Flanking Sequence Of Gene Research Articles

PAX2 Activates WNT4 Expression during Mammalian Kidney Development

The transcription factor PAX2 is expressed during normal kidney development and is thought to influence outgrowth and branching of the ureteric bud. Mice with homozygous null Pax2 mutations have developmental defects of the midbrain-hindbrain region, optic nerve, and ear and are anephric. During nephrogenesis, PAX2 is also expressed by mesenchymal cells as they cluster and reorganize to form proximal elements of each nephron, but the function of PAX2 in these cells is unknown. In this study we hypothesized that PAX2 activates expression of WNT4, a secreted glycoprotein known to be critical for successful nephrogenesis. PAX2 protein was identified in distal portions of the "S-shaped" body, and the protein persists in the emerging proximal tubules of murine fetal kidney. PAX2 activated WNT4 promoter activity 5-fold in co-transfection assays with JTC12 cells derived from the proximal tubule. Inspection of the 5'-flanking sequence of the human WNT4 gene identified three novel PAX2 recognition motifs; each exhibited specific PAX2 protein binding in electromobility shift assays. Two motifs were contained within a completely duplicated 0.66-kb cassette. Transfection of JTC12 cells with a PAX2 expression vector was associated with a 7-fold increase in endogenous WNT4 mRNA. In contrast, Wnt4 mRNA was decreased by 60% in mesenchymal cell condensates of fetal kidney from mice with a heterozygous Pax2 mutation. We speculated that a key function of PAX2 is to activate WNT4 gene expression in metanephric mesenchymal cells as they differentiate to form elements of the renal tubules.

Analysis of the interactions of Nrf-2, PMF-1, and CSN-7 with the 5′-flanking sequence of the mouse 4E-BP1 gene

Nuclear factor erythroid 2-related factor 2 (Nrf-2) binds to a specific polyamine responsive element (PRE) in the promoter region of the spermidine–spermine acetyltransferase (SSAT) gene, a key component of the polyamine catabolic pathway. Regulation of SSAT gene transcription requires the additional interaction of Nrf-2 with polyamine modulated factor 1 (PMF-1). Likewise, transcription of the eukaryotic initiation factor 4E binding protein 1 (4E-BP1) gene is regulated in a polyamine-dependent manner, but the actual mechanism has not previously been determined. Analysis of the 5′-flanking sequence of the murine 4E-BP1 gene indicated the presence of several potential PRE sites, which might be involved in regulating its transcription. Our goal in this research was to determine potential interactions between Nrf-2, PMF-1, the human homologue of the Arabidopsis signalosome complex (CSN-7), and these potential PRE sites. Four PCR fragments containing regions with considerable homology (78%) to the human PRE were generated from the 5′-flanking sequence of the mouse 4E-BP1 gene and the fragments were used in electrophoretic gel mobility shift and supershift assays. Purified Nrf-2 interacted with all four of these fragments, and similar gel shifts were observed with both cytoplasmic and nuclear fractions of NIH-3T3 cells. However, polyamine depletion with difluoromethylornithine (DFMO) eliminated the gel shift. Supershift assays indicated that the shift was due to the binding of Nrf-2, and the binding was competitive with a known Nrf-2 binding sequence. Purified PMF-1 did not bind any of the PCR fragments alone, but when added with Nrf-2, decreased the magnitude of the gel shift for one of the fragments (PRE located at − 2060 relative to the transcription start site). CSN-7 did not interact with the sequences, nor did it inhibit protein/DNA interaction. These data indicate a possible mechanism by which polyamines enhance the binding of a Nrf-2/PMF-1 complex to the 5′-flanking region of the 4E-BP1 gene. Since polyamines increase expression of the 4E-BP1 gene, it seems likely that formation of this complex is involved in its transcriptional regulation.

