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At least 469 records · Page 26Linked to original sources
PubMed2005

Disruption in the tropomodulin1 (Tmod1) gene compromises cardiomyocyte development in murine embryonic stem cells by arresting myofibril maturation.

Tropomodulins (Tmods) comprise a family of capping proteins for actin filament pointed ends. To decipher the significance of Tmod1 functions during de novo myofibrillogenesis, we generated Tmod1 null embryonic stem (ES) cells and studied their differentiation into cardiomyocytes. Strikingly, in vitro cardiomyocyte differentiation of wild type (WT) ES cells faithfully recapitulates in vivo cardiomyocyte differentiation, allowing us to evaluate the phenotypes of Tmod1 knockout (KO) myofibrils irrespective of embryonic lethality of Tmod1 KO mice. Immunofluorescence and electron microscopy studies revealed that Tmod1 null cardiac myocytes were round, morphologically immature, and contained underdeveloped myofibrils that were shorter, narrower, and had fewer thin filaments than those in WT cells. Unexpectedly, clear gaps in the staining pattern for F-actin at the H-zone were detected in most KO cells, indicating the presence of filaments at uniform lengths. This indicates that additional mechanisms other than capping proteins are responsible for thin filament length maintenance in cardiac myocytes. Also unexpectedly, approximately 40% of the KO cardiac myocytes exhibited contractile activity. Our data indicate that differentiating ES cells are a powerful system to investigate the functional properties of contractile proteins and that Tmod1 functions are critical for late stages of myofibrillogenesis, and for the maturation of myofibrils.

Animals↗
PubMed2005

The nanos translational control element represses translation in somatic cells by a Bearded box-like motif.

Developmental control of translation is frequently mediated by regulatory elements that reside within 3' untranslated regions (3' UTRs). Two stem-loops within the nanos 3' UTR translational control element (TCE) act independently to direct translational repression of maternal nanos mRNA in the ovary or embryo. We have previously shown that the nanos TCE can also function in select somatic sites. Using an ectopic expression screen, we now identify a new site of TCE function, the dorsal pouch epithelium. Analysis of TCE mutants reveals that TCE activity in the dorsal pouch does not depend on either of the stem-loops required for maternal TCE function, but instead requires a third feature-a sequence that closely matches the Bearded box, a regulatory motif found in the 3' UTRs of several Notch pathway genes. In addition, we identify pleiohomeotic mRNA as an endogenous candidate for regulation by Bearded box-like motifs in the dorsal pouch. Together, these results suggest that the TCE has appropriated a conserved regulatory motif to expand its function to somatic tissues.

3' Untranslated Regions↗
PubMed2005

The chitin synthase genes chs-1 and chs-2 are essential for C. elegans development and responsible for chitin deposition in the eggshell and pharynx, respectively.

It is widely accepted that chitin is present in nematodes. However, its precise role in embryogenesis is unclear and it is unknown if chitin is necessary in other nematode tissues. Here, we determined the roles of chitin and the two predicted chitin synthase genes in Caenorhabditis elegans by chitin localization and gene disruption. Using a novel probe, we detected chitin in the eggshell and discovered elaborate chitin localization patterns in the pharyngeal lumen walls. Chitin deposition in these two sites is likely regulated by the activities of chs-1 (T25G3.2) and chs-2 (F48A11.1), respectively. Reducing chs-1 gene activity by RNAi led to eggs that were fragile and permeable to small molecules, and in the most severe case, absence of embryonic cell division. Complete loss of function in a chs-1 deletion resulted in embryos that lacked chitin in their eggshells and failed to divide. These results showed that eggshell chitin provides both mechanical support and chemical impermeability essential to developing embryos. Knocking down chs-2 by RNAi caused a defect in the pharynx and led to L1 larval arrest, indicating that chitin is involved in the development and function of the pharynx.

Animals↗
PubMed2004

Topology of genes and nontranscribed sequences in human interphase nuclei.

