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PubMed2006

Genomic structure, promoter analysis and expression of the porcine (Sus scrofa) TLR4 gene.

Toll-like receptor 4 (TLR4) is essential for initiating the innate response to lipopolysaccharide (LPS) from Gram-negative bacteria by acting as a signal-transducing receptor. As the pig industry faces a unique array of related pathogens, it is anticipated that the genotype of swine TLR4 could be of crucial importance in future strategies aimed at improving genetic resistance to infectious diseases. In order to help in investigating TLR4 as a candidate disease-resistance gene in pigs, we established its genomic structure and produced sufficient flanking intronic sequences to enable simple PCR amplification of the coding portions of the gene. Expression in different porcine tissues was studied and showed splicing variations in mRNA sequences. The cDNA sequence for poTLR4 contains an open reading frame of 2526bp that codes for 841 aa, 98 and 568bp in the 5'- and 3'-UTRs, respectively. Overall, the general organization of porcine, human, murine, and avian TLR4 genes is quite similar: three exons with the third one very long. A high level of conservation of the size and the sequence, especially for the two last exons and particularly in the sequence corresponding to the LRRs and TIR domain, is observed between species. The important antimicrobial properties of these proteins may account for a conservative selection pressure on these TLR4 coding sequences. Several putative binding sites described in the human and murine promoter of TLR4 genes have been identified in the 5'-flanking region of poTLR4. Conversely, this region lacks a TATA box, consensus initiator sequences, or GC-rich regions. The basic sequence data gathered will allow the establishment of an inventory of naturally occurring variation in porcine TLR4, so that alleles can be tested for disease association studies.

Animals↗
PubMed2002

Novel homozygous splice acceptor site GnRH receptor (GnRHR) mutation: human GnRHR "knockout".

Mutations in the GnRH receptor (GnRHR) have been shown to be responsible for a significant number of autosomic recessive and, less commonly, sporadic cases of idiopathic hypogonadotropic hypogonadism. We describe a woman with complete GnRH resistance secondary to a novel homozygous GnRHR gene mutation, transmitted as an autosomal recessive trait. The propositus presented with primary amenorrhea and absent thelarche and pubarche. Dynamic tests demonstrated absent spontaneous gonadotropin pulsatility, and no response to either exogenous pulsatile (10 microg/pulse at 90-min intervals over 6 h) or acute (100 microg) GnRH administration. However, she responded to exogenous gonadotropin administration, with a resulting normal pregnancy. Genomic DNA extracted from peripheral blood was PCR amplified using amplimers spanning intron-exon boundaries for the three exons of GnRHR and revealed a homozygous splice junction mutation (G to A transversion) at the intron 1-exon 2 boundary. Her unaffected sister, with a totally normal phenotype, was heterozygous for this mutation. After lymphocyte Epstein-Barr virus transformation, RNA was extracted and subjected to RT-PCR, using primers located in the first and third exons. Results showed a transcript lacking all of exon 2 (exon 2 skipping), with splicing of exon 1 to exon 3. This created a frame shift, generating a coding sequence for three new amino acids, followed by a stop codon. Although it is not clear whether the mutant receptor is actually expressed, the resultant mRNA sequence was presumed to produce a truncated receptor with no binding or signaling capacity.

Adolescent↗
PubMed1985

Human liver fatty acid binding protein cDNA and amino acid sequence. Functional and evolutionary implications.

Human liver fatty acid binding protein (L-FABP) cDNA clones were identified in a liver cDNA library. The two longest clones were completely sequenced. The nucleotide sequence predicts a protein of 127 amino acid residues. Identity of the clones was confirmed by limited amino acid sequence analysis of purified human L-FABP peptides and Edman degradation of radiolabeled in vitro translated FABP. Statistical analysis of the amino acid and mRNA sequences of human L-FABP, rat L-FABP, rat intestinal (I-) FABP, and mouse 422 protein indicates that the human and rat L-FABPs are highly homologous and that L-FABP and I-FABP diverged a long time ago (approximately 650-690 million years ago), although they are more closely related to each other than either of them is to 422 protein. Secondary structure predictions from the primary sequence of human and rat L-FABP reveal a region (residues 12-30) that might be the putative fatty acid binding domain of the two L-FABPs. Knowledge of the primary amino acid sequence of L-FABP and possible functional domains will be pivotal in further defining and understanding the mechanism of ligand binding and transfer by this protein.

