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PubMed1998

Global regulation by the small RNA-binding protein CsrA and the non-coding RNA molecule CsrB.

Csr (carbon storage regulator) is a recently discovered global regulatory system that controls bacterial gene expression post-transcriptionally. Its effector is a small RNA-binding protein referred to as CsrA or, in phytopathogenic Erwinia species, RsmA (repressor of stationary phase metabolites). Numerous genes whose expression occurs in the stationary phase of growth are repressed by csrA/rsmA, and csrA activates certain exponential-phase metabolic pathways. Glycogen synthesis and catabolism, gluconeogenesis, glycolysis, motility, cell surface properties and adherence are modulated by csrA in Escherichia coli, while the production of several secreted virulence factors, the plant hypersensitive response elicitor HrpN(Ecc) and, potentially, other secondary metabolites are regulated by rsmA in Erwinia carotovora. CsrA represses glycogen synthesis by binding to and destabilizing glgCAP mRNA and is hypothesized to repress other genes by a similar mechanism. The second component of the Csr system is CsrB (AepH in Erwinia species), a non-coding RNA molecule that forms a large globular ribonucleoprotein complex with approximately 18 CsrA subunits and antagonizes the effects of CsrA in vivo. Highly repeated sequence elements found within the loops of predicted stem-loops and other single-stranded segments of CsrB RNA may facilitate CsrA binding. Current information supports a model in which CsrA exists in an equilibrium between CsrB and CsrA-regulated mRNAs, which predicts that CsrB levels may be a key determinant of CsrA activity in the cell. The presence of csrA homologues in phylogenetically diverse species further suggests that this novel kind of regulatory system is likely to play a broad role in modulating eubacterial gene expression.

Amino Acid Sequence↗
PubMed2000

Characterization of two novel regulatory genes affecting Salmonella invasion gene expression.

A Salmonella typhimurium chromosomal deletion removing approximately 19 kb of DNA at centisome 65 reduces invasion of cultured epithelial cells as well as the expression of lacZY operon fusions to several genes required for the invasive phenotype. As the deleted region contains no genes previously known to affect Salmonella invasion, we investigated the roles of individual genes in the deleted region using a combination of cloning, complementation and directed mutation. We find that the deletion includes two unrelated regulatory genes. One is the Salmonella homologue of Escherichia coli barA (airS ), which encodes a member of the multistep phosphorelay subgroup of two-component sensor kinases. The action of BarA is coupled to that of SirA, a member of the phosphorylated response regulator family of proteins, and includes both HilA-dependent and HilA-independent components. The other regulatory gene removed by the deletion is the Salmonella homologue of E. coli csrB, which specifies a regulatory RNA implicated in controlling specific message turnover in E. coli. These results identify a protein that is likely to play a key role in the environmental control of Salmonella invasion gene expression, and they also suggest that transcriptional control of invasion genes could be subject to refinement at the level of message turnover.

Bacterial Proteins↗
PubMed1999

Rice ENOD40: isolation and expression analysis in rice and transgenic soybean root nodules.

The early nodulin ENOD40 has been proposed as playing a pivotal role in the organogenesis of legume root nodules. We have isolated the ENOD40 gene homologues ObENOD40 and OsENOD40 from the wild and cultivated rice genotypes Oryza brachyantha and Oryza sativa, respectively. Rice ENOD40s contain a sequence at the 5' end (region I) for encoding an oligopeptide that is highly conserved in all legume ENOD40s. Furthermore, at the 3' end (region II), the nucleotide sequence of rice ENOD40s exhibited a considerable homology to the corresponding region in legume ENOD40s. Among various organs of the rice plant, expression of OsENOD40 was detected only in stems. In situ hybridization studies revealed that, within the stem, transcription of OsENOD40 is confined to parenchyma cells surrounding the protoxylem during the early stages of development of lateral vascular bundles that conjoin an emerging leaf. Expression pattern of OsENOD40 promoter-GUS fusion in nodules developed on transgenic hairy roots of soybean was also found to be restricted to peripheral cells of nodule vascular bundles, thus evidencing that rice ENOD40 promoter activity is essentially the same as that of soybean ENOD40. Taken together, these results strongly suggest that OsENOD40 and legume ENOD40s share common, if not identical, functions in differentiation and/or function of vascular bundles.

