The two embryonic U1 small nuclear RNAs of Xenopus laevis are encoded by a major family of tandemly repeated genes

1984 ◽  
Vol 4 (12) ◽  
pp. 2580-2586
Author(s):  
E Lund ◽  
J E Dahlberg ◽  
D J Forbes
Keyword(s):  
Xenopus Laevis ◽  
Large Family ◽  
Distinct Species ◽  
Single Copy ◽  
Haploid Genome ◽  
Small Nuclear Rnas ◽  
Cell Embryo ◽  
Rna Genes ◽  
Repeated Genes ◽  
Tandem Arrays

We have identified a large family of U1 RNA genes in Xenopus laevis that encodes two distinct species of U1 RNA. These genes are expressed primarily at the onset of transcription in the 4,000-cell embryo (D. J. Forbes, M. W. Kirschner, D. Caput, J. E. Dahlberg, and E. Lund, Cell 38:681-689, 1984). The two types of embryonic U1 RNA genes are interspersed and are organized in large tandem arrays. The basic 1.9-kilobase repeating unit contains a single copy of each of the embryonic genes and is reiterated ca. 500-fold per haploid genome. This repetitive U1 DNA accounts for more than 90% of all U1 DNA in X. laevis. In addition to this major family, there exist several minor families of dispersed U1 RNA genes, which presumably encode the oocyte and somatic species of X. laevis U1 RNA. Although the embryonic genes are normally inactive in stage VI oocytes, they are expressed when cloned copies are injected into oocyte nuclei.

scholarly journals The two embryonic U1 small nuclear RNAs of Xenopus laevis are encoded by a major family of tandemly repeated genes.

1984 ◽  
Vol 4 (12) ◽  
pp. 2580-2586 ◽  
Author(s):  
E Lund ◽  
J E Dahlberg ◽  
D J Forbes
Keyword(s):  
Xenopus Laevis ◽  
Large Family ◽  
Distinct Species ◽  
Single Copy ◽  
Haploid Genome ◽  
Small Nuclear Rnas ◽  
Cell Embryo ◽  
Rna Genes ◽  
Repeated Genes ◽  
Tandem