Conserved regulatory elements identified from a comparative puroindoline gene sequence survey of Triticum and Aegilops diploid taxa

Kernel texture (‘hardness’) is an important trait that determines end-use quality of wheat ( Triticum aestivum L. and Triticum turgidum ssp. durum [Desf.] Husn.). Variation in texture is associated with the presence/absence or sequence polymorphism of two proteins, puroindoline a and puroindoline b. This work describes the flanking and coding region sequences of puroindoline genes from 25 accessions representing wild diploid taxa of the Triticeae related to the three genomes of T. aestivum. Analysis of variation at the nucleotide level included hard and soft T. aestivum wheat cultivars. Various degrees of insertions/deletions and point mutations were found, that did not affect the overall sequence structure identity. Nucleotide sequence comparisons and database searches facilitated the identification of the 5′ proximal regulating regions, revealing the presence of several putative control elements. An absolute conservation of some known regulatory elements for tissue specificity was observed, while different rates of conservation of reiterated motifs with possible enhancer functions, and the exclusive presence of some elements either in puroindoline a or puroindoline b were also found. A total of 24 new puroindoline alleles (unique sequences) were identified. Despite some primary structure variation, the main features of puroindolines, i.e. the signal peptide, the cysteine backbone, the tryptophan-rich domain, the hydrophobicity and basic identity of the proteins were all conserved.

DNA Methylation-dependent Epigenetic Regulation of Dimethylarginine Dimethylaminohydrolase 2 Gene in Trophoblast Cell Lineage

Trophoblast cell lineage is established through the first cellular differentiation in mammalian embryogenesis, and its developmental potential is restricted to the extraembryonic tissues contributing solely to the placenta. Several lines of evidence suggest a relative lack of importance of DNA methylation in gene regulation in the extraembryonic tissues when compared with embryonic ones. Here we analyzed the dynamics of epigenetic status in the upstream region of mouse Ddah2 gene, which was found to be specifically repressed in a stem cell population of trophoblast cell lineage. We found a tissue-dependent differentially methylated region in the regulatory region of the Ddah2 gene. This region was hypermethylated in trophoblast stem cells and was hypomethylated in differentiated cells both in vivo and in vitro. This change was well correlated with Ddah2 expression. In addition, in vitro methylation confined to the differentially methylated region was sufficient to repress promoter activity in the reporter assay. Furthermore, a repressive pattern of histone modifications was formed around the differentially methylated region in undifferentiated trophoblast stem cells with repressed Ddah2. Our data suggest that DNA methylation-mediated chromatin remodeling is involved in the regulation of the Ddah2 gene expression and thus is important even in trophoblast cell lineage.

CpG methylation at the USF-binding site is important for the liver-specific transcription of the chipmunk HP-27 gene

The chipmunk hibernation-specific HP-27 gene is expressed specifically in the liver and has a CpG-poor promoter. To reveal how the liver-specific transcription of the HP-27 gene is regulated, we performed yeast one-hybrid screening of a chipmunk liver cDNA library. A 5'-flanking sequence of the HP-27 gene, extending from -170 to -140 and containing an E-box (5'-CACGTG-3'), is essential for the liver-specific transcription of HP-27. We used this sequence as bait and found that a ubiquitously expressed transcription factor, USF (upstream stimulatory factor), bound to the E-box. In COS-7 cells, USF activated transcription from the HP-27 gene promoter. We then used bisulphite genomic sequencing to analyse the methylation status of the four CpG dinucleotides that lie in the 5'-flanking sequence of the HP-27 gene up to -450, to investigate how the ubiquitously expressed USF activates transcription of the HP-27 gene only in the liver, while its transcription is repressed elsewhere. The only difference in methylation in the tissues tested was in the CpG dinucleotide in the USF-binding site, which was hypomethylated in the liver, but highly methylated in the kidney and heart. The specific methylation of the CpG dinucleotide at the USF-binding site impeded both the binding of USF and its transcriptional activation of the HP-27 gene. Chromatin immunoprecipitation using anti-USF antibodies revealed that USF bound to the HP-27 gene promoter in the liver, but not in the kidney or heart. Thus CpG methylation at the USF-binding site functions in establishing and maintaining tissue-specific transcription from the CpG-poor HP-27 gene promoter.

