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Bp Upstream (bp + upstream)
Selected AbstractsStructure and promoter analysis of the mouse membrane-bound transferrin-like protein (MTf) geneFEBS JOURNAL, Issue 5 2001Kazuko Nakamasu Recently, we purified membrane-bound transferrin-like protein (MTf) from the plasma membrane of rabbit chondrocytes and showed that the expression levels of MTf protein and mRNA were much higher in cartilage than in other tissues [Kawamoto T, Pan, H., Yan, W., Ishida, H., Usui, E., Oda, R., Nakamasu, K., Noshiro, M., Kawashima-Ohya, Y., Fujii, M., Shintani, H., Okada, Y. & Kato, Y. (1998) Eur. J. Biochem.256, 503,509]. In this study, we isolated the MTf gene from a constructed mouse genomic library. The mouse MTf gene was encoded by a single-copy gene spanning ,,26 kb and consisting of 16 exons. The transcription-initiation site was located 157 bp upstream from the translation-start codon, and a TATA box was not found in the 5, flanking region. The mouse MTf gene was mapped on the B3 band of chromosome 16 by fluorescence in situ hybridization. Using primary chondrocytes, SK-MEL-28 (melanoma cell line), ATDC5 (chondrogenic cell line) and NIH3T3 (fibroblast cell line) cells, we carried out transient expression studies on various lengths of the 5, flanking region of the MTf gene fused to the luciferase reporter gene. Luciferase activity in SK-MEL-28 cells was higher than in primary chondrocytes. Although no luciferase activity was detectable in NIH3T3 cells, it was higher in chondrocytes than in ATDC5 chondrogenic cells. These findings were consistent with the levels of expression of MTf mRNA in these cells cultured under similar conditions. The patterns of increase and decrease in the luciferase activity in chondrocytes transfected with various 5, deleted constructs of the MTf promoter were similar to that in ATDC5 cells, but differed from that in SK-MEL-28 cells. The findings obtained with primary chondrocytes suggest that the regions between ,693 and ,444 and between ,1635 and ,1213 contain positive and negative cis -acting elements, respectively. The chondrocyte-specific expression of the MTf gene could be regulated via these regulatory elements in the promoter region. [source] Phylogenetic reconstruction of Gram-positive organisms based on comparative sequence analysis of molecular chaperones from the ruminal microorganism Ruminococcus flavefaciens FD-1FEMS MICROBIOLOGY LETTERS, Issue 1 2003Dionysios A. Antonopoulos Abstract Primers designed on the basis of nucleotide sequences conserved in DnaK and GroEL from Gram-positive organisms were used to PCR amplify internal regions of the cognate genes from the anaerobic ruminal cellulolytic bacterium Ruminococcus flavefaciens FD-1. Genome walking was then utilized to elucidate the remainder of the sequences in addition to upstream and downstream regions. The full sequence of the gene encoding the GroES protein (groES) was found directly upstream from groEL. The deduced amino acid sequence of the groEL gene showed the highest homology with the amino acid sequence of the Clostridium thermocellum GroEL protein (72% amino acid identity). Similarly, translation of the groES nucleotide sequence showed highest homology to the C. thermocellum GroES protein (61% amino acid identity). Analysis of the upstream region of this chaperonin operon revealed a CIRCE regulatory element 45 bp upstream from the putative start of the groES ORF. The deduced amino acid sequence of the putative dnaK gene showed the highest homology with the amino acid sequence of the Clostridium acetobutylicum DnaK protein (68% amino acid identity). Phylogenetic analyses based on the translated sequences reiterate this relationship between R. flavefaciens and the Clostridia. However, when the nucleotide sequences of Gram-positive organisms are analyzed, a different topology occurs of the relationship between high- and low-G+C Gram-positive organisms to the 16S rRNA interpretation. [source] Deletion hotspot in the argininosuccinate lyase gene: association with topoisomerase II and DNA polymerase , sites ,HUMAN MUTATION, Issue 11 2006John Christodoulou Abstract Molecular analysis of argininosuccinate lyase (ASAL) deficiency has led to the identification of a deletion hotspot in the ASL gene. Six individuals with ASAL deficiency had alleles that led to a complete absence of exon 13 from the ASL mRNA; each had a partial deletion of exon 13 in the genomic DNA. In all six patients, the deletions begin 18 bp upstream of the 3, end of exon 13. In four cases, the deletions were 13 bp in length, and ended within exon 13, whereas in two other patients the