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Results for “regulatory element transcripts”

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PubMed2006

Regulatory sequences of orthologous petD chloroplast mRNAs are highly specific among Chlamydomonas species.

The 5' untranslated regions (UTR) of chloroplast mRNAs often contain regulatory sequences that control RNA stability and/or translation. The petD chloroplast mRNA in Chlamydomonas reinhardtii has three such essential regulatory elements in its 362-nt long 5' UTR. To further analyze these elements, we compared 5' UTR sequences from four Chlamydomonas species (C. reinhardtii, C. incerta, C. moewusii and C. eugametos) and five independent strains of C. reinhardtii. Overall, these petD 5' UTRs have relatively low sequence conservation across these species. In contrast, sequences of the three regulatory elements and their relative positions appear partially conserved. Functionality of the 5' UTRs was tested in C. reinhardtii chloroplasts using beta-glucuronidase reporter genes, and the nearly identical C. incerta petD functioned for mRNA stability and translation in C. reinhardtii chloroplasts while the more divergent C. eugametos petD did not. This identified what may be key features in these elements. We conclude that these petD regulatory elements, and possibly the corresponding trans-acting factors, function via mechanisms highly specific and surprisingly sensitive to minor sequence changes. This provides a new and broader perspective of these important regulatory sequences that affect photosynthesis in these algae.

5' Untranslated Regions↗

PubMed1996

Cell type-specific expression of the mouse peripherin gene requires both upstream and intragenic sequences in transgenic mouse embryos.

Peripherin is a neuron-specific type III intermediate filament protein expressed in well-defined populations of neurons projecting towards peripheral targets. To investigate the molecular mechanisms by which a gene is expressed in a specific subset of neurons, we used a transgenic approach in order to define peripherin gene sequences that are necessary for cell-type specific expression. Transgenic mice carrying different various genomic regions of the mouse peripherin gene fused to the Escherichia coli lacZ reporter gene were generated. We used three different peripherin/lacZ constructs containing either 5.8 kb upstream sequences, or both 5.8 kb upstream and 1.1 kb intragenic sequences, or 1.1 kb intragenic sequences associated with an heterologous promoter. Analysis of lacZ gene expression in transgenic mouse embryos showed that cell type-specific expression of the mouse peripherin gene requires both upstream and intragenic sequences. Analysis of transgenic mouse lines expressing the construct containing both upstream and intragenic sequences showed that this transgene contains all regulatory elements essential for both spatial and temporal expression of the mouse peripherin gene during embryogenesis. Furthermore, lacZ+ positive cells isolated from these transgenic lines by fluorescence-activated cell sorting (FACS) can be stained with a peripherin antibody, demonstrating that the transgene containing both upstream and intragenic sequences is expressed in peripherin neurons. These mouse peripherin upstream and intragenic sequences can now be used to identify cis-acting regulatory elements and transcription factors involved in peripherin gene regulation.

Animals↗

PubMed2006

Induction of hepatic choriogenin mRNA expression in male marine medaka: a highly sensitive biomarker for environmental estrogens.

Teleost choriogenins, precursors of the inner layer subunits of egg envelope, have been recently introduced as sensitive biomarkers for exposure to estrogenic compounds. In this study, two full-length cDNAs-ojChgH and ojChgL which encode the choriogenin H and L forms, respectively, were cloned from the marine medaka, Oryzias javanicus. The deduced protein sequences of ojChgH and ojChgL are highly similar to the corresponding homologues in the freshwater medaka (O. latipes) with identities of 77.2 and 87.6%, respectively. Phylogenetic analysis indicated that ojChgH and ojChgL are members of two different classes of liver-specific ZP-domain containing proteins (ZPB and ZPC, respectively). Computer analysis of ca. 2 kb of the 5'-flanking sequences of ojChgH and ojChgL revealed that both genes contain a number of putative estrogen response elements (EREs) and/or half-site EREs. In vivo mRNA expression patterns of the genes were examined by quantitative real-time RT-PCR. ojChgH is expressed exclusively in the liver while ojChgL is co-expressed in the liver (major) and ovary (minor). Exposure of fish to waterborne 17beta-estradiol (E2) at environmentally relevant concentrations (1, 5, 10 and 100 ng/L) resulted in dose-dependent induction of both genes in the liver, with higher sensitivity and magnitude of induction in males than in females. In the male liver, induction of ojChgH is more sensitive to E2 than that of ojChgL and two other estrogen-responsive genes, estrogen receptor alpha (ojERalpha) and vitellogenin (ojVTG). The lowest-observed-effect concentration (LOEC) of E2 on induction of hepatic ojChgH mRNA is 1 ng/L. In the ovary, expression of ojChgL is non-responsive to E2 treatment. In conclusion, the present study suggested that induction of hepatic ojChgH mRNA in male fish may be a highly sensitive biomarker for exposure to environmental estrogens.