Amino Acid Sequence↗
PubMed1996

Expression of H19 and Igf2 genes in uniparental mouse ES cells during in vitro and in vivo differentiation.

Genomic imprinting is a process that results in the differential expression of genes according to their parental inheritance. Two imprinted genes, insulin-like growth factor 2 (Igf2) and H19 are closely linked on mouse chromosome 7, and are expressed from the paternal and maternal alleles, respectively. The genes show striking similarity in their tissue-specific expression patterns, which led to the proposal that their transcription is controlled by a common regulatory domain that enables only one gene to be active from each chromosome. Evidence is accumulating, however, that the expression of H19 and Igf2 genes is not always from their respective maternal and paternal alleles. This suggests that their expression is regulated independently of imprinting in some tissues and teratomas. We have analysed the extent of non-imprinted expression of H19 and Igf2 in uniparental mouse embryonic stem (ES) cells during in vitro differentiation, and differentiation in teratomas using Northern blot and in situ hybridisation analysis. The expression patterns observed indicate that both imprinting and non-imprinting mechanisms regulate transcription of these genes. Expression of one or the other gene was observed in certain cell types in differentiated cultures and in teratomas, suggesting that imprinting regulates the expression of H19 and Igf2 genes in some differentiating cell lineages. At the same time, in other subpopulations of cells, co-expression of both genes was observed, demonstrating that the expression of these genes is not always regulated by genomic imprinting.

Animals↗
PubMed2002

Xist expression and macroH2A1.2 localisation in mouse primordial and pluripotent embryonic germ cells.

The molecular mechanism underlying X chromosome inactivation in female mammals involves the non-coding RNAs Xist and its antisense partner Tsix. Prior to X inactivation, these RNAs are transcribed in an unstable form from all X chromosomes, both in the early embryo and in undifferentiated embryonic stem (ES) cells. Upon differentiation, the expression of these unstable transcripts from all alleles is silenced, and Xist RNA becomes stabilised specifically on the inactivating X chromosome. This pattern of expression is then maintained throughout subsequent somatic cell divisions. Once established, the inactive state of the X chromosome is remarkably stable, the only natural case of reactivation occurring in XX primordial germ cells (PGCs) when they enter the genital ridge. To gain insight into the X reactivation process, we have analysed Xist gene expression using RNA FISH in PGCs and also in PGC-derived embryonic germ (EG) cells. XX EG cells were shown to express unstable Xist/Tsix from both X chromosomes. In contrast, no unstable Xist/Tsix transcripts were detected in XX PGCs at any stage. Instead, a proportion of XX PGCs isolated from the genital ridge between 11.5 and 13.5 dpc (the period during which X chromosome reactivation occurs) showed an accumulation of stable Xist RNA on one X. The number of these cells decreased progressively and was nearly extinguished by 13.5 dpc. As a late marker for the inactive state, we analysed localisation of the histone H2A variant macroH2A1.2. Although macroH2A1.2 expression was observed in PGCs, no significant localisation to the inactive X was detected at any stage. We discuss these results in the context of understanding X chromosome reactivation.

Animals↗
PubMed2000

H19 sense and antisense transgenes modify insulin-like growth factor-II mRNA levels.

The oppositely-imprinted genes insulin-like growth factor-II (IGF2) and H19, a putative tumor suppressor, often show coordinate, reciprocal regulation and are believed to play a role in carcinogenesis. To explore the possible interactions between these genes, we stably transfected diHepG2 cells with a plasmid containing either the sense or the antisense H19 cDNA sequences and verified their expression by Northern analysis and by RNase protection analysis. Levels of H19, IGF2 and gamma-actin mRNA were quantified by competitive RT-PCR analysis. Although H19 sense transgene overexpression (n = 24 clones) did not decrease the low, basal levels of IGF2 mRNA compared to control cells, levels of IGF2 mRNA were positively correlated with the levels of H19 antisense mRNA (P < 0.0001, n = 40 clones). Furthermore, the increase in IGF2 mRNA level was accompanied by an elevation of IGF-II peptide in conditioned media. To see if H19 mRNA had a specific effect on transcription, we also performed transient transfections with reporter gene constructs containing IGF2 promoter 3 in the presence of sense or antisense H19 cDNA sequences under control of a cytomegalovirus promoter. We show a lower reporter gene activity from reporter gene constructs in the presence of sense H19 cDNA than from those with antisense or neomycin. Our results suggest that H19 participates in the repression of IGF2, at least in part through effects on IGF2 transcription, an effect which may contribute to its action as a tumor suppressor.