deletions were 25 bp and extended into intron 13. The sequence at which these deletions begin overlaps both a putative topoisomerase II recognition site and a DNA polymerase , mutation/frameshift site. Moreover, the topoisomerase II cut site is situated precisely at the beginning of the deletions, which are flanked by small (2- and 3-bp) direct repeats. We note that a similar concurrence of these two putative enzyme sites can be found in a number of other deletion sites in the human genome, most notably the ,F508 deletion in the CFTR gene. These findings suggest that the joint presence of these two enzyme sites represents a DNA sequence context that may favor the occurrence of small deletions. Hum Mutat 27(11), 1065,1071, 2006. © 2006 Wiley-Liss, Inc. [source] BUB1 infrequently mutated in human breast carcinomas,,HUMAN MUTATION, Issue 5 2003Anita Langerřd Abstract The BUB1 gene is a key player in the mitotic spindle checkpoint machinery that monitors proper segregation of sister chromatides during mitosis. It has been suggested that mutations in BUB1 may disrupt the spindle checkpoint and thereby cause chromosomal instability, which is a hallmark of solid tumors including those from the breast. From a series of breast carcinomas we selected 20 cases with genomic instability, as scored by Comparative Genome Hybridization (CGH), and without somatic TP53 (p53) mutations, and sequenced the entire coding region of the BUB1 gene. Two different constitutional sequence variants were found; a base substitution in exon 5, c.481G>A (CAG>CAA, a synonymous change encoding Gln144) in two samples, and a base substitution 8 bp upstream of exon 10, c.1007-8T>C in two other samples. No somatic mutations were detected. These results indicate that genomic instability scored as copy number alterations by CGH in TP53 wild type breast carcinomas is not caused by somatic mutations in the BUB1 gene. © 2003 Wiley-Liss, Inc. [source] Rapid denaturing high-performance liquid chromatography (DHPLC) for mutation scanning of the transforming growth factor ,3 gene using a novel proof-reading polymeraseINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2003A. Bayat Summary We have utilized a novel variation on the conventional denaturing high-performance liquid chromatography (DHPLC) technology, which we term rapid DHPLC, combining changes in instrumentation, cartridge technology and analysis conditions to enable significant increases in throughput to be achieved. In addition, the use of a novel proof-reading polymerase for sample amplification with a low misincorporation rate enables simplification of the DHPLC patterns and hence enhanced mutation detection recognition. This scheme for increasing DHPLC throughput has been tested by scanning the transforming growth factor (TGF) ,3 gene for the presence of mutations for which there is limited published or on-line data available regarding the presence of gene polymorphisms. TGF, isoforms have multiple roles in cell division, growth, proliferation, transformation and differentiation. TGF,3 is a TGF, cytokine isoform, and has an important role in embryogenesis, cell differentiation and wound healing. The TGF,3 gene consists of seven exons and six introns spanning 43 000 bp of the human genome on chromosome 14q23,24. The rapid DHPLC approach enabled scanning of all seven exons and part of the promoter region (1000 bp upstream from exon 1 in the 5,-flanking regions) of the TGF,3 gene in 95 Caucasian individuals in only 8 days, in comparison to the 17 days it would have previously taken. Mutations were clearly identified in the promoter region of the TGF,3 gene but were absent from the exonic regions. Understanding the genetic variations affecting the TGF,3 gene is important as this molecule has multiple regulatory functions on a variety of cell types. [source] Transcriptional analysis of the gdhA gene in Streptococcus thermophilusJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2009C. Lazzi Abstract Aims:, To study the transcriptional analysis of glutamate dehydrogenase gene, involved in the amino acid conversion to aroma compound in Streptococcus thermophilus. Methods and Results:, Analysis of the gdhA gene nucleotide sequence of S. thermophilus CNRZ1066 revealed that the coding region is 1353 nucleotides long. The deduced amino acids sequence exhibits the putative GDH active site and some conserved domains characteristic of family I of hexameric GDHs. Phylogenetic analysis revealed that the gdh gene of S. thermophilus clustered with the orthologues of other streptococci such as Streptococcus mutans, Streptococcus agalactiae and Streptococcus infantarius. Studying