Amino Acid Sequence↗
PubMed1997

Programmed cell death by hok/sok of plasmid R1: coupled nucleotide covariations reveal a phylogenetically conserved folding pathway in the hok family of mRNAs.

The hok/sok system of plasmid R1 mediates plasmid maintenance by killing of plasmid-free cells. Translation of the stable toxin-encoding hok mRNA is repressed by the unstable Sok antisense RNA. Using genetic algorithm simulations and phylogenetic comparisons, we analyse five plasmid-encoded and two chromosome-encoded hok-homologous mRNAs. A similar folding pathway was found for all mRNAs. Metastable hairpins at the very 5'-ends of the mRNAs were predicted to prevent the formation of structures required for translation and antisense RNA binding. Thus the folding of the mRNA 5'-ends appears to explain the apparent inactivity of the nascent transcripts. In the full-length mRNAs, long-range 5' to 3' interactions were predicted in all cases. The 5' to 3' interactions lock the mRNAs in inactive configurations. Translation of the mRNAs is activated by 3' exonucleolytic processing. Simulation of the 3' processing predicted that it triggers rearrangements of the mRNA 5'-ends with the formation of translational activator and antisense RNA target hairpins. Alignment of the mRNA sequences revealed a large number of nucleotide covariations that support the existence of the proposed secondary structures. Furthermore, coupled covariations support the folding pathway and provide evidence that the mRNA 5'-ends pair with three different partners during the proposed series of dynamic RNA rearrangements.

Apoptosis↗
PubMed1978

Characterization of beta-globin mRNA in the beta0 thalassemias.

A number of cases of beta0 thalassemia have been examined for the presence or absence of beta-globin mRNA. Total RNA extracted from peripheral blood was hybridized to purified complementary DNA specific for beta-globin mRNA, and to beta-cDNA probes specific for the 5' and 3' noncoding regions of beta-globin mRNA. Three clear-cut categories of beta0 thalassemia were identified. The first type had no detectable beta-globin mRNA. A second typed had beta-globin mRNA sequences which hybridized incompletely to the cDNA probes and probably represented mRNAs with grossly altered structures. A third type appeared to have essentially intact, though untranslatable, beta-globin mRNA. Depurination products from 5' and 3' beta-cDNAs synthesized from this latter mRNA were identical to those from normal beta-globin mRNA, but the relative yields were different, suggesting a possible defect near the initiation codon.

Adolescent↗
PubMed1980

Structure and developmental expression of the chick alpha-actin gene.

Recombinant DNA clones containing chick alpha-actin mRNA sequence have been isolated and used as probes to analyze the structure and developmental expression of the chick alpha-actin gene. The full length, 2000 nucleotide alpha-actin mRNA is detected in poly(A) RNA at early and late stages of in vivo leg muscle development. As expected, the alpha-actin mRNA is present at very low levels at early myogenic stages but is a high abundance species in terminally differentiated muscle. However, most of the alpha-actin mRNA from fused leg muscle is shorter than 2000 nucleotides, and occurs in relatively discrete size classes. An alpha-actin-like mRNA can be detected in poly(A) RNA from early embryonic brain, indicating that transcription of the alpha-actin gene may not be strictly muscle-specific at all stages of development. We have identified at least 3, very short (< 100 base pairs) intervening sequences in the alpha-actin gene which was isolated from a chick genomic library. The structure of the chick alpha-actin gene differs, therefore, from the structures of actin genes from yeast and Drosophila, both of which contain a single, relatively long, intervening sequence.

Actins↗
PubMed2003

[Cloning and analysis of three genes encoding type II CHH family neuropeptides from Fennropenaeus chinensis].