Amino Acid Sequence↗

PubMed2005

T-DNA tagging and characterization of a cryptic root-specific promoter in Arabidopsis.

From a T-DNA tagged Arabidopsis population, a line, M-57 showing GUS (beta-glucuronidase) expression in the vascular regions of young roots was identified. Southern analysis revealed presence of a single T-DNA insert. Using inverse PCR, the plant sequence flanking the T-DNA insertion was cloned. The insertion was identified to be in the intergenic area between loci At4G13940 and At4G13930, coding for SAHH (S-Adenosyl-l-Homocysteine Hydrolase) and SHMT (Serine Hydroxy Methyl Transferase) genes, respectively. A 452-bp fragment immediately upstream of the T-DNA insertion when cloned and mobilized as a GUS fusion was capable of driving a similar root-specific expression of reporter gene in transgenic Arabidopsis plants and their progenies. This cryptic promoter element does not show the presence of any known root-specific promoter element.

Arabidopsis↗

PubMed2005

Hepatocyte-specific deletion of the keap1 gene activates Nrf2 and confers potent resistance against acute drug toxicity.

Nrf2 is a key regulator of many detoxifying enzyme genes, and cytoplasmic protein Keap1 represses the Nrf2 activity under quiescent conditions. Germ line deletion of the keap1 gene results in constitutive activation of Nrf2, but the pups unexpectedly died before weaning. To investigate how constitutive activation of Nrf2 influences the detoxification system in adult mice, we generated mice bearing a hepatocyte-specific disruption of the keap1 gene. Homozygous mice were viable and their livers displayed no apparent abnormalities, but nuclear accumulation of Nrf2 is elevated. Microarray analysis revealed that, while many detoxifying enzyme genes are highly expressed, some of the typical Nrf2-dependent genes are only marginally increased in the Keap1-deficient liver. The mutant mice were significantly more resistant to toxic doses of acetaminophen than control animals. These results demonstrate that chronic activation of Nrf2 confers animals with resistance to xenobiotics without affecting the morphological and physiological integrity of hepatocytes.

Acetaminophen↗

PubMed2006

Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance.

The context-dependent expression of genes is the core for biological activities, and significant attention has been given to identification of various factors contributing to gene expression at genomic scale. However, so far this type of analysis has been focused either on relation between mRNA expression and non-coding sequence features such as upstream regulatory motifs or on correlation between mRNA abundance and non-random features in coding sequences (e.g., codon usage and amino acid usage). In this study multiple regression analyses of the mRNA abundance and all sequence information in Desulfovibrio vulgaris were performed, with the goal to investigate how much coding and non-coding sequence features contribute to the variations in mRNA expression, and in what manner they act together. Using the AlignACE program, 442 over-represented motifs were identified from the upstream 100bp region of 293 genes located in the known regulons. Regression of mRNA expression data against the measures of coding and non-coding sequence features indicated that 54.1% of the variations in mRNA abundance can be explained by the presence of upstream motifs, while coding sequences alone contribute to 29.7% of the variations in mRNA abundance. Interestingly, most of contribution from coding sequences is overlapping with that from upstream motifs; thereby a total of 60.3% of the variations in mRNA abundance can be explained when coding and non-coding information was included. This result demonstrates that upstream regulatory motifs and coding sequence information contribute to the overall mRNA expression in a combinatorial rather than an additive manner.

Base Sequence↗

PubMed2005

Control of dendritic diversity.

The dendritic trees of different neuronal types display an astonishing diversity in structure and function. How this diversity is generated remains incompletely understood. However, recent studies have revealed some of the underlying mechanisms by which intrinsic programs of cell-type specification and extrinsic factors exert their effects on the dendritic cytoskeleton to regulate patterns of growth and branching.

Animals↗

PubMed2005

Regulation of p53 translation and induction after DNA damage by ribosomal protein L26 and nucleolin.

Increases in p53 protein levels after DNA damage have largely been attributed to an increase in the half-life of p53 protein. Here we demonstrate that increased translation of p53 mRNA is also a critical step in the induction of p53 protein in irradiated cells. Ribosomal protein L26 (RPL26) and nucleolin were found to bind to the 5' untranslated region (UTR) of p53 mRNA and to control p53 translation and induction after DNA damage. RPL26 preferentially binds to the 5'UTR after DNA damage, and its overexpression enhances association of p53 mRNA with heavier polysomes, increases the rate of p53 translation, induces G1 cell-cycle arrest, and augments irradiation-induced apoptosis. Opposite effects were seen when RPL26 expression was inhibited. In contrast, nucleolin overexpression suppresses p53 translation and induction after DNA damage, whereas nucleolin downregulation promotes p53 expression. These findings demonstrate the importance of increased translation of p53 in DNA-damage responses and suggest critical roles for RPL26 and nucleolin in affecting p53 induction.