the structural organization of the gdhA locus the amino acid similarity of GDHs was higher than 87%, but the locus organization was not conserved. A dominant transcript of approximately 1·4 kbp was revealed by Northern blot hybridization, suggesting that gdhA mRNA is monocystronic. Primer extension showed that transcription start point of gdhA was localized 43 bp upstream of the potential start codon (ATG). Conclusions:, The gdhA represents a monocistronic operon highly conserved in phylogenetic-related bacteria. Significance and Impact of the Study:, A deeper knowledge of gdh transcriptional mechanisms could lead to develop S. thermophilus industrial starter cultures with optimized aromatic properties. [source] A RUNX/AML-binding motif residing in a novel 13-bp DNA palindrome may determine the expression of the proximal promoter of the human uPA geneJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 9 2005E. KOPF Summary., Urokinase-type plasminogen activator (uPA) is a multifunctional extracellular serine protease implicated in different events including fibrinolysis, tissue remodeling, and hematopoiesis. The human uPA gene contains a major promoter region at around 2000 bp upstream from the transcription start site (+1), and a second regulatory region spanning nucleotides ,90/+32 within the proximal promoter. Here, an inspection of this region revealed a novel 13-bp palindrome residing at position +8/+20. Interestingly, the palindrome contains the DNA consensus-binding hexamer for the RUNX/AML family of transcription factors that play a role in hematopoiesis, leukemia, and several developmental processes. Measuring the expression for promoter,reporter constructs after transfection revealed that deletion of the palindrome abrogated most of the proximal promoter activity in 293A cell. Additionally, electrophoretic mobility shift assays have shown that the palindrome could bind the RUNX1 component in nuclear extracts of myeloid cell lines exclusively through its RUNX motif. The palindrome was found in five additional human genes, two of which (MYH11 and MLLT1) have been linked to chromosomal rearrangements leading to leukemia. The data presented here have implicated, for the first time, RUNX/AML in the regulation of the uPA gene. The significance of the novel palindrome regarding gene regulation through the RUNX motif deserves further investigation. [source] Activation of enteropathogenic Escherichia coli (EPEC) LEE2 and LEE3 operons by LerMOLECULAR MICROBIOLOGY, Issue 4 2000Vanessa Sperandio Enteropathogenic Escherichia coli (EPEC) produces attaching and effacing lesions (AE) on epithelial cells. The genes involved in the formation of the AE lesions are contained within a pathogenicity island named the locus of enterocyte effacement (LEE). The LEE comprises 41 open reading frames organized in five major operons: LEE1, LEE2, LEE3, LEE4 and tir. The first gene of the LEE1 operon encodes a transcription activator of the other LEE operons that is called the LEE-encoded regulator (Ler). The LEE2 and LEE3 operons are divergently transcribed with overlapping ,10 promoter regions, and gene fusion studies have shown that they are both activated by Ler. Deletion analysis, using lacZ reporter fusions, of the LEE2 and LEE3 promoters demonstrated that deletions extending closer to the LEE2 transcription start site than ,247 bp lead to loss of activation by Ler, whereas only 70 bp upstream of the LEE3 transcription start site is required for Ler-mediated activation. We have purified Ler as a His-tagged protein and used it to perform DNA-binding assays with LEE2 and LEE3. We observed that Ler bound to a DNA fragment containing the ,300 to +1 region of LEE2; however, it failed to bind to a DNA fragment containing the ,300 to +1 region of LEE3, suggesting that Ler activates both operons by only binding to the regulatory region upstream of LEE2. The Ler-activatable LEE3::lacZ fusions extended to what would be ,246 bp of the LEE2 operon. A lacZ fusion from the ,300 to +1 region of LEE3 failed to be activated by Ler, consistent with our hypothesis that Ler activates the expression of LEE2 and LEE3 by binding to a region located downstream of the LEE3 transcription start site. DNase I footprinting revealed that Ler protected a region of 121 bp upstream of LEE2. Purified Ler mutated in the coiled-coil domain was unable to activate transcription and to bind to the LEE2 regulatory region. These data indicate that Ler may bind as a multimer to LEE2 and activate both divergent operons by a novel mechanism potentially involving changes in the DNA structure. [source] A Rox1-independent hypoxic pathway