Knowledge about the functional impact of the topological organization of DNA sequences within interphase chromosome territories is still sparse. Of the few analyzed single copy genomic DNA sequences, the majority had been found to localize preferentially at the chromosome periphery or to loop out from chromosome territories. By means of dual-color fluorescence in situ hybridization (FISH), immunolabeling, confocal microscopy, and three-dimensional (3D) image analysis, we analyzed the intraterritorial and nuclear localization of 10 genomic fragments of different sequence classes in four different human cell types. The localization of three muscle-specific genes FLNA, NEB, and TTN, the oncogene BCL2, the tumor suppressor gene MADH4, and five putatively nontranscribed genomic sequences was predominantly in the periphery of the respective chromosome territories, independent from transcriptional status and from GC content. In interphase nuclei, the noncoding sequences were only rarely found associated with heterochromatic sites marked by the satellite III DNA D1Z1 or clusters of mammalian heterochromatin proteins (HP1alpha, HP1beta, HP1gamma). However, the nontranscribed sequences were found predominantly at the nuclear periphery or at the nucleoli, whereas genes tended to localize on chromosome surfaces exposed to the nuclear interior.

Base Sequence↗
PubMed2005

Characterization of turkey and chicken ghrelin genes, and regulation of ghrelin and ghrelin receptor mRNA levels in broiler chickens.

Ghrelin, a peptide hormone produced by the stomach in mammals, stimulates growth hormone release and food intake. Recently, ghrelin was identified and characterized in chicken proventriculus and shown to stimulate growth hormone release but inhibit feed intake. The purpose of this work was to identify and further characterize the ghrelin gene in chickens and in turkeys. Using molecular cloning techniques we have sequenced cDNAs corresponding to chicken (White Leghorn) and turkey ghrelin mRNAs. A total of 844 (chicken) or 869 (turkey) bases including the complete coding regions (CDS), and the 5'- and 3'-untranslated regions (UTRs) were determined. Nucleotide sequence (CDS) predicted a 116 amino acid precursor protein (preproghrelin) for both the chicken and the turkey that demonstrated complete conservation of an N-terminal 'active core' (GSSF) including a serine (position 3 of the mature hormone) known to be a modification (acylation) site important for ghrelin bioactivity. Additional nucleotide sequence was found in the 5'-UTRs of both Leghorn and turkey cDNAs that was not present in broilers or the red jungle fowl. The turkey ghrelin gene, sequenced from genomic DNA templates, contained five exons and four introns, a structure similar to mammalian and chicken ghrelin genes. Ghrelin was highly expressed in proventriculus with much lower levels of expression in other tissues such as pancreas, brain, and intestine. RT-PCR was used to quantify ghrelin mRNA levels relative to 18S rRNA in 3-week-old male broiler chickens. The level of ghrelin mRNA increased in proventriculus in response to fasting but did not decline with subsequent refeeding. Plasma ghrelin levels did not change significantly in response to fasting or refeeding and did not appear to reflect changes in proventriculus ghrelin mRNA levels. Ghrelin mRNA levels declined in broiler pancreas after a 48 h fast and increased upon refeeding. Expression of the gene encoding the receptor for ghrelin (growth hormone secretagogue receptor, GHS-R) and a variant form was detected in a variety of tissues collected from 3-week-old male broiler chickens possibly suggesting autocrine/paracrine effects. These results offer new information about the avian ghrelin and ghrelin receptor genes and the potential role that this system might play in regulating feed intake and energy balance in poultry.

Amino Acid Sequence↗
PubMed2004

Analysis of the human VPS13 gene family.