Activation of Human CYP2C9 Promoter and Regulation by CAR and PXR in Mouse Liver

The activity of various genomic segments at the 5'-flanking region of the human CYP2C9 gene in driving gene expression and their involvement in pregnane X receptor (PXR) and constitutive androstane receptor (CAR) mediated activation were evaluated in mouse hepatocytes. Using the genomic sequence of human CYP2C9 as a template, segments covering different regions of CYP2C9 5'-flanking sequences starting from the translation start site were amplified by PCR and inserted into a pGL-3 luciferase vector. Plasmid DNA containing the 0.2K, 1K, 2K, 3K, 5K, or 10K upstream sequences of the CYP2C9 gene were transfected into mouse liver by hydrodynamic delivery, and the activity of each fragment in driving reporter gene expression was assessed. With the exception of the 10K fragment, the level of luciferase activity in transfected mouse liver was similar among the constructs examined. Cotransfection of these reporter constructs with the pCMX-PXR or pCMX-CAR plasmids resulted in a slight increase in luciferase gene expression that could be significantly enhanced by chemical inducers. In mice cotransfected with pCMX-PXR, pregnenolone-16 alpha-carbonitrile (PCN) induced a 20-fold increase in the luciferase level compared to a 70-fold increase induced by rifampicin. Similarly, when animals were cotransfected with the pCMX-CAR plasmid, phenobarbital and 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene enhanced luciferase gene expression by 10- and 57-fold, respectively. The element responsible for PXR- and CAR-mediated activation of luciferase gene expression by chemical inducers was found to reside in the -2000 to -1000 bp region of the 5'-flanking sequence of the CYP2C9 gene. These results prove that PXR and CAR are transcription factors regulating CYP2C9 gene expression.

Agrobacterium T-DNA-mediated integration and gene replacement in the brown rot pathogen Monilinia fructicola

A transformation system utilizing Agrobacterium tumefaciens was developed for targeted gene disruption in Monilinia fructicola, a fungal pathogen that causes brown rot disease of stone fruits. Transformation with a vector containing the neomycin phosphotransferase II (nptII) cassette flanked with 4 kb cutinase gene (Mfcut1) flanking sequences resulted in an average of 13 transformants per 10(5) spores. When assayed by PCR and DNA blot analyses, more than 50% of the transformants recovered had integrated in the targeted Mfcut1 locus. Both target-gene-specific and non-specific integrations carried direct (head-to-tail) repeat T-DNA integrations. Sequence analysis of these T-DNA integrations revealed that 26 bp of the T-DNA right border were missing at the junctions between direct repeats in all cases. The recombination event during non-specific T-DNA integration in this fungus was unlike that reported in Agrobacterium-mediated transformation in plants.

3′ gene regulatory elements required for expression of the Plasmodiumfalciparum developmental protein, Pfs25

Development of sexual stage parasites within the mosquito vector is a crucial step in the transmission of Plasmodium parasites. The expression of the P25 and P28 proteins on the surface of Plasmodium parasites in the mosquito midgut is required for development and hence disease transmission. 3′ gene-flanking sequences are essential for expression of these critical proteins but the nucleotide elements required are poorly defined. Transient gene transfection experiments using constructs containing deletions of the 3′ gene-flanking region of the Plasmodium falciparum P25 homologue, pfs25, reveal that elements necessary for protein expression are within 315 nucleotides (nt) of the stop codon. A T-rich region 137–231 nt from the stop codon is required for expression. The nonamer AATAAAATG, 360 nt downstream from the stop codon, enhances expression by 51 percent. Using 3′ RACE analysis, multiple polyadenylation sites from endogenous and plasmid-derived pfs25 transcripts were identified. Dissimilarities between the identified elements and those of metazoans support the hypothesis that definition of P25/28 3′ gene regulatory processes may eventually permit the development of agents which block malaria transmission but are non-toxic to humans.

Induction of experimental autoimmune encephalomyelitis in transgenic mice expressing ovalbumin in oligodendrocytes

We have used the 5' flanking sequence of the myelin basic protein gene known to include the core promoter and a strong oligodendrocyte (ODC)-specific enhancer to target expression of the well-studied model antigen ovalbumin (OVA) to ODC in transgenic mice. OVA protein was detected in a tissue- and cell-specific manner in these "ODC-OVA" mice. Without immunization, CD4 T cells and B cells remained ignorant of the neo-self antigen expressed in the central nervous system (CNS), as indicated by unimpaired development and lack of activation of OVA/IA(b)-specific TCR transgenic T cells in these mice, and the ability to mount normal OVA-specific recall and antibody responses. Upon immunization with OVA in complete Freund's adjuvant, about half of the transgenic mice developed neurological symptoms characteristic of experimental autoimmune encephalomyelitis (EAE). Mononuclear infiltrates in the brain and spinal cord contained both macrophages and T cells, similar to classical models of EAE induced by immunization with CNS antigens in adjuvant. The wealth of immunological reagents available to study and manipulate the OVA-specific response should make this new model useful for the investigation of components and mechanisms involved in CNS-specific autoimmunity.