On the basis of sequence similarity, the crustean hyperglycemic hormone (CHH) family peptides have been classified into two types of hormones: type I and type II. Molt-inhibiting hormone (MIH) is a neuropeptide member of type II CHH family. Molting in shrimp is controlled by MIH and ecdysone. By inhibiting the synthesis of ecdysone in the Y-organ, MIH indirectly suppresses the molting activity of shrimp. In this study, we reported the cloning and characterization of 3 gene fragments encoding type II CHH family neuropeptides of the shrimp Fennropenaeus chinensis. According to the complementary DNA sequence of the mult-inhibiting hormone of Fennropenaeus chinensis, 3 primers were designed and synthesized. MP1 and MP2 are sense primers, and MP3 is anti-sense primer. Polymerase chain reaction was performed using genomic DNA of Fennropenaeus chinensis as template. Three PCR products were obtained using primers MP1 and MP3. Their sizes are about 600 bp, 850 bp, 1050 bp, respectively. A 580 bp PCR product was obtained using primers MP2 and MP3. All the 4 PCR products were cloned into pMD18-T vector. The recombinant clones were sequenced using ABI 310 Genetic Analyzer. After sequencing, all the DNA sequences were searched in the GenBank by Blast program to find similar gene sequences. The searching results revealed 3 DNA fragment sequences were of high similarity with CHH family neuropeptide genes from various crustean species. The 3 DNA fragments were named as NP1, NP2, and NP3. Their sizes were 540 bp, 601 bp, and 826 bp, respectively. Using the mRNA sequences with the most similarity to the 3 sequence fragments as reference, the gene structure of the 3 DNA fragment sequences was analyzed. The exons of 3 sequence fragments were aligned with their similar sequences by Clustal W program. Both NP1 and NP2 consisted of 1 intron and 2 exons. NP3 consisted of 2 introns and 3 exons. Sequence analysis suggested that these 3 products belonged to sequence fragments of neuropeptide gene of type II crustacean hyperglycemic hormone family. The exons of NP1, NP2, and NP3 had highest similarity respectively with mRNA of Pem-SCP-C2 and Pem-SGP-C1 both from Penaeus monodon, and FenchMIH from Fennropenaeus chinensis. The identities were 91.5%, 92.8%, 88.9%, respectively. The results suggest NP3 is a fragment of molt-inhibiting hormone gene of Fennropenaeus chinensis NP1 and NP2 are two fragments of neuropeptide genes of type II crustacean hyperglycemic hormone family, which were found in Fennropenaeus chinensis for the first time.

Amino Acid Sequence↗
PubMedDate not supplied

mRNA Metabolism and hereditary disorders: a tale of surveillance and escape.

The exploration of the molecular origin of hereditary diseases focused on genes and proteins for many years. Recently, mRNA has gained increasing attention. Most human genes contain introns and a considerable proportion of transcripts are not only alternatively spliced but also regulated posttranscriptionally in manifold ways. mRNA processing as well as a complex network of interactions between the steps of gene expression and associated quality control mechanisms are guided by a multitude of regulative mRNA sequence elements. Therefore it is not surprising that mutations of such elements can cause or modify human disease. The purpose of this review is the illustration of principles of physiological and dysregulated mRNA metabolism as well as a survey of new analytical tools and therapeutic approaches.

Base Sequence↗
PubMed2004

Hammerhead ribozyme targeting connective tissue growth factor mRNA blocks transforming growth factor-beta mediated cell proliferation.