The gene mutated in chorea-acanthocytosis (CHAC; approved gene symbol VPS13A) encodes chorein, a protein similar to yeast Vps13p. We detected several similar putative human proteins by BLAST analysis of chorein. We characterized the structure of three new genes encoding these CHAC-similar proteins, located on chromosomes 1p36, 8q22, and 15q21. The most similar gene in yeast to all four human genes is Vps13, and therefore the human genes were named VPS13A (CHAC, 9q21), VPS13B (8q22), VPS13C (15q21), and VPS13D (1p36). VPS13B has recently been reported as COH1, altered in Cohen syndrome. For each gene, we describe several alternative splicing variants; at least two transcripts per gene are major forms. The expression pattern of these genes is ubiquitous, with some tissue-specific differences between several transcript variants. Protein sequence comparisons suggest that intramolecular duplications have played an important role in the evolution of this gene family.

Alternative Splicing↗
PubMed2004

Cloning, genomic structure, and expression profiles of TULIP1 (GARNL1), a brain-expressed candidate gene for 14q13-linked neurological phenotypes, and its murine homologue.

Previously, we have described the clinical and molecular characterization of a de novo 14q13.1-q21.1 microdeletion, less than 3.5 Mb in size, in a patient with severe microcephaly, psychomotor retardation, and other clinical anomalies. Here we report the characterization of the genomic structure of the human tuberin-like protein gene 1 (TULIP1; approved gene symbol GARNL1), a CpGisland-associated, brain-expressed candidate gene for the neurological findings in our patient, and its murine homologue. The human TULIP1 gene was mapped to chromosome band 14q13.2 by fluorescence in situ hybridization of BAC clone RP11-355C3 (GenBank Accession No. AL160231), containing the 3' region of the gene. TULIP1 spans about 271 kb of human genomic DNA and is divided into 41 exons. An untranscribed, processed pseudogene of TULIP1 was found on human chromosome band 9q31.1. The active locus TULIP1, encoding a predicted protein of 2036 amino acids, is expressed ubiquitously in pre- and postnatal human tissues. The murine homologue Tulip1 spans about 220 kb of mouse genomic DNA and is also divided into 41 exons, encoding a predicted protein of 2035 amino acids. No pseudogene could be found in the available mouse sequence data. Several splicing variants were found. Considering the location, expression profile, and predicted function, TULIP1 is a strong candidate for several neurological features seen in 14q deletion patients. Additionally we searched for mutations in the coding region of TULIP1 in subjects from a family with idiopathic basal ganglia calcification (IBGC; Fahr disease), previously linked to chromosome 14q. We identified two novel SNPs in the intron-exon boundaries; however, they did not segregate only with affected subjects in the predicted model of an autosomal dominant disease such as IBGC.

Amino Acid Sequence↗
PubMed2005

Molecular cloning and functional characterization of mouse Nxf family gene products.

Tap, a member of the evolutionarily conserved nuclear RNA export factor (NXF) family of proteins, has been implicated in the nuclear export of bulk poly(A)+ RNAs. cDNAs encoding the mouse NXF proteins (Tap, NXF7, NXF2, and NXF3) were prepared and the gene products were characterized in terms of their genomic organization, expression patterns, and biochemical properties. Mouse Tap was found to be ubiquitously expressed, whereas tissue- and developmental stage specific expression of mouse Nxf2, Nxf3, and Nxf7 was observed. Although mouse Tap and NXF2 bound to the phenylalanine-glycine repeat sequences of nucleoporins, NXF7 and NXF3 did not. GFP-tagged mouse Tap and NXF2 were localized predominantly in the nucleus. In contrast, GFP-tagged NXF7 and NXF3 were localized exclusively in the cytoplasm. As shown for the human counterpart, disruption of the leucine-rich nuclear export signal or leptomycin B treatment abolishes the cytoplasmic localization of mouse NXF3. p15/NXT1, an essential cofactor for human Tap in the export of mRNAs, was able to bind to mouse Tap, NXF2, and NXF3, but NXF7 did not form a stable heterodimeric complex. Transient transfection experiments indicated that only mouse Tap and NXF2 enhance the nuclear export of an otherwise inefficiently exported mRNA substrate. The orthologous relationship between human and mouse Nxf genes is discussed on the basis of these data.