LaNe RAGE: a new tool for genomic DNA flanking sequence determination

The determination of genomic DNA sequence flanking a known region is often problematic. Existing technologies depend on multiple, efficient enzyme-catalysed preparative processing steps and/or rely on relatively inefficient 'one-sided' PCR mechanisms. I demonstrate the application of a simple 'two-sided' PCR-based approach, lariat-dependent nested PCR for rapid amplification of genomic DNA ends (LaNe RAGE), applied to the mouse GAPDH and PGK1 gene flanking sequences. This demonstration offers great promise in applications such as genome walking, transposon mutagenesis mapping and DNA fingerprinting.

Genomic structure and alternative transcript of bovine fatty acid synthase gene (FASN): comparative analysis of the FASN gene between monogastric and ruminant species

Fatty acid synthesis differs considerably between monogastric and ruminant species. Fatty acid synthase (FASN) plays a central role in de novo lipogenesis in mammals. FASN has seven active sites which help to catalyse all the reaction steps in the conversion of acetyl-CoA and malonyl-CoA to palmitate. In this work, the bovine fatty acid synthase gene (FASN) was cloned, characterized and compared to the human and rat orthologs. Comparative analysis reveals evolutionarily conserved exon regions and gene flanking sequences. Analysis of the DNA sequence in the 5′ flanking region of the FASN bovine gene revealed a potential TATA box, CAAT box and 5 Sp1 binding sites located in a CpG island. RT-PCR and Western blot analysis showed that FASN expression was higher in brain, testis and adipose tissue than in liver and heart. The longer form of the FASN cDNA includes a 7,542-bp sequence which encodes a protein with 2,513 amino acids. An alternative transcript was discovered in bovine and ovine tissues devoid of part of exon 9. The removal of part of exon 9 by post-transcriptional splicing causes a frameshift in the open reading frame and results in a premature termination codon. We hypothesize that in ruminants, FASN may be regulated by the ratio between the two transcripts. The small transcript is mostly produced in tissues with low fatty acid synthesis.

Promoter activity of sea lamprey proopiocortin and proopiomelanotropin genes in AtT-20/D16v cells

Adrenocorticotropic hormone (ACTH) and melanophore-stimulating hormone (MSH) are produced in the pars distalis and pars intermedia, respectively, throughout vertebrates. These hormones together with β-endorphin are encoded on a single gene proopiomelanocortin ( POMC) in gnathostomes, but in the sea lamprey, an agnathan, ACTH and MSH are encoded on two separate genes, proopiocortin ( POC) and proopiomelanotropin ( POM), respectively. Moreover, the nucleotide sequences of 5′-flanking regions of the POC and POM genes are significantly different from each other. To investigate the potential promoter activities of the POC and POM genes, we constructed promoter reporter plasmids by fusing the 5′ flanking sequences (nucleotides −1151 to +31 and −2510 to +51, respectively) to a firefly luciferase gene. Transient transfection studies in AtT-20/D16v cells, which derived from a mouse pituitary tumor cell line, revealed that the 5′-flanking sequence of the POC gene did not exhibit promoter activity, whereas that of the POM gene showed the activity at high levels nearly equivalent to SV40 promoter. Analysis of a series of the 5′-deleted reporter for the POM gene in the AtT-20/D16v cells demonstrated that the 422 bp 5′-flanking sequence was sufficient for promoter activity, while the sequence from −853 to −574 may contain negatively acting regulatory elements. Because the POC and POM genes are supposed to have differentiated from a common ancestor, during evolution, the POC gene may lack essential element(s) for expression in the AtT-20/D16v cells.