5' Untranslated Regions↗

PubMed2006

The expanding cosmos of nuclear receptor coactivators.

About 200 coactivators play a central role in promoting gene expression mediated by nuclear receptors. This diverse group of proteins are key integrators of signals from steroid hormones and have been implicated in cancer and other diseases.

Active Transport, Cell Nucleus↗

PubMed2006

Picking pyknons out of the human genome.

In a recent paper in PNAS, Rigoutsos et al. (2006) describe a nonrandom pattern of repeated elements, called pyknons, which are found more frequently in the 3' untranslated regions of genes than in other regions of the human genome. Although it is unclear how pyknons might have arisen, it is possible that they may be involved in a new form of gene regulation.

3' Untranslated Regions↗

PubMed2006

Flipping riboswitches.

Riboswitches are common cis-acting regulatory elements in bacteria. They are made of nascent RNA that changes its conformation in response to direct binding of cognate metabolites. The publication of five high-resolution crystal structures provides a comprehensive view of how riboswitches sense their ligands and points to new challenges in this emerging field.

Bacteria↗

PubMed2006

Identification and analysis of putative regulatory sequences for the MYF5/MYF6 locus in different vertebrate species.

The myogenic factors (MYF) 5 and 6 are integral to the initiation and development of skeletal muscle and to the maintenance of its phenotype. Thus, they are candidate genes for growth- and meat quality-related traits. We performed a comparative sequence analysis of the MYF5/MYF6 locus in swine, cattle, dog, chicken and zebrafish on the basis of structural and functional information from human and mouse. Beside the characterization of upstream regulatory elements recently identified in mice, we demonstrate the existence of further highly conserved elements (E1 to E4) which may play a role in the regulation of MYF5 and MYF6 expression. Comparative sequence analysis of putative regulatory sequences in swine revealed a total of 21 single nucleotide polymorphisms (SNP) including 1 and 6 SNPs new for the promoters of MYF5 and MYF6, respectively. The conserved organization of the locus in vertebrates indicates a common basic mechanism of muscle development. However, the existence of numerous regulatory elements at large distances to MYF5 and MYF6 points to a very complex pattern of the gene regulation with significant differences between species.

Animals↗

PubMed2006

Polymorphism in the 5' upstream regulatory and 3' untranslated regions of the HLA-G gene in relation to soluble HLA-G and IL-10 expression.

The nonclassical human leukocyte antigen (HLA) class Ib gene HLA-G may be important for the induction and maintenance of immune tolerance between the mother and the semi-allogeneic fetus during pregnancy. Expression of HLA-G can influence cytokine and cytotoxic T-lymphocyte responses. Different HLA-G mRNA isoform expression patterns have been associated with HLA-G polymorphism, especially with a 14-bp insertion deletion polymorphism in the 3' untranslated region (3'UTR) of the HLA-G gene. A significantly high level of interleukin-10 (IL-10) secretion is observed in homozygous +14/+14-bp HLA-G peripheral blood mononuclear cells after lipopolysaccharide (LPS) stimulation. This study finds that polymorphism in the 5' upstream regulatory region (5'URR) of the HLA-G gene may also be implicated in differences in IL-10 secretion. However, this may also be due to linkage disequilibrium with the 14-bp polymorphism. A single-nucleotide polymorphism located -477 bp from the start site of exon 1 had a significant association with IL-10 concentrations but not after correction (p=0.011; pc=0.154). This polymorphism is located next to a heat shock element. Eighteen 5'-URR/3'-UTR HLA-G haplotypes were defined; one common homozygous genotype based on these haplotypes was significantly associated with a high IL-10 level after LPS stimulation compared to certain other genotypes. This study indicates that polymorphism in the 5'-URR of the HLA-G gene may have functional significance, although a new line of investigations is needed to elucidate these findings.

3' Untranslated Regions↗

PubMed2005

Epidermal langerhans cell-deficient mice develop enhanced contact hypersensitivity.

Epidermal Langerhans cells (LCs), a distinct skin-resident dendritic cell population, acquire antigen in the skin and migrate to draining lymph nodes where they are thought to initiate adaptive immune responses. To examine the functional requirement of LCs in skin immunity, we generated BAC transgenic mice in which the regulatory elements from human Langerin were used to drive expression of diphtheria toxin. The resulting mice have a constitutive and durable absence of epidermal LCs but are otherwise intact. Unexpectedly, we found that contact hypersensitivity (CHS) was amplified rather than abrogated in the absence of LCs. Moreover, we showed that LCs act during the priming and not the effector phase. Thus, LCs not only were dispensable for CHS, but they served to regulate the response, a previously unappreciated function.