Amino Acid Sequence↗
PubMed2004

Chimeric CYP21P/CYP21 and TNXA/TNXB genes in the RCCX module.

Two types of chimeric RCCX modules found in chromosome 6p21.3 are the chimeras CYP21P/CYP21 and TNXA/TNXB. The CYP21P-specific sequence of chimera CYP21P/CYP21 has the 5'-end in common, but differs in the 3'-end of CYP21-specific genes. The sequence organization of the gene array is C4A-CYP21P/CYP21-TNXB, whereas chimera TNXA/TNXB is caused by a CYP21 deletion, and a partial TNXB replaced by the TNXA gene shows the C4A-CYP21P-TNXA/TNXB sequence. Therefore, chimeras CYP21P/CYP21 and TNXA/TNXB are two distinct hybrid genes produced in the RCCX module in HLA class III. In addition, the haplotype of CYP21 with chimera CYP21P/CYP21 causes 21-hydroxylase deficiency in congenital adrenal hyperplasia (CAH), while chimera TNXA/TNXB is associated with Ehlers-Danols syndrome as well as CAH.

Adrenal Hyperplasia, Congenital↗
PubMed2004

Viburnum phylogeny: evidence from the duplicated nuclear gene GBSSI.

DNA sequencing studies of the granule-bound starch synthase gene (GBSSI) indicate the presence of two loci in Viburnum. Gene trees from separate and combined phylogenetic analyses of the GBSSI paralogues are generally congruent with each other and with trees from previous analyses, especially those of Donoghue et al. [Syst. Bot. 29 (2004) 188] based on nuclear ribosomal ITS and chloroplast trnK intron DNA sequences. Specifically, our GBSSI trees confirm (i) the monophyly of some and non-monophyly of other traditionally recognized taxonomic sections, (ii) the presence of three major supra-sectional lineages within Viburnum, and (iii) the resolution of many species relationships within the section-level clades. Analyses of GBSSI also provide greater resolution of relationships within the largest supra-sectional lineage. Relationships at the base of the Viburnum phylogeny remain uncertain; in particular, the position of the root, relationships among the supra-sectional clades, and the exact placement of several smaller groups (e.g., Viburnum clemensiae, Viburnum urceolatum, and section Pseudotinus). In two lineages each GBSSI paralogue is represented by two distinct sequences. The presence of additional copies appears to be correlated with polyploidy in these clades. Placement of the homoeologues in our gene trees suggests the possibility of a hybrid origin for these polyploids.

Base Sequence↗
PubMed2002

Human peptidylarginine deiminase type II: molecular cloning, gene organization, and expression in human skin.

Peptidylarginine deiminases (PADs) are posttranslational modification enzymes that convert protein arginine to citrulline residues in a calcium ion-dependent manner. Rodents have four isoforms of PAD (types I, II, III, and IV), each of which is distinct in substrate and tissue specificity. In fact, the only tissue in which all four PAD mRNAs have been detected is the epidermis. In this study, we found PAD activity in HSC-1 human cutaneous squamous carcinoma cells in vitro, and this activity increased during cultivation. Using a homology-based strategy, we cloned a full-length cDNA encoding human PAD type II. The cDNA was 2348 bp long and encoded a 665-amino-acid sequence with a predicted molecular mass of 75 kDa. The predicted protein shared 93% identity with the rat and mouse PAD type II sequence. Alignment of the amino acid sequences from both species revealed notable conservation in the C-terminal region, suggesting the presence of a functional region such as an enzyme catalytic site and/or a calcium-binding domain. Gene organization analysis established that human PAD type II on chromosome 1p35.2-p35.21 spanned more than 50 kb and contained 16 exons and 15 introns. A recombinant PAD protein subsequently produced in Escherichia coli proved to be enzymatically active, with substrate specificities similar to those of the rat PAD type II. In an immunohistochemical study of human skin, the type II enzyme was expressed by all the living epidermal layers, suggesting that PAD type II is functionally important during terminal differentiation of epidermal keratinocytes.