Molecular cloning and expression analysis of the replacement histone H3 gene of Italian ryegrass ( Lolium multiflorum)

The replacement histone H3 gene and its 5'-flanking sequence were isolated from Italian ryegrass by polymerase chain reaction and inverse polymerase chain reaction, respectively. Expression analysis showed that this gene is constitutively expressed in the entire plant. The expression level in leaves was found to be significantly low when compared with that in other tissues. However, the gene expression level in leaves was increased by the treatment with abscisic acid and abiotic stresses such as cold, heat and high-salinity (NaCl). The motif search of the 5'-flanking sequence of the replacement histone H3 gene revealed the presence of several potential cis-acting elements that could respond to the above-mentioned abiotic stresses. In addition to defence-related elements, we also found type I and II-/III-like elements, which are highly conserved motifs in the 5'-regulatory sequence of plant histone genes that are expressed specifically during the S-phase. Experiments using transgenic Italian ryegrass plants proved that the isolated 5'-flanking sequence of the replacement histone H3 gene, which was fused to a beta-glucuronidase reporter gene, was fully functional for inducing gene expression under various abiotic stress conditions.

Characterization of Promoter Elements of the Human HYAL-2 Gene

The regulated catabolism of hyaluronan is critical to the function of many connective tissues. In cartilage, hyaluronan catabolism occurs locally by resident chondrocytes. To determine whether the expression of lysosomal hyaluronidases contributes to this regulation, the promoter elements associated with HYAL-2 gene expression were characterized. Human articular chondrocytes were found to express all three lysosomal hyaluronidases, HYAL-1, HYAL-2, and HYAL-3. HYAL-2 was the predominant gene product. Using 5' RACE (rapid amplification of cDNA ends) analysis, multiple transcription initiation sites were identified including a novel initiation site located within intron 1 of the gene expressed by human articular chondrocytes. The presence of multiple transcriptional initiation sites is a typical feature of TATA-less promoter regions, such as those of HYAL-2. Approximately 4000 bp of 5' flanking sequence of the HYAL-2 gene was characterized. Transient transfection of C-28/I2 cells with various 5' deletion constructs indicated that the region between +959 to +1158 (within intron 1) contains the basal promoter for HYAL-2 in chondrocytes. In addition, the region +224 to +958 contained a negative modulator that could control the basal expression level of HYAL-2. Treatment of human articular chondrocytes or C-28/I2 cells with various catabolic cytokines did not alter HYAL-2 mRNA expression, luciferase promoter expression, or hyaluronidase enzymatic activity. Thus, in chondrocytes HYAL-2 appears to be constitutively expressed and not inducibly regulated by catabolic agents. As such, it appears that the expression of lysosomal hyaluronidase participates little in the overall regulation of hyaluronan catabolism.

The Pro-atherogenic Cytokine Interleukin-18 Induces CXCL16 Expression in Rat Aortic Smooth Muscle Cells via MyD88, Interleukin-1 Receptor-associated Kinase, Tumor Necrosis Factor Receptor-associated Factor 6, c-Src, Phosphatidylinositol 3-Kinase, Akt, c-Jun N-terminal Kinase, and Activator Protein-1 Signaling

We recently demonstrated that the chemokine CXCL16 is expressed in aortic smooth muscle cells (ASMC) and induces ASMC adhesion and proliferation (Chandrasekar, B., Bysani, S., and Mummidi, S. (2004) J. Biol. Chem. 279, 3188-3196). Here we reort that interleukin (IL)-18 positively regulates CXCL16 transcription in rat ASMC. We characterized the cis-regulatory region of CXCL16 and identified a functional activator protein-1 (AP-1) binding motif. Deletion or mutation of this site attenuated IL-18-mediated CXCL16 promoter activity. Gel shift, supershift, and chromatin immunoprecipitation assays confirmed AP-1-dependent CXCL16 expression. CXCL16 promoter-reporter activity was increased by constitutively active c-Fos and c-Jun and decreased by dominant negative or antisense c-Fos and c-Jun. Src kinase inhibitors PP1 and PP2, phosphatidylinositol 3-kinase (PI3K) inhibitors wortmannin and LY294002, Akt inhibitor, the c-Jun N-terminal kinase (JNK) inhibitor SP600125, antisense JNK and dominant negative MyD88, interleukin-1 receptor-associated kinase (IRAK)-1, IRAK4, and phosphatidylinositol 3-kinase expression all attenuated IL-18-mediated AP-1 binding and reporter activity, CXCL16 promoter-reporter activity, and CXCL16 expression. Thus IL-18 induced CXCL16 expression via a MyD88 --> IRAK1-IRAK4-TRAF6 (tumor necrosis factor receptor-associated factor 6) --> c-Src--> PI3K --> Akt --> JNK --> AP-1 pathway. Importantly, IL-18 stimulated ASMC proliferation in a CXCL16-dependent manner. These data provide for the first time a mechanism of IL-18-mediated CXCL16 gene transcription and CXCL16-dependent ASMC proliferation and suggest a role for IL-18-CXCL16 cross-talk in atherogenesis and restenosis following angioplasty.