Actins↗
PubMed2000

The single-stranded DNA- and RNA-binding proteins pur alpha and pur beta link BC1 RNA to microtubules through binding to the dendrite-targeting RNA motifs.

Neural BC1 RNA is distributed in neuronal dendrites as RNA-protein complexes (BC1 RNPs) containing Translin. In this study, we demonstrated that the single-stranded DNA- and RNA-binding protein pur alpha and its isoform, pur beta, which have been implicated in control of DNA replication and transcription, linked BC1 RNA to microtubules (MTs). The binding site was within the 5' proximal region of BC1 RNA containing putative dendrite-targeting RNA motifs rich in G and U residues, suggesting that in the cytoplasm of neurons, these nuclear factors are involved in the BC1 RNA transport along dendritic MTs. The pur proteins were not components of BC1 RNP but appeared to associate with MTs in brain cells. Therefore, it is suggested that they may transiently interact with the RNP during transport. In this respect, the interaction of pur proteins with BC1 RNA could be regulated by the Translin present within the RNP, because the binding mode of these two classes of proteins (pur proteins and Translin) to the dendrite-targeting RNA motifs was mutually exclusive. As the motifs are well conserved in microtubule-associated protein 2a/b mRNA as well, the pur proteins may also play a role(s) in the dendritic transport of a subset of mRNAs.

Animals↗
PubMed2003

Imprinted mesodermal specific transcript (MEST) and H19 genes in renal development and diabetes.

BACKGROUND: Imprinted genes, mesodermal specific cDNA or transcript (MEST) and H19, are implicated in peri-implantation embryogenesis, and their expression was assessed in embryonic kidneys undergoing glucose-induced dysmorphogenesis. METHODS: MEST and H19 mRNA expression was assessed by Northern blot analysis in embryonic kidneys of mice harvested at day 15 to day 19 of gestation and of 1-week-old mice obtained from hyperglycemic mothers. A full-length mouse MEST cDNA was isolated, subcloned into an expression vector, a recombinant protein prepared and an antibody raised; the latter was used to assess protein expression by immunoprecipitation and immunofluorescence microscopy in day 13 metanephric explants subjected to high glucose ambience. Also, MEST mRNA expression was assessed in high d glucose-treated explants by competitive reverse transcription-polymerase chain reaction (RT-PCR) analyses and by in situ tissue autoradiography. RESULTS: A high expression of MEST and H19 with respective transcript size of approximately 2.7 and approximately 2.4 kb was observed in fetal kidneys, and their expression decreased during the successive stages of gestation and was undetectable in the postnatal period. At day 13, the MEST mRNA was expressed in the mesenchyme, while H19 was expressed in the ureteric bud branches and epithelial elements of the metanephros. Their expression decreased with progression of gestation. By competitive RT-PCR and Northern blot and in situ autoradiographic analyses, both MEST and H19 expressions decreased in day 13 explants treated with high glucose and in the kidneys of fetuses obtained from diabetic mothers. The MEST protein expression was observed in the metanephric epithelial elements and ureteric bud branches instead of in the mesenchyme, and its expression decreased in glucose-treated dysmorphogenetic explants, as assessed by immunofluorescence and immunoprecipitation methods. CONCLUSION: MEST and H19 imprinted genes are strategically located in the mammalian embryonic metanephros. They are developmentally regulated and their concomitant decreased expression in high glucose ambience or diabetic state did not follow the prevailing dogma of reciprocal inactivation/activation of imprinted genes, and such a decrease may be responsible for the perturbed epithelial:mesenchymal interactions leading to dysmorphogenesis of the mammalian metanephros.

Animals↗
PubMed2004

Analysis of trinucleotide repeats in different SCA loci in spinocerebellar ataxia patients and in normal population of Taiwan.