in yeast.MOLECULAR MICROBIOLOGY, Issue 4 2000Antagonistic action of the repressor Ord, activator Yap1 for hypoxic expression of the SRP1/TIR1 gene Hypoxic SRP1/TIR1 gene expression depends on the absence of haem but is independent of Rox1-mediated repression. We have found a new hypoxic pathway involving an antagonistic interaction between the Ixr1/Ord1 repressor and the Yap1 factor, a transcriptional activator involved in oxidative stress response. Here, we show that Ord1 repressed SRP1 gene expression under normoxia and hypoxia, whereas Yap1 activated it. Ord1 and Yap1 have been shown to bind the SRP1 promoter in a region extending from ,299 to ,156 bp upstream of the start codon. A typical AP-1 responsive element lying from ,247 to ,240 bp allows Yap1 binding. Internal deletion of sequences within the SRP1 promoter were introduced. Two regions were characterized at positions ,299/,251 and ,218/,156 that, once removed, resulted in a constitutive expression of SRP1 in a wild-type strain under normoxic conditions. Deletion of both these two sequences allowed the bypass of YAP1 requirement in a ,yap1 strain, whereas these two internal deletions did not yield increased expression in a ,ord1 strain compared with the full-length promoter. Both a single ,ord1 mutant and a doubly disrupted ,yap1 ,ord1 strain yielded normoxic constitutive SRP1 expression and increased hypoxic SRP1 induction, thereby demonstrating that ord1 is epistatic to yap1. Thus, Yap1 is not directly involved in SRP1 induction by hypoxia, but is necessary to counteract the Ord1 effect. [source] A novel mechanism for control of antigenic variation in the haemagglutinin gene family of Mycoplasma synoviaeMOLECULAR MICROBIOLOGY, Issue 4 2000A. H. Noormohammadi High-frequency phase and antigenic variation of homologous lipoprotein haemagglutinins has been seen in both the major avian mycoplasma pathogens, Mycoplasma synoviae and Mycoplasma gallisepticum. The expression and, hence, antigenic variation of the pMGA gene family (encoding these lipoproteins in M. gallisepticum) is controlled by variation in the length of a trinucleotide repeat motif 5, to the promoter of each gene. However, such a mechanism was not detected in preliminary observations on M. synoviae. Thus, the basis for control of variation in the vlhA gene family (which encodes the homologous haemagglutinin in M. synoviae) was investigated to enable comparison with its homologue in M. gallisepticum and with other lipoprotein gene families in mycoplasmas. The start point of transcription was identified 119 bp upstream of the initiation codon, but features associated with control of transcription in other mycoplasma lipoprotein genes were not seen. Comparison of three copies of vlhA revealed considerable sequence divergence at the 3, end of the gene, but conservation of the 5, end. Southern blot analysis of M. synoviae genomic DNA revealed that the promoter region and part of the conserved 5, coding sequence occurred as a single copy, whereas the remainder of the coding sequence occurred as multiple copies. A 9.7 kb fragment of the genome was found to contain eight tandemly repeated regions partially homologous to vlhA, all lacking the putative promoter region and the single-copy 5, end of vlhA, but extending over one of four distinct overlapping regions of the 3, coding sequence. Examination of sequential clones of M. synoviae established that unidirectional recombination occurs between the pseudogenes and the expressed vlhA, with duplication of pseudogene sequence and loss of the corresponding region previously seen in the expressed gene. Expression of the 5, end of two variants of the vlhA gene showed that they differed in their reaction with monoclonal antibodies specific for this region. These data suggest that the control of vlhA antigenic variation in M. synoviae is achieved by multiple gene conversion events using a repertoire of coding sequences to generate a chimeric expressed gene, with the greatest potential for variation generated in the region encoding the haemagglutinin. Thus, completely distinct mechanisms have been adopted to control antigenic variation in homologous gene families. [source] The transcription factor CREM, and cAMP regulate promoter activity of the Na,K-ATPase ,4 isoformMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 11 2006Marianna Rodova Abstract The Na,K-ATPase is an essential enzyme of the plasma membrane that plays a key role in numerous cell processes that depend on the transcellular gradients of Na+ and K+. Among the various isoforms of the catalytic subunit of the Na,K-ATPase, ,4 exhibits the most limited pattern of