse glypican-4 (Gpc4), an analysis of its promoter and its transcriptional regulation in the 3T3-F442A adipocyte cell line. The Gpc4 gene consists of nine exons separated by eight introns. A series of deletion mutants and 4391 bp of the 5′-flanking region were cloned into pGL3-BASIC upstream of the luciferase reporter gene and transfected into 3T3-F442A adipocytes. Analysis of a 4.3-kb DNA fragment at the 5′-flanking region of this gene revealed that the Gpc4 promoter is a TATA-less promoter with a large cluster of GC boxes. Competitive electrophoretic mobility shift and supershift assays identified a cluster of nine functional GC boxes binding Sp1 and Sp3 in this region. Transactivation experiments in insect cells showed that both Sp1 and Sp3 are major activators of the Gpc4 promoter. Gpc4 is expressed in adipocytes where its expression is highest in confluent 3T3-F442A adipoblasts and decreases dramatically as cells differentiate. Sp protein analyses demonstrated a major decrease in Sp3 protein in differentiated adipocytes as compared to undifferentiated adipoblasts. These experiments show that Gpc4 is developmentally regulated in 3T3-F442A adipocytes and suggest that Sp transcription factors play a significant role in the regulated expression of Gpc4.
    No preview · Article · Aug 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: Diverse physiological effects of the androgen receptor (AR), a nuclear transcription factor, and its mapping position within a quantitative trait loci (QTL) region on chromosome X propose it as an interesting candidate gene for pig reproduction and performance. Therefore, the aims of this study were isolation of the gene and detection of polymorphisms as a tool for association study and analysis of functional properties of the porcine AR. The mRNA and promoter sequences were obtained and screened for polymorphisms. Based on comparative sequencing, eight single nucleotide polymorphisms (SNPs), TG- and T-insertion/deletetion polymorphisms (INDELs) upstream transcription initiation sites, three SNPs in the 5′-untranslated region (UTR), one microsatellite (CCTTT)n in the intron of 5′-UTR, and a CAG-INDEL in exon 1 were detected. Two haplotypes originated from Duroc and Berlin Miniature Pig were segregating in the DUMI-F2 resource population. Characterization of the porcine AR promoter showed two conserved transcription start sites, a consensus sequence of GC-box and a homopurine/homopyrimidine stretch at similar locations compared to the human, rat and mouse as well as sequences similar to androgen response elements (ARE). The AR mRNA expression levels determined by real-time RT-PCR in various tissues of female pigs were high in ovary (100%) and adrenal gland (83.9% relative to ovary), moderate in uterus (61.6%) and liver (47.4%), and low in pituitary gland (1.3%) as well as in tonsil, muscle, mammary gland, leukocyte and jejunum (less than 1%). Detection of the AR mRNA transcripts in liver revealed that hemizygous males carrying the AR haplotype descended from Berlin Miniature pig had higher relative AR expressions than did those with the Duroc haplotype. Here we showed that the porcine AR is a highly polymorphic gene. Polymorphisms identified in the present study affect the predicted amino acid sequence as well as consensus transcription factor binding sites and are associated with the allele-specific differences of the AR mRNA transcript level in liver, reinforcing AR as a potential candidate gene for traits related to pig reproduction and performance.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: The collagenous repeat-containing sequence of 26-kDa protein (CORS-26) was recently described as a new gene that is induced during adipocyte differentiation. Since the transcription factors specificity protein-1 (SP-1) and PPARγ have been demonstrated to modulate transcriptional activation of adipocytic genes, we investigated the putative role of SP-1 and PPARγ in the regulation of the murine CORS-26 promoter. Computer-based sequence analysis revealed two putative SP-1 binding sites and binding sites for PPARγ and Pit-1 within the TATA-box containing promoter. Electrophoretic mobility shift assays (EMSA) with nuclear extracts from 3T3-L1 adipocytes and appropriate promoter fragments demonstrated that SP-1 binds specifically to both SP-1 binding sites. Specificity was demonstrated by (i) the appearance of supershift bands, (ii) competition experiments and, (iii) by using oligonucleotides carrying mutated SP-1 binding sites. Functional promoter activity was analyzed by Luciferase reporter gene assays and SP-1 was shown to exert inhibitory effects on the transcriptional activation of the murine CORS-26 gene. Additionally, specific binding activity of PPARγ and Pit-1 to the CORS-26 promoter was demonstrated. Taken together, the present data demonstrate the functionality of the proximal murine CORS-26 promoter, which is regulated specifically by two SP-1 binding sites via SP-3-independent repressive effects of SP-1 on transcriptional activation. Pit-1 and PPARγ can bind specifically to the promoter and might play an additive functional role in gene regulation of murine CORS-26.