PURPOSE: Excessive scarring following trauma or surgery of cornea, conjunctiva or retina can greatly impair visual outcome. At present, no agents are clinically available that selectively reduce activity of genes that regulate fibrosis. Connective tissue growth factor (CTGF) has been linked to fibrosis in several tissues, including cornea and conjunctiva. In this study, hammerhead ribozymes targeting CTGF mRNA were synthesized, kinetic parameters were measured, and the effect on TGF-beta-mediated cell proliferation was measured in cultured human fibroblasts. METHODS: The mRNA sequence of human CTGF was scanned for potential hammerhead ribozyme cleavage sites, and predicted secondary folding structures around the sites were calculated. Synthetic 12mer ribozymes and 33mer oligonucleotide mRNA targets corresponding to two sites were synthesized, and kinetic constants calculated from Hanes-Wolff plots of in vitro cleavage reactions. The ribozyme with higher percentage cleavage and kinetic rate was cloned into an expression plasmid (pTR-UF21) and stably transfected into cultured human fibroblasts. An inactive ribozyme plasmid served as a negative control. The effects of the ribozyme on expression of TGF-beta-induced CTGF mRNA and protein levels were measured using ELISA and real-time TaqMan quantitative RT-PCR. Finally, the effect of the CTGF ribozyme on TGF-beta-mediated proliferation of fibroblasts was measured using a non-radioactive cell proliferation microtiter assay. RESULTS: Of the eight potential hammerhead ribozyme cleavage sites in human CTGF mRNA, two sites (CHR 745, and CHR 859) were identified with optimal secondary folding. CHR 859 cleaved 94% of the target mRNA, compared to 46% cleavage for CHR 745 after 16 hr of reaction. CHR 859 had a K(m) of 1.56 microM and a K(cat) of 2.97 min(-1), while CHR 745 had a K(m) of 7.80 microM and a K(cat) of 5.7 min(-1). The turnover numbers (K(cat)/K(m)) of CHR 859 and CHR 745 were 1.9 x 10(6) M min(-1) and 7.4 x 10(5) M min(-1), respectively, indicating CHR 859 is 2.6 times more efficient than CHR 745 in destroying CTGF mRNA. Stable transfection of CHR 859 into human fibroblasts reduced CTGF mRNA levels 55% and protein levels 72% compared to the inactive ribozyme control. Furthermore, TGF-beta-induced cell proliferation was reduced 90% in fibroblasts stably transfected with CHR 859 compared to control cell groups. CONCLUSIONS: The CHR 859 hammerhead ribozyme cleaved human CTGF mRNA with high kinetic efficiency in vitro, effectively reduced levels of CTGF mRNA and protein in cultured human fibroblasts, and blocked TGF-beta-induced cell proliferation without nonspecific toxicity. These data support the concept that CTGF mediates TGF-beta-induced cell proliferation, and imply that regulating CTGF expression with ribozymes may be effective in reducing ocular scarring.

Base Sequence↗
PubMed1982

The yeast frameshift suppressor gene SUF16-1 encodes an altered glycine tRNA containing the four-base anticodon 3'-CCCG-5'.

The SUF16 frameshift suppressor locus encodes a glycine tRNA. The SUF16-1 suppressor tRNA is inferred by DNA sequence analysis to contain the four-base anticodon sequence 3'-CCCG-5' in place of the wild-type anticodon 3'-CCG-5'. SUF16-1 mediates translation of the four-base messenger RNA (mRNA) sequence 5'-GGGU-3' but apparently fails to act at the sequence 5'-GGGG-3'. A molecular model is presented that accounts for the observed specificity of tRNA-mediated frameshift suppression in Saccharomyces cerevisiae.

Anticodon↗
PubMed1981

Isolation of a cDNA clone for mouse urinary proteins: age- and sex-related expression of mouse urinary protein genes is transcriptionally controlled.

A recombinant cDNA plasmid derived from mouse urinary protein (MUP) mRNA was isolated and used to determine the level of control of the developmentally regulated and the sex-linked expression of MUP genes by monitoring the transcription of MUP mRNA sequences in isolated liver nuclei. No transcription of MUP genes could be detected in liver nuclei of prepubescent animals whose livers do not contain measurable MUP mRNA. Transcription of MUP genes in the livers of adult male mice was 6-fold higher than in the livers of adult female mice, proportional to the difference in MUP mRNA concentrations. Transcriptional control mechanisms are therefore implicated as responsible for both the developmentally and the sex-linked changes in the expression of MUP genes.

Age Factors↗
PubMed1986

Differential effects of polyadenylation regions on gene expression in mammalian cells.

The steady-state level attained for any protein in mammalian cells is in part determined by its steady-state level of mRNA. Sequence information in and around the 3' end of an RNA which is involved in specifying and regulating polyadenylation [poly(A)] may have important consequences on mRNA levels, and ultimately on expression of the protein product. In this report we compare the effects on gene expression which result from placing several different poly(A) regions, or no poly(A) region, downstream from a marker gene (galactokinase or galK) that can be readily assayed in mammalian cells. Our results demonstrate that the presence of a poly(A) region is important for efficient gene expression and that the use of the poly(A) region of bovine growth hormone (bGH) reproducibly results in three times higher expression than that of SV40 early or human collagen poly(A) regions. We further demonstrate that changing the promoter region on these chimeric transcription units does not change the effect of the poly(A) region. Neither does changing the assay gene, since comparison of the same poly(A) regions behind another marker gene (xanthine-guanine phosphoribosyl transferase or xgprt) leads to identical differences in expression. When we examine the levels of poly(A)+ RNA that result from each transcription unit, we find that they correlate precisely with the gene expression levels. Apparently the 3' end of an RNA is a determinant of steady-state mRNA levels and, in turn, the subsequent production of the protein product.