expression, being restricted to male germ cells. Activity of ,4 is essential for sperm function, and ,4 is upregulated during spermatogenesis. The present study addressed the transcriptional control of the human Na,K-ATPase ,4 gene, ATP1A4. We describe that a 5, untranslated region of the ATP1A4 gene (designated ,339/+480 based on the ATP1A4 transcription initiation site) has promoter activity in luciferase reporter assays. Computer analysis of this promoter region revealed consensus sites (CRE) for the cyclic AMP (cAMP) response element modulator (CREM). Accordingly, dibutyryl cAMP (db-cAMP) and ectopic expression of CREM,, a testis specific splice variant of CREM were able to activate the ATP1A4 promoter driven expression of luciferase in HEK 293 T, JEG-3 and GC-1 cells. Further characterization of the effect of db-cAMP and CREM, on deleted constructs of the ATP1A4 promoter (,339/+80, and +25/+480), and on the ,339/+480 region carrying mutations in the CRE sites showed that db-cAMP and CREM, effect required the CRE motif located 263 bp upstream the transcription initiation site. EMSA experiments confirmed the CRE sequence as a bonafide CREM, binding site. These results constitute the first demonstration of the transcriptional control of ATP1A4 gene expression by cAMP and by CREM,, a transcription factor essential for male germ cell gene expression. Mol. Reprod. Dev. 73: 1435,1447, 2006. © 2006 Wiley-Liss, Inc. [source] Roles of the conserved CCAAT and GC boxes of the human and mouse type II transforming growth factor-, receptor genesMOLECULAR REPRODUCTION & DEVELOPMENT, Issue 4 2003Cory T. Bernadt Abstract Embryonal carcinoma (EC) cells are used widely to study the molecular mechanisms that regulate the transcription of genes during mammalian embryogenesis. The type II transforming growth factor-, receptor (T,R-II) gene is expressed at very low levels by mouse EC cells prior to differentiation. Differentiation of EC cells results in increases of both the steady-state levels of T,R-II mRNA and the activity of the T,R-II promoter. Several cis -regulatory elements have been shown previously to regulate the T,R-II gene. This study focuses on the role of a CCAAT box and three GC boxes in the regulation of the human and mouse T,R-II promoters in EC-differentiated cells. We demonstrate that the CCAAT box and two flanking GC boxes, Sp A and Sp B, function as positive regulatory elements in the human T,R-II promoter, and that the transcription factor complex NF-Y positively regulates the human T,R-II promoter through the CCAAT box motif. We also show that the CCAAT box and the downstream GC box Sp B, which are conserved between the human and mouse promoters, behave as positive regulatory elements in the mouse T,R-II promoter. In addition, we demonstrate that the transcription factor Sp1 can bind to the Sp B GC box in vitro. Finally, we show that a GC box located 25 bp upstream of the major transcription start site of the T,R-II gene plays a minimal role in the function of the T,R-II promoter in EC-differentiated cells. Together, our studies highlight important differences and similarities in the cis -regulatory elements that regulate the human and mouse T,R-II promoters. Mol. Reprod. Dev. 65: 353,365, 2003. © 2003 Wiley-Liss, Inc. [source] Expression and promoter activity of the desiccation-specific Solanum tuberosum gene, StDS2PLANT CELL & ENVIRONMENT, Issue 9 2002R. Dóczi Abstract Environmental stresses induce the expression of several plant genes via multiple and cross-talking signalling pathways. Previously it was shown that ScDS2, a gene of the wild potato species, Solanum chacoense, is highly inducible by dehydration but not by abscisic acid (ABA), the mediator of many plant stress responses. Herein it is shown that ScDS2 -related genes are present in the cultivated potato, Solanum tuberosum (StDS2) and also in the non-tuberizing Solanum species, Solanum brevidens (SbDS2). We show that expression of StDS2 is dehydration-specific, is not inducible by cold, heat, salt, hypoxia or oxidative stresses, and is independent of ABA. Signalling of StDS2 induction, however, is dependent on the synthesis of novel proteins because cycloheximide can block StDS2 expression. To analyse the promoter region of StDS2 a genomic library of Solanum tuberosum was established and 1140 and 498 bp regions of the StDS2 promoter were isolated. The promoter fragments were fused to the , -glucuronidase (GUS) reporter gene and tested in transgenic potato plants. Both promoter fragments were able to induce GUS activity in response to dehydration. This result suggests that drought-specific cis -elements are located