Adoptive Transfer↗

PubMed2006

Survey of polymorphic sequence variation in the immediate 5' region of human DNA repair genes.

Systematic screens have revealed extensive DNA sequence variation existing in the human population. Studies of the role of polymorphic genetic variants in explaining the association of family history with risk of common disease have generally focused on variants predicted to disrupt protein structure and activity. Recent studies have identified genetic variation in the level of expression of many genes, variation that is potentially biologically relevant in explaining individual variation in disease risk. In a survey of data available for 108 DNA repair genes that have been systematically screened for sequence variation, an average of 3.3 SNPs per gene were found to exist at a variant allele frequency of at least 0.02 in the region 2kb upstream from the 5'-untranslated region. One-third of the genes harbored a SNP with an allele frequency of at least 0.02 within a predicted promotor element. These variants are distributed among promoter elements that average 20 elements per gene. The frequency of polymorphic SNPs in CpG islands was 0.8 per gene, while the frequency of SNPs in the 5'-UTR was 0.7 per gene. The recognition of extensive genetic variation with potential to impact levels of gene expression, and thereby exacerbate the impact of amino acid substitution variants on the activity of proteins, increases the complexity of analyses required to explain the molecular genetic basis for the familial contribution to the sporadic incidence of common disease.

5' Untranslated Regions↗

PubMed2006

A Drosophila ortholog of the human MRJ modulates polyglutamine toxicity and aggregation.

In the Drosophila eye, proteins with an expanded polyglutamine (polyQ) tract form nuclear and cytoplasmic inclusions and produce cytotoxicity, demonstrated as loss of eye pigmentation and structural integrity. An EP P-element that suppressed the loss of eye pigmentation was inserted 9.7 kb upstream of dmrj, a gene that encodes an ortholog of a brain-enriched cochaperone, the human MRJ (mammalian relative of DnaJ). Despite the large distance between them, quantitative polymerase chain reaction indicated that the EP could overexpress dmrj. In the retina and other neurons, transgenic dMRJ suppressed polyQ toxicity and colocalized with its inclusions. In the photoreceptors, expression of another suppressor with a J domain, dHDJ1, but not dMRJ, prior to expression of expanded polyQs dramatically promoted cytoplasmic aggregation. However, both proteins increased the level of detergent-soluble, monomeric polyQ-expanded proteins. These findings exemplify the functional similarities and differences between J domain proteins in suppressing polyQ toxicity.

Amino Acid Sequence↗

PubMed2006

Regulatory sequences of the PRNP gene influence susceptibility to sporadic Creutzfeldt-Jakob disease.

The prion diseases are fatal neurodegenerative disorders that afflict both humans and animals. They comprise kuru, Creutzfeldt-Jakob disease (CJD), Gerstmman-Straussler-Scheinker syndrome (GSS), and fatal familial insomnia (FFI). Both GSS, FFI and approximately 10% of CJD cases are genetically linked disorders, whereas 90% of CJD cases are not associated with mutations in the PRNP coding region, therefore other factors must be involved in pathogenesis of these forms of CJD. There is strong evidence that in transgenic mice the level of PrP gene expression influences the initiation and progression of the prion diseases. Moreover, in in vitro experiments demonstrated that mutations in the regulatory region of PRNP gene altered gene expression, therefore it may be expected that PrP expression level influences the susceptibility to CJD. In order to investigate whether single nucleotide polymorphisms within regulatory region of PRNP may modulate genetic susceptibility to sporadic CJD we examined an association of the C/G polymorphism at position -101 with the sCJD. In our study -101G polymorphism is over-represented among sCJD PRNP codon 129M/V cases compared with the control group. Our data suggest that polymorphism at position -101 in the regulatory region of PRNP may be a risk factor for sCJD among codon 129 heterozygotes.

Creutzfeldt-Jakob Syndrome↗

PubMed2006

Maps, codes, and sequence elements: can we predict the protein output from an alternatively spliced locus?

Alternative splicing choices are governed by splicing regulatory protein interactions with splicing silencer and enhancer elements present in the pre-mRNA. However, the prediction of these choices from genomic sequence is difficult, in part because the regulators can act as either enhancers or silencers. A recent study describes how for a particular neuronal splicing regulatory protein, Nova, the location of its binding sites is highly predictive of the protein's effect on an exon's splicing.

Alternative Splicing↗