Animals↗
PubMed2001

Full-length cDNAs: more than just reaching the ends.

The development of functional genomic resources is essential to understand and utilize information generated from genome sequencing projects. Central to the development of this technology is the creation of high-quality cDNA resources and improved technologies for analyzing coding and noncoding mRNA sequences. The isolation and mapping of cDNAs is an entrée to characterizing the information that is of significant biological relevance in the genome of an organism. However, a bottleneck is often encountered when attempting to bring to full-length (or at least full-coding) a number of incomplete cDNAs in parallel, since this involves the nonsystematic, time consuming, and labor-intensive iterative screening of a number of cDNA libraries of variable quality and/or directed strategies to process individual clones (e.g., 5' rapid amplification of cDNA ends). Here, we review the current state of the art in cDNA library generation, as well as present an analysis of the different steps involved in cDNA library generation.

Automation↗
PubMed2004

Structural features and transcript-editing analysis of sugarcane (Saccharum officinarum L.) chloroplast genome.

The complete nucleotide sequence of the chloroplast genome of sugarcane (Saccharum officinarum) was determined. It consists of 141,182 base-pairs (bp), containing a pair of inverted repeat regions (IR(A), IR(B)) of 22,794 bp each. The IR(A) and IR(B) sequences separate a small single copy region (12,546 bp) and a large single copy (83,048 bp) region. The gene content and relative arrangement of the 116 identified genes (82 peptide-encoding genes, four ribosomal RNA genes, 30 tRNA genes), with the 16 ycf genes, are highly similar to maize. Editing events, defined as C-to-U transitions in the mRNA sequences, were comparable with those observed in maize, rice and wheat. The conservation of gene organization and mRNA editing suggests a common ancestor for the sugarcane and maize plastomes. These data provide the basis for functional analysis of plastid genes and plastid metabolism within the Poaceae. The sugarcane chloroplast DNA sequence is available at GenBank under accession NC005878.

Base Sequence↗
PubMed1985

Liver-specific RNA metabolism in hepatoma cells: variations in transcription rates and mRNA levels.

The transcription rate and abundance of several liver-specific mRNAs as well as mRNAs common to many cell types were compared in a series of rodent hepatoma cell lines, normal liver cells, and primary hepatocyte cultures. The rat hepatoma cell line, Fao, which displays a liver-specific phenotype, contained eight of eight liver-specific mRNAs examined. However, the transcription rates of most liver-specific mRNAs were found to be low (1 to 30%) compared with normal liver in this and other differentiated cell lines. This low rate is similar to the transcription rates of liver-specific mRNA sequences measured in primary cultures of hepatocytes. Several variant cell lines that had lost differentiated traits contained few or none of the liver-specific mRNAs; clonal descendents which had regained differentiated function regained the tissue-specific mRNAs as a group, but at various concentrations. Because all of the changes observed in mRNA levels were not accompanied by parallel changes in transcription of the same sequences, differential posttranscriptional stabilization of the liver-specific mRNAs must also occur in the different cell lines. These results qualify the utility of cultured cell lines in the study of tissue-specific transcriptional control, but raise the possibility that posttranscriptional mechanisms act in cooperation with transcriptional controls to bring the level of tissue-specific mRNAs closer to those found in liver cells.

Albumins↗
PubMed2002

brachyury Target genes in the early sea urchin embryo isolated by differential macroarray screening.