within 498 bp upstream to the StDS2 coding sequence. [source] Sequence and Intranuclear Location of the Extrachromosomal rDNA Plasmid of the Amoebo-Flagellate Naegleria gruberiTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2007SHINICHIRO MARUYAMA ABSTRACT. Several lower eukaryotic genomes have distinctive organization of rDNA on extrachromosomal molecules: the rDNAs of the amoebo-flagellate Naegleria gruberi (Heterolobosea) are encoded on an extrachromosomal circular plasmid. Although the presence of a circular rDNA plasmid in N. gruberi has now been accepted, its sequence and intracellular location are still unclear. We have now sequenced the entire 14,128 bp of the extrachromosomal circular rDNA plasmid. It contains a single rRNA gene unit composed of 18S, 5.8S, and 28S rRNA genes, but no tRNA or 5S RNA genes. We predict that there are two open reading frames. The region that flanks the rRNA gene unit is A/T-rich, except for a highly G/C-rich region that is approximately 900 bp upstream of the rRNA genes. Fluorescence in situ hybridization of N. gruberi cells revealed that the rDNA plasmids cluster within the nucleolus, suggesting that they are highly organized for the efficient transcription of rRNAs. The N. gruberi rDNA plasmid has a unique high-order cluster structure that provides both a molecular basis for understanding chromosomal organization in basal eukaryotes, and a vehicle for constructing stable transgenic vectors. [source] Identification of polymorphisms in the ovine Shadow of prion protein (SPRN) gene and assessment of their effect on promoter activity and susceptibility for classical scrapieANIMAL GENETICS, Issue 2 2010E. Lampo Summary Shadow of prion protein (SPRN) is an interesting candidate gene thought to be involved in prion pathogenesis. In humans, an association has already been discovered between mutations in SPRN and the incidence of variant and sporadic Creutzfeldt-Jakob disease. However, in sheep, the effect of mutations in SPRN is largely unknown. Therefore, we analysed the presence of mutations in the entire ovine SPRN gene, their association with scrapie susceptibility and their effect on SPRN promoter activity. In total, 26 mutations were found: seven in the promoter region, four in intron 1, seven in the coding sequence and eight in the 3, untranslated region. The mutations detected in the coding sequence and the promoter region were subsequently analysed in more detail. In the coding sequence, a polymorphism causing a deletion of two alanines was found to be associated with susceptibility for classical scrapie in sheep. Furthermore, a functional analysis of deletion constructs of the ovine SPRN promoter revealed that the region 464 to 230 bp upstream of exon 1 (containing a putative AP-2 and putative Sp1 binding sites) is of functional importance for SPRN transcription. Six mutations in the SPRN promoter were also found to alter the promoter activity in vitro. However, no association between any of these promoter mutations and susceptibility for classical scrapie was found. [source] Genomic structure, chromosomal localization and expression profile of a porcine long non-coding RNA isolated from long SAGE librariesANIMAL GENETICS, Issue 4 2009H. Ren Summary Long non-coding RNA (long ncRNA) is a novel class of ncRNA that may be involved in critical cellular processes. A considerable number of mammalian long ncRNAs have now been isolated but only a small number of these nucleic acids have been functionally well characterized. In this study, to determine the structure, regulation and function of long ncRNA in pigs, TncRNA was isolated from this mammal and its potential function during pig foetus development was identified. We anticipated that this would provide new insights into functional genomic studies in the pig. Using LongSAGE libraries generated from Chinese indigenous Tongcheng and Landrace pigs at three prenatal stages, a novel porcine long ncRNA was identified, TncRNA, which was found to be differentially expressed during myogenesis. The full-length cDNA for this gene is 3409 bp, and it harbours a typical polyadenylation signal sequence located 18 bp upstream from the 3, poly (A) tail. Genomic sequence analysis showed that pig TncRNA is alternatively spliced and several transcripts were detected. Using the INRA,University of Minnesota porcine radiation hybrid panel, TncRNA was assigned to SSC2 and found to be closely linked to the microsatellite marker SW256. Porcine TncRNA was found to be expressed in all tissues examined but in variable amounts. Comparisons between the expression profiles of TncRNA at different development stages in