Amino Acid Sequence↗
PubMed2003

Genomic structure, expression, and transcriptional regulation of human Gal beta 1,3 GalNAc alpha 2,3-sialyltransferase gene.

In this report, we describe transcriptional regulation of the human Gal beta 1,3 GalNAc alpha 2,3-sialyltransferase II (hST3Gal II) gene. The results of 5'-RACE showed that the forms of two mRNAs differed only in the 5'-untranslated region (Types 1 and 2). According to analysis of the genomic structure, the transcriptional regulation of Type 1 and Type 2 mRNA isoforms depended on the p1 and p2 promoters, respectively. Both the mRNA isoforms were detected in various human tissues except colon, skeletal muscle, and peripheral blood leukocytes by RT-PCR analysis. In colon tissue, the Type 2 mRNA was detected, however, Type 1 mRNA was not detected. To elucidate the molecular basis of hST3Gal II gene expression, we isolated and characterized the function of the genomic region of hST3Gal II containing the p1 and p2 promoters. The activity of p2 promoter is much higher than that of the p1 promoter in the colon adenocarcinoma cell line, COLO205. These results suggest that the hST3Gal II gene is expressed specifically by alternative promoter utilization and is regulated in a tissue-restricted fashion at the level of transcription.

5' Flanking Region↗
PubMed2003

Ghrelin gene in cichlid fish is modulated by sex and development.

We have identified the complementary and genomic DNA sequences of the novel growth hormone-releasing peptide, ghrelin, in the cichlid fish (tilapia Oreochromis niloticus). The tilapia ghrelin precursor cDNA was 855 bp long, consisting of 119 bp of 5(')-untranslated region, 324 bp open reading frame, and 412 bp of 3(')-untranslated region. The serine residues at positions 2 and 3 of the "active core" (GSSF) of the ghrelin mature peptide are conserved between tilapia and the mammalian species. The tilapia ghrelin gene has four exons and three introns and resembles the structure of other known ghrelin genes. RT-PCR analysis revealed ghrelin mRNA predominantly expressed in the stomach but absent in the brain, pituitary, heart, kidney, ovary, and testis. Real-time PCR analysis showed an age/body size dependent increase in gastric ghrelin, which stagnated at 7 cm body size (onset of maturation). Ghrelin mRNA levels were unchanged in food-deprived sexually mature animals but were significantly higher in females compared to males. The present study shows that the structure of ghrelin peptide is highly conserved, and the reported differences in somatic and gonadal growth in tilapia could be a consequence of age- and sex-related synthesis of gastric ghrelin.

Age Factors↗
PubMed2002

Involvement of in vivo induced cheY-4 gene of Vibrio cholerae in motility, early adherence to intestinal epithelial cells and regulation of virulence factors.

Using a global transcription profile approach cheY-4 of Vibrio cholerae was identified as an in vivo induced gene. In the present study, duplication of the gene in the chromosome resulted in increased motility, increased chemotactic response towards isolated intestinal mucus layer and stronger adhesion to human intestinal epithelial cell line at an early phase of infection compared to wild type and a null mutant strain. In contrast to the cheY-4 null mutant, duplication of cheY-4 gene resulted in increased expression of ctxAB and tcpA, the two major virulence genes of V. cholerae.

Animals↗
PubMed2003

Comparative analysis of mouse hepcidin 1 and 2 genes: evidence for different patterns of expression and co-inducibility during iron overload.