Brachyury is a transcription factor that functions in gastrulation and endoderm development throughout the Bilateria. Here, we identify genes that are expressed downstream of brachyury during gastrulation of the sea urchin embryo. Screens with two different complex probes generated by subtractive hybridization were carried out on high-density arrays of embryonic cDNA libraries. An mRNA sequence population from embryos expressing brachyury at its peak stage of expression was subtracted with message sequence from embryos in which Brachyury function had been "knocked-out" by injection of a morpholine-substituted antisense oligonucleotide to generate a differential probe for brachyury target genes. Another probe was made by using an mRNA population from embryos that mis-express brachyury at a stage just prior to the normal onset of expression, subtracted with message sequence taken from normal embryos at this stage. Screens carried out with these probes target overlapping but distinct sets of downstream genes. After partial sequence characterization, promising genes were independently analyzed by quantitative real-time PCR and by in situ hybridization. Two major classes of genes emerge in this study: genes expressed in the subset of the secondary mesenchyme cells (SMC) that will become pigment cells, and genes that are expressed in portions of the endoderm coincident with brachyury expression. The latter genes are candidates for direct transcriptional targets of Brachyury. Some of the endodermal genes that respond to Brachyury are cytoskeletal modulators that may play a role in gut morphogenesis. This finding is consistent with the block in gastrulation induced by interfering with Brachyury function in sea urchins, and with known or suggested Brachyury function in other species. Other endodermal target genes are expressed in the archenteron and might be terminal differentiation enzymes of the gut. Brachyury expression patterns for Strongylocentrotus purpuratus reported in this paper are entirely consistent with data from other echinoderm species. Brachyury expression in the vegetal plate is confined to the presumptive endodermal cells. Therefore, the SMC genes are likely to be indirect targets of Brachyury-induced signaling from the surrounding endoderm to the central mesoderm, or the effects on these genes may be indirect consequences of gross disruption of the vegetal plate. These results and other data suggest that the brachyury gene transduces information about the state of endodermal specification to genes that modulate morphogenesis and genes that perform terminal functions in the gut.

Animals↗
PubMed1991

Structure of the gene encoding columbid annexin Icp35.

The cp35 gene, encoding an annexin I (AnxI) cropsac 35-kDa protein (cp35) from the pigeon, consists of 13 exons and twelve introns. The borders of exons 2-13 were mapped by comparison with the known cDNA sequence. A 5-kb sequence containing exons 1, 2, and 3, and 1.4 kb of 5'-flanking DNA, is presented. The transcription start point was mapped by S1 nuclease protection. The region of the cp35 mRNA sequence, which we had previously shown to be profoundly different from mammalian anxI, is located in the first half of exon 3. Whereas human anxI is known to be single copy, Southern analysis of pigeon genomic DNA and genomic clones demonstrated multiple anxI genes in the pigeon, diverging significantly in their 5'-termini. Pigeon vimentin, on the other hand, is encoded by a single-copy gene as it is in other birds and mammals. These experiments have demonstrated that the cp35 mRNA is transcribed from its individual gene and is not a product of alternative processing of the pigeon homolog of mammalian anxI. We speculate that the diversification of anxI genes in Columbid birds allowed the recruitment of one of these genes (cp35) for unique regulation by prolactin in the absence of post-translational regulation via residues encoded by exons 2 and 3.

Animals↗
PubMed1996

A novel gene expressed in rat ameloblasts codes for proteins with cell binding domains.

Two variants of an mRNA sequence are identified that are expressed at high levels in rat ameloblasts during the formation of the enamel matrix. The sequences contain open reading frames for 407 and 324 amino acid residues, respectively. The encoded proteins, which we call amelins, are rich in proline, glycine, leucine, and alanine residues and contain the peptide domain DGEA, an integrin recognition sequence. The sequences coding for the C-terminal 305 amino acid residues, the 3' nontranslated part, and a microsatellite repeat at the nontranslated 5' region are identical in both mRNA variants. The remaining 5' regions contain 338 nucleotides unique to the long variant, 54 common nucleotides, and 46 nucleotides present only in the short variant. Eleven nucleotides have the potential to code for 5 amino acids of both proteins in different reading frames. The reading frame of the longer variant includes codons for a typical N-terminal signal peptide. The amelins are likely to be constituents of the enamel matrix and the only proteins that have so far been implicated in binding interactions between the ameloblast surface and its extracellular matrix.

Ameloblasts↗