Tongcheng and Landrace pigs revealed up-regulation of this molecule in prenatal skeletal muscle, and differential expression in 90-day-old foetal skeletal muscle between these two pig breeds. This is the first report to describe a long ncRNA in pig. Moreover, the distinct expression pattern and structure of porcine TncRNA suggest that it performs complex and critical functions during foetal development. [source] Nucleotide diversity on the ovine Y chromosomeANIMAL GENETICS, Issue 5 2004J. R. S. Meadows Summary To investigate the impact of male-mediated introgression during the evolution of sheep breeds, a sequencing approach was used to identify single nucleotide polymorphisms (SNPs) from the male-specific region of the ovine Y chromosome (MSY). A total of 4380 bp, which comprised nine fragments from five MSY genes was sequenced within a panel of 14 males from seven breeds. Sequence alignment identified a single segregating site, an A/G SNP located approximately 1685 bp upstream of the ovine SRY gene. The resulting estimation of nucleotide diversity (,Y = 0.90 ± 0.50 × 10,4) falls towards the lower end of estimates from other species. This was compared with the nucleotide diversity estimated from the autosomal component of the genome. Sequence analysis of 2933 bp amplified from eight autosomal genes revealed a nucleotide diversity (,A = 2.15 ± 0.27 × 10,3) higher than previously reported for sheep. Following adjustment for the contrasting influence of effective population size and a male biased mutation rate, comparison revealed that approximately 10% of the expected nucleotide diversity is present on the ovine Y chromosome. [source] The modulator is a constitutive enhancer of a developmentally regulated sea urchin histone H2A geneBIOESSAYS, Issue 9 2002Giovanni Spinelli Going back to the late 1970s and early 1980s, we trace the Xenopus oocyte microinjection experiments that led to the emergence of the concept of "modulator". The finding that the modulator could transactivate transcription from far upstream and in either orientation suggested that a new genetic element, different from the classical prokaryotic promoter sequences, had been discovered. This particular enhancer transactivates transcription of the sea urchin early (,) histone H2A gene which is regulated in early sea urchin development. We summarise the data from sea urchin microinjection experiments that confirm and extend the results obtained with Xenopus oocytes. We conclude that the H2A enhancer is bipartite, is located approx. 100 bp upstream of the TATAAATA box in the H2A gene of two sea urchin species and enhances transcription when placed at a position far upstream or far downstream of the gene unless an insulator intervenes between enhancer and promoter. Evidence from microinjection experiments with sea urchin embryos suggests that the developmental control of H2A expression resides not with the enhancer, which is constitutively active, but with a striking chromatin structure with two positioned nucleosomes near the 3, end of the gene. Within this structure, there is an insulator element. BioEssays 24:850,857, 2002. © 2002 Wiley Periodicals, Inc. [source] The prevalence of, and molecular defects underlying, inherited protein S deficiency in the general populationBRITISH JOURNAL OF HAEMATOLOGY, Issue 5 2004Nicholas J. Beauchamp Summary The molecular basis of protein S (PS) deficiency was investigated in seven of eight donors identified with persistently low plasma PS levels from a survey of PS levels in 3788 Scottish blood donors. PROS1 gene analysis identified at least one defect in six donors. Five were heterozygous for the Heerlen polymorphism predicting a Ser460Pro substitution. Haplotype analysis revealed the possibility that this allele was inherited with the same haplotype in four of the five donors, suggesting a founder effect for the Heerlen allele in this population. One Heerlen allele carrier was also heterozygous for a 3 bp deletion 68,72 bp upstream of exon 2. Platelet PROS1 transcript analysis showed no reduction in mRNA expression from the affected allele in this donor. A T to G transversion 3 bp upstream of exon 12 was identified in one donor, which is predicted to reduce the efficiency of PS mRNA splicing. However, PROS1 transcript analysis showed no evidence of exon skipping or cryptic splicing. No PROS1 gene defect was detected in the remaining donor. This genetic information enabled us to refine our estimate of the prevalence of heritable PS deficiency in the Scottish population to between 0·16% and 0·21%, predominantly resulting from the presence of the Heerlen allele. [source] | |||||||||||||