OBJECTIVE: To identify various subtypes of spinocerebellar ataxias (SCAs) among autosomal dominant cerebellar ataxia (ADCA) patients referred to our research center, SCA1, SCA2, SCA3/MJD (Machado-Joseph disease), SCA6, SCA7, SCA8 and SCA12 loci were assessed for expansion of trinucleotide repeats. PATIENTS AND METHODS: A total of 211 ADCA patients, including 202 patients with dominantly inherited ataxia from 81 Taiwanese families and nine patients with sporadic ataxia, were included in this study and subjected to polymerase chain reaction (PCR) analysis. The amplified products of all loci were analyzed on both 3% agarose gels and 6% denaturing urea-polyacrylamide gels. PCR-based Southern blots were also applied for the detection of SCA7 locus. RESULTS: The SCA1 mutation was detected in six affected individuals from one family (1.2%) with expanded alleles of 50-53 CAG repeats. Fourteen individuals from nine families (11%) had a CAG trinucleotide repeat expansion at the SCA2 locus, while affected SCA2 alleles have 34-49 CAG repeats. The SCA3/MJD CAG trinucleotide repeat expansion in 60 affected individuals from 26 families (32%) was expanded to 71-85 CAG repeats. As for the SCA7 locus, there were two affected individuals from one family (1.2%) possessed 41 and 100 CAG repeats, respectively. However, we did not detect expansion in the SCA6, SCA8 and SCA12 loci in any patient. CONCLUSIONS: The SCA3/MJD CAG expansion was the most frequent mutation among the SCA patients. The relative prevalence of SCA3/MJD in Taiwan was higher than that of SCA2, SCA1 and SCA7.

Adolescent↗
PubMed2000

H19 and IGF-2 allele-specific expression in hepatoblastoma.

Patterns of allele-specific expression of H19 and insulin-like growth factor-2 (IGF-2) were examined in tissue obtained from 30 children diagnosed with hepatoblastoma. All informative tumours demonstrated monoallelic expression of H19. In contrast, variable patterns of allele-specific expression of IGF-2 were seen in tumours from children of different ages.

Alleles↗
PubMed2000

Altered expression of members of the IGF-axis in hepatoblastomas.

Previous reports have demonstrated that expression of insulin-like growth factor 2 (IGF2) is altered in hepatoblastoma. Using RNAase protection analysis (RPA), we examined the gene expression for IGF1, IGF2, IGF1R, M6P/IGF2R, IGFBP-1 and IGFBP-2 in a series of hepatoblastomas with corresponding normal liver from the same individuals. The results show that the expression of the IGF-axis members included in the present study are altered between tumour and normal, and indicate that the IGF-axis may be involved in hepatoblastoma development.

Genes, Tumor Suppressor↗
PubMed2000

Decreased expression of p57(KIP2)mRNA in human bladder cancer.

To identify targets of genetic and epigenetic alterations on chromosome 11p15.5 in human bladder cancer, expression of the imprinted KIP2, IGF2 and H19 genes was studied by quantitative RT-PCR in 24 paired samples of urothelial carcinomas and morphologically normal mucosa obtained by cystectomy, and in bladder carcinoma cell lines. The most frequent alteration in tumour tissue was decreased expression of KIP2 identified in 9/24 (37%) specimens. Decreased IGF2 and H19 mRNA levels were found in five (21%) and three (13%) tumours, respectively. One tumour each overexpressed IGF2 and H19. Loss of H19 expression was only found associated with loss of KIP2 expression, whereas decreased expression of IGF2 mRNA occurred independently. Almost all bladder carcinoma cell lines showed significant changes in the expression of at least one gene with diminished expression of KIP2 mRNA as the most frequent alteration. IGF2 mRNA levels were diminished in several lines, but increased in others. The KIP2 gene could be an important target of genetic and epigenetic alterations in bladder cancer affecting the maternal chromosome 11p15.5. However, reminiscent of the situation in Wilms' tumours, expression of the IGF2 gene on the paternal chromosome can also be disturbed in bladder cancers.

Aged↗
PubMed2001

hTR repressor-related gene on human chromosome 10p15.1.