High level of endothelial cell-specific gene expression by a combination of the 5′ flanking region and the 5′ half of the first intron of the VE-cadherin gene

AbstractTo develop a tool to obtain a high level of gene expression specifically in endothelial cells (ECs), we assessed enhancer activity of fragments in the first intron of the VE-cadherin gene using 3 different experimental systems: luciferase assay in the F2 EC line, green fluorescent protein (GFP) expression in ECs generated in embryonic stem (ES) cell differentiation culture, and GFP expression in transgenic mice. Although the 2.5-kbp (kilobase pair) 5′ flanking sequence of the VE-cadherin gene is EC specific, adding 4 kbp of the 5′ half of the first intron affected an enhancement of the gene expression level in all 3 assay systems. No other fragments tested in this study could confer such effects. Compared with other gene expression units, the unit described in this study would be the most optimum one available to date for EC-specific gene expression. Because this unit can express genes in VE-cadherin+ progenitors of hematopoietic cells but not in fully committed hematopoietic cells, it will be useful to manipulate specifically the uncommitted progenitor stage during hematopoietic cell differentiation. (Blood. 2005; 105:4657-4663)

Evolutionary History of 4.5SH RNA

4.5SH RNA is a 94-nt small RNA with unknown function. This RNA is known to be present in the mouse, rat, and hamster cells; however, it is not found in human, rabbit, and chicken. In the mouse genome, the 4.5SH RNA gene is a part of a long (4.2 kb) tandem repeat ( approximately 800 copies) unit. Here, we found that 4.5SH RNA genes are present only in rodents of six families that comprise the Myodonta clade: Muridae, Cricetidae, Spalacidae, Rhizomyidae, Zapodidae, and Dipodidae. The analysis of complementary DNA derived from the rodents of these families showed general evolutionary conservation of 4.5SH RNA and some intraspecific heterogeneity of these RNA molecules. 4.5SH RNA genes in the Norway rat, mole rat, hamster and jerboa genomes are included in the repeated sequences. In the jerboa genome these repeats are 4.0-kb long and arranged tandemly, similar to the corresponding arrangements in the mouse and rat genomic DNA. Sequencing of the rat and jerboa DNA repeats containing 4.5SH RNA genes showed fast evolution of the gene-flanking sequences. The repeat sequences of the distantly related rodents (mouse and rat vs. jerboa) have no apparent similarity except for the 4.5SH RNA gene itself. Conservation of the 4.5SH RNA gene nucleotide sequence indicates that this RNA is likely to be under selection pressure and, thus, may have a function. The repeats from the different rodents have similar lengths and contain many simple short repeats. The data obtained suggest that long insertions, deletions, and simple sequence amplifications significantly contribute in the evolution of the repeats containing 4.5SH RNA genes. The 4.5SH RNA gene seems to have originated 50-85 MYA in a Myodonta ancestor from a copy of the B1 short interspersed element. The amplification of the gene with the flanking sequences could result from the supposed cellular requirement of the intensive synthesis of 4.5SH RNA. Further Myodonta evolution led to dramatic changes of the repeat sequences in every lineage with the conservation of the 4.5SH RNA genes only. This gene, like some other relatively recently originated genes, could be a useful model for studying generation and evolution of non-protein-coding genes.