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: Metastin is encoded by a putative human metastasis suppressor gene KiSS-1, and is the cognate ligand of a G-protein-coupled receptor designated OT7T175. To study the physiological function(s) of metastin, we cloned rat and mouse KiSS-1 cDNAs both encoding 130-amino acid KiSS-1 proteins. Sequence analysis suggested that processing of the rat and mouse KiSS-1 proteins produces 52-amino-acid peptides, each with an amidated carboxyl terminal and with a single possible disulfide bond, corresponding to rat and mouse metastins. The carboxyl-terminal sequence of metastin, known to be essential for functional receptor interaction, was found to be highly conserved among humans and rodents. Real-time PCR analysis indicated that rat KiSS-1 mRNA showed the highest expression level in the cecum and colon. Since KiSS-1 mRNA and metastin are known to be abundant in human placenta, we further studied the localization of KiSS-1 and OT7T175 mRNAs in rat placenta by in situ hybridization. KiSS-1 and OT7T175 mRNAs were specifically detected in trophoblast giant cells at embryonic day 12.5, and the transcripts in the cells gradually decreased during placental maturation. These results suggest that metastin/OT7T175 signaling may participate in implantation of the mammalian embryo, placenta formation, and maintenance of pregnancy.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: The responsiveness of the 1.13 kb proximal human muscle glycogen phosphorylase (MGP) gene promoter to the chicken ovalbumin upstream promoter-transcription factor (COUP-TF) repressor, known to be ablated during muscle cell differentiation, was examined. Constitutive expression of COUP-TFI repressed the activity of the promoter in C2C12 muscle cells and sequential deletion analysis mapped the sensitive region between nucleotides −362 and −185, which included a putative consensus COUP-TF binding half-site at −198/−193. Mutation of this site abolished transcriptional response to COUP-TFI of the −362 construct. A −209/−180 probe bound in vitro to COUP-TFI and to protein extracts from proliferating but not fusing myoblasts. Thus, COUP-TF may be involved in repression of the human MGP gene promoter at the myoblast stage.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: Poly (A) tails are found at the 3′ ends of almost all eukaryotic mRNAs. They are bound by two different poly (A) binding proteins, PABPC in the cytoplasm and PABPN1 in the nucleus. PABPC functions in the initiation of translation and in the regulation of mRNA decay. In both functions, an interaction with the m7G cap at the 5′ end of the message plays an important role. PABPN1 is involved in the synthesis of poly (A) tails, increasing the processivity of poly (A) polymerase and contributing to defining the length of a newly synthesized poly (A) tail.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: Response to oxidative stress has been hitherto scarcely studied in the respiratory yeast Kluyveromyces lactis. The genes coding for reductases of glutathione and thioredoxin, KlGLR1 and KlTRR1, respectively, have been cloned and characterized in this work. H2O2 treatment increased transcription and enzyme activity of KlTRR1 but not of KlGLR1, suggesting a different situation from that reported for the fermentative yeast Saccharomyces cerevisiae. A consensus for Yap1p binding is functional in the KlTRR1 promoter.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: A cDNA encoding a Rel/NF-κB homologue was cloned from a beetle, Allomyrina dichotoma, by reverse transcriptase-polymerase chain reactions (RT-PCR) taking advantage of the conserved Rel homology domain (RHD) to synthesize primers. The Rel/NF-κB homologue was designated A. dichotoma (A.d.) Rel A. The amino acid sequence of the A.d. Rel A RHD was compared with those of insect RHDs. The result showed that it has 70% identity with Tribolium castaneum Dorsal, 66% with Drosophila melanogaster Dorsal, 61% with Anopheles gambiae Gambif1, and 55% with D. melanogaster Dif. A putative phosphorylation site in the RHD, RRPS, and two putative nuclear localization signals were conserved in A.d. Rel A. A recombinant fusion protein containing the A.d. Rel A RHD was confirmed to bind specifically to the NF-κB site of a gene encoding A.d. coleoptericin A, an antibacterial peptide from A. dichotoma. The activity of A.d. Rel A in modulating a gene construct of the A.d. coleoptericin A promoter-luciferase reporter by expressing the A.d. coleoptericin A cDNA in a Bombyx mori cell line was analyzed. The result showed that A.d. Rel A strongly activates the A.d. coleoptericin A gene construct, whereas A.d. Rel A failed to activate the gene construct containing the mutated NF-κB site, suggesting the importance of the interaction between the NF-κB site and A.d. Rel A in the signal transduction for gene expression of antibacterial peptides in A. dichotoma.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: Focal adhesion kinase (FAK) gene encodes focal adhesion kinase that localizes at contact points of cells with extracellular matrix. It was shown that FAK expression is increased in a variety of malignancies, both at early and advanced stages of tumorigenesis. To understand mechanisms of FAK gene expression and regulation, we cloned and characterized the 5′ promoter region of the FAK gene. The 1.2-kb fragment with FAK promoter was placed upstream of the luciferase reporter gene in a pGL3-Basic vector and transfected into different cell lines. Endogenous high-FAK-expressing cell lines showed high levels of luciferase activity in contrast to low-FAK-expressing cells, indicating on transcriptional level of FAK regulation. Serial deletion constructs revealed that a ∼600 base pair region (−564 to +47) is required for the maximal FAK promoter activity. The 5′-flanking region of FAK is GC-rich and contains several potential transcription factor binding sites, including two NF-kappa B and p53 binding sites. Inhibition of NF-kappa B with NF-kappa B super-repressor decreased FAK luciferase activity. Induction with TNF-α increased luciferase activity confirming a role of NF-kappa B transcription factor in the FAK transcriptional activation. The binding of NF-kappa B and p53 transcription factors to the FAK promoter region was demonstrated by electrophoretic mobility shift assay (EMSA). Cotransfection of NF-kappa B and p53 plasmids with FAK promoter luciferase constructs demonstrate induction and inhibition, respectively, of FAK luciferase activity. The results provide a molecular basis for analysis of FAK transcriptional regulation.