In contrast to the human genome, the mouse genome contains two HEPC genes encoding hepcidin, a key regulator of iron homeostasis. Here we report a comparative analysis of sequence, genomic structure, expression and iron regulation of mouse HEPC genes. The predicted processed 25 amino acid hepcidin 2 peptide share 68% identity with hepcidin 1 with perfect conservation of eight cysteine residues. Both HEPC1 and HEPC2 genes have similar genomic organization and have probably arisen from a recent duplication of chromosome 7 region, including the HEPC ancestral gene and a part of the adjacent USF2 gene. Insertion of a retroviral intracisternal A-particle element was found upstream of the HEPC1 gene. Both genes are highly expressed in the liver and to a much lesser extent in the heart. In contrast to HEPC1, a high amount of HEPC2 transcripts was detected in the pancreas. Expression of both genes was increased in the liver during carbonyl-iron and iron-dextran overload. Overall our data suggest that both HEPC1 and HEPC2 genes are involved in iron metabolism regulation but could exhibit different activities and/or play distinct roles.

Amino Acid Sequence↗
PubMed2003

Genomic organization and transcription of the human retinol dehydrogenase 10 (RDH10) gene.

A cDNA clone up-regulated in hydraulic lung edema in rabbit showed high similarity with human RDH10 mRNA, which encodes a protein involved in retinoic acid metabolism. We defined the organization of the human gene, which includes a unique transcriptional start site, a coding region with six translated exons and a 3' untranslated region containing at least two used polyadenylation sites. The two poly(A) signals are responsible for the production of the 3 and 4 kb RDH10 mRNA isoforms detected in several human tissues and cell lines.

3' Untranslated Regions↗
PubMed2003

The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts.

We report the complete sequence of the mitochondrial genome of Penicillium marneffei, the first complete mitochondrial DNA sequence of a thermal dimorphic fungus. This 35 kb mitochondrial genome contains the genes encoding ATP synthase subunits 6, 8, and 9 (atp6, atp8, and atp9), cytochrome oxidase subunits I, II, and III (cox1, cox2, and cox3), apocytochrome b (cob), reduced nicotinamide adenine dinucleotide ubiquinone oxireductase subunits (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), ribosomal protein of the small ribosomal subunit (rps), 28 tRNAs, and small and large ribosomal RNAs. Analysis of gene contents, gene orders, and gene sequences revealed that the mitochondrial genome of P. marneffei is more closely related to those of molds than yeasts.

Base Sequence↗
PubMed2005

Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences.

V(D)J recombination is the process by which the variable region exons encoding the antigen recognition sites of receptors expressed on B and T lymphocytes are generated during early development via somatic assembly of component gene segments. In response to antigen, somatic hypermutation (SHM) and class switch recombination (CSR) induce further modifications of immunoglobulin genes in B cells. CSR changes the IgH constant region for an alternate set that confers distinct antibody effector functions. SHM introduces mutations, at a high rate, into variable region exons, ultimately allowing affinity maturation. All of these genomic alteration processes require tight regulatory control mechanisms, both to ensure development of a normal immune system and to prevent potentially oncogenic processes, such as translocations, caused by errors in the recombination/mutation processes. In this regard, transcription of substrate sequences plays a significant role in target specificity, and transcription is mechanistically coupled to CSR and SHM. However, there are many mechanistic differences in these reactions. V(D)J recombination proceeds via precise DNA cleavage initiated by the RAG proteins at short conserved signal sequences, whereas CSR and SHM are initiated over large target regions via activation-induced cytidine deaminase (AID)-mediated DNA deamination of transcribed target DNA. Yet, new evidence suggests that AID cofactors may help provide an additional layer of specificity for both SHM and CSR. Whereas repair of RAG-induced double-strand breaks (DSBs) involves the general nonhomologous end-joining DNA repair pathway, and CSR also depends on at least some of these factors, CSR requires induction of certain general DSB response factors, whereas V(D)J recombination does not. In this review, we compare and contrast V(D)J recombination and CSR, with particular emphasis on the role of the initiating enzymes and DNA repair proteins in these processes.

Animals↗