Regulation of Complement C3 Expression by the Bile Acid Receptor FXR

The farnesoid X receptor (FXR; NR1H4) is an intracellular bile acid-sensing transcription factor that plays a critical role in the regulation of synthesis and transport of bile acids as well as lipid metabolism. Although the reciprocal relationship between bile acid and triglyceride levels is well known, the mechanism underlying this link is not clearly defined. In this study, we demonstrate that FXR regulates the expression of at least two secreted factors, complement component C3 and FGF15, the rat ortholog of FGF19, known to influence lipid metabolism. The analysis of the human complement C3 gene reveals the presence of functional FXR response elements in the proximal promoter of C3. Furthermore, rats given a single dose of an FXR agonist exhibit an increase in the plasma concentration of complement C3 protein. These studies demonstrate a mechanism by which FXR, a nuclear receptor with a limited tissue expression pattern, regulates secretion of factors that ultimately can affect lipid metabolism in an endocrine or paracrine manner.

Identification of functional SNPs in the 5-prime flanking sequences of human genes

BackgroundOver 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be associated with a cell phenotype. These functional SNPs are consequently important in understanding human health. Information related to functional SNPs in candidate disease genes is critical for cost effective genetic association studies, which attempt to understand the genetics of complex diseases like diabetes, Alzheimer's, etc. Robust methods for the identification of functional SNPs are therefore crucial. We report one such experimental approach.ResultsSequence conserved between mouse and human genomes, within 5 kilobases of the 5-prime end of 176 GPCR genes, were screened for SNPs. Sequences flanking these SNPs were scored for transcription factor binding sites. Allelic pairs resulting in a significant score difference were predicted to influence the binding of transcription factors (TFs). Ten such SNPs were selected for mobility shift assays (EMSA), resulting in 7 of them exhibiting a reproducible shift. The full-length promoter regions with 4 of the 7 SNPs were cloned in a Luciferase based plasmid reporter system. Two out of the 4 SNPs exhibited differential promoter activity in several human cell lines.ConclusionsWe propose a method for effective selection of functional, regulatory SNPs that are located in evolutionary conserved 5-prime flanking regions (5'-FR) regions of human genes and influence the activity of the transcriptional regulatory region. Some SNPs behave differently in different cell types.

Transfection and expression of exogenous gene in laying hens oviduct in vitro and in vivo

To examine whether or not the regulatory sequence of chicken ovalbumin gene can drive transgene expression specifically in hen oviduct, the authors constructed an oviduct-specific expression vector (pOV), containing 3.0 kilobases (kb) of the 5'-flanking sequence and 3.0 kb of the 3'-flanking sequence of the chicken ovalbumin gene. Jellyfish green fluorescence protein (EGFP) reporter gene and bacterial LacZ reporter gene were respectively inserted into the downstream of the 5'-regulatory region. The recombinants were named as pOVEGFP and pOVLacZ. Two transfer systems, in vitro and in vivo, were used to verify the function of the vector. In vitro, the plasmid DNA pOVEGFP and pEGFP-N1 were transfected respectively by the polyethyleneimine procedure into the primary chicken oviduct epithelium (PCOE) and fibroblasts cells isolated from laying hens. In vivo, the recombinant vector pOVLacZ was injected into egg-laying hens via wing vein and the tissues were collected for RT-PCR analysis. The results showed that expression of pEGFP-N1 was achieved at low level in oviduct epithelial cells and at high level in fibroblasts, but that the recombinant vector was not expressed in both cells. RT-PCR analysis showed that the LacZ gene was transcribed in the oviduct, but not in the heart, liver, kidney and spleen of the injected hens. Accordingly, the beta-galactosidase activity was only detected in the oviduct magnum (116.7 mU/ml) and eggs (16.47 mU/ml). These results indicated that the cloned regulation regions of chicken ovalbumin gene could drive exogenous gene expression specifically in the oviducts of hens. In vivo gene injection via wing vein may serve as a rapid production system of recombinant proteins in chicken eggs. In addition, the cultured primary oviduct cells from laying hens were not efficient temporary expression systems for analyzing the function of regulating elements of ovalbumin gene.