Somatic cells express genes that suppress telomerase activity and these genes may be inactivated in tumour cells. We postulated that cancer cells acquire immortality by activation of telomerase by the loss of such a gene. We have reported recently that a telomerase repressor gene may be located on 10p15.1 by deletion mapping using microcell-mediated chromosome transfer (MMCT), radiated microcell fusion (RMF), fluorescent in situ hybridization (FISH) and STS analysis. To independently confirm this result, we correlated expression of RNA component of telomerase (hTR) as a marker of telomerase expression by in situ hybridization with allelic loss in pulmonary carcinoid tumours. Unlike most malignant tumours, pulmonary carcinoids (which are low-grade malignant tumours) are heterogeneous for telomerase expression. Loss of 5 closely spaced polymorphic markers on 10p15.1, especially D10S1728, were highly correlated with hTR expression. In an additional experiment, 10p15.1 showed higher and more significant correlation than any region of 3p where it has been predicted as another chromosomal location of telomerase repressor with allelic loss of the region. Our findings strongly suggest that 10p15.1 harbours a gene involved in repression of telomerase RNA component in human somatic cells and each putative repressor (on 3p and 10p) may act independently.

Carcinoid Tumor↗
PubMed2001

Equality of the sexes: mammalian dosage compensation.

X chromosome inactivation achieves dosage equivalence for most X-linked genes between the two X chromosomes in females and the single X chromosome in males. In this article the evidence for random inactivation of an X chromosome is reviewed, along with the exceptions that result in nonrandom inactivation. Another exception to X chromosome inactivation is the presence of genes that escape inactivation and are expressed from both the active and inactive X chromosomes. The phenotypic consequences of such expression from the inactive X chromosome are discussed. The major players in the process of inactivation are presented. Initiation of inactivation requires the functional RNA, XIST, and the subsequent stable inactivation of the X chromosome relies upon the recruitment of many other factors, the majority of which are generally associated with heterochromatin.

Animals↗
PubMed2001

Ring X and other structural X chromosome abnormalities: X inactivation and phenotype.

Patients who carry a structural abnormality of the X chromosome are a fascinating group who have provided opportunities to evaluate genotype/phenotype correlation in relation to X chromosome content and inactivation. Turner syndrome (TS) is most commonly associated with a 45,X karyotype and presents with an array of phenotypes, the main ones being poor viability in utero, ovarian failure and infertility, short stature, lymphedema, and other congenital malformations but usually not mental retardation. In some TS patients the karyotype shows both a normal X and a structurally rearranged X chromosome. These structural abnormalities, which include deletions, duplications, inversions, translocations, and rings, are associated with chromosome breaks and significant imbalance of gene content of the X chromosome. However, such abnormalities are generally well tolerated because of the preferential inactivation of the abnormal X, which can restore, at least in part, a balanced genetic makeup. This beneficial effect of X inactivation results in a mild phenotype in most patients with structural abnormalities of the X, similar to that found in TS patients with a 45,X karyotype. However, in cases of ring X chromosomes and of X/autosome translocations the incidence of mental retardation and other congenital abnormalities can be significantly higher than in TS. These abnormal phenotypes can be ascribed to failed or partial X inactivation and/or incomplete selection in favor of cells with normal balance of gene expression. In this article, we present phenotype/genotype correlation in female patients with structural abnormalities of the X and address the role of X inactivation and cell selection in the phenotypic findings. Our review emphasizes a subset of rare patients with ring X chromosomes who have provided evidence of a direct role for X inactivation in determining phenotypes.

Chromosome Deletion↗
PubMed2002

Soybean ENOD40 encodes two peptides that bind to sucrose synthase.

ENOD40 is expressed at an early stage in root nodule organogenesis in legumes. Identification of ENOD40 homologs in nonleguminous plants suggests that this gene may have a more general biological function. In vitro translation of soybean ENOD40 mRNA in wheat germ extracts revealed that the conserved nucleotide sequence at the 5' end (region I) encodes two peptides of 12 and 24 aa residues (peptides A and B). These peptides are synthesized de novo from very short, overlapping ORFs. Appropriate ORFs are present in all legume ENOD40s studied thus far. In this case small peptides are directly translated from polycistronic eukaryotic mRNA. The 24-aa peptide B was detected in nodules by Western blotting. Both peptides specifically bind to the same 93-kDa protein, which was affinity purified from soybean nodules. Using peptide mass fingerprinting, we identified this binding protein as nodulin 100, which is a subunit of sucrose synthase. Based on our data we suggest that ENOD40 peptides are involved in the control of sucrose use in nitrogen-fixing nodules.

Amino Acid Sequence↗