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: Chromatin structure at the silencer region of the epsilon-globin promoter was investigated using novel nitrogen mustards as probes of protein–DNA interactions. Sites of protection and enhancement that corresponded to known transcription factor binding sites were detected in both K562 and HeLa cells at this gene region. Protection was observed at several sites including the GATA-1/YY1 motifs. Of particular interest was a large 155 bp footprint that was observed at the epsilon-globin gene silencer region of the promoter. This large footprint was consistent with the presence of a positioned nucleosome core in intact human cells at this silencer region. Additionally, the DNA sequence at the epsilon-globin silencer and promoter was compared for 11 mammalian species. Significant areas of conservation were found that correlated with known transcription factor binding motifs. This phylogenetic footprinting analysis was compared to the genomic footprinting data at the epsilon-globin silencer region.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: The structure and regulation of the murine microsomal glutathione transferase gene (MGST1) from the 129/SvJ strain is described and demonstrates considerable difference in nucleotide sequence and consequently in restriction enzyme sites as compared to other mouse strains. A comparison of the amino acid sequence for MGST1 revealed one difference in exon 2 between the 129/SvJ strain (arginine at position 5) and the sequence previously reported for the Balb/c strain (lysine). The promoter region immediately upstream of the dominant first exon is functional, transcriptionally responds to oxidative stress, and is highly homologous to the human region. Oxidative stress also induced the production of endogenous MGST1 mRNA. The tissue-specific expression of MGST1 mRNA was studied, and as anticipated, was indeed highest in liver. There was, however, marked mRNA expression in several tissues not previously studied including smooth muscle, epidymus, ovaries, and endocrine glands in which the expression of various peroxidases is also very high (salivary and thyroid). Overall, there was a good agreement between the mRNA content detected and previous reports of MGST1 activity with the exception of brain tissue.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: A method was developed to detect the time course of the overall presence of intermediate species during K+-induced DNA quadruplex assembly from single-stranded d(TG4) oligonucleotides in experiments in which only the combined circular dichroisms (CD) of all species present could be measured directly. The presence of intermediate species is determined unambiguously but quantitative estimates can be made only to the extent that the CD characteristics of all intermediates are known. The method consists of (i) obtaining CD spectra of known concentrations of initial and final species to determine their molar ellipticity coefficients, (ii) carrying out CD measurements of the kinetics of quadruplex assembly reactions at two different wavelengths, chosen to give optimal differentiation between the initial and final species, and (iii) using the results of (ii) to detect discrepancies between the rates of consumption of single strands and the generation of quadruplex to infer the presence of intermediate species. The analysis was facilitated by the validation and use of biphasic exponential expressions obtained from the SAS nonlinear curve fitting procedure NLIN in place of the raw CD data. The general method is described, then applied to data from [d(TG4)4(K+)3] quadruplex assembly experiments.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: We analyzed the promoter regions of the adult rat β (IIβ, IIIβ, and 0β)-globin genes. The results indicated that (1) the activities of the minimal promoters of these three genes are proportional to the gene expression levels in vivo, and (2) erythroid-specific repressor regions are located immediately upstream of the minimal promoter sequences and are regulated by the same transcription factor.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression
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    ABSTRACT: In the present study, we analyzed the influence of retinoic acids on the expression of α-1 acid glycoprotein (AGP). We show that in rat primary hepatocytes, 9-cis retinoic acid and all-trans retinoic acid increase AGP gene expression at the transcriptional level. Transient transfections of rat primary hepatocytes with a reporter construct driven by the rat AGP gene promoter indicated that retinoids regulate AGP gene expression via the −763/−138 region of the AGP promoter. Furthermore, cotransfection experiments with retinoic acid receptor alpha (RARα) and retinoid X receptor alpha (RXRα) expression vectors in NIH3T3 cells demonstrated that both RXRα/RXRα homodimer and RXRα/RARα heterodimer are competent for ligand-induced transactivation of the AGP promoter. Unilateral deletion and site-directed mutagenesis identified two retinoic-acid responsive elements (RARE), RARE-I and RARE-II, which interestingly correspond to a direct repeat of two TGACCT-related hexanucleotides separated by a single bp only (DR1-type response element). Cotransfection assays showed that RXRα and RARα activate AGP gene transcription through these two elements either as a homodimer (RXRα/RXRα) or as a heterodimer (RXRα/RARα). The RXRα/RXRα homodimer acts most efficiently through the RARE-I response element to promote AGP transactivation, whereas the RXRα/RARα heterodimer mediates transactivation better via the RARE-II responsive element.
    No preview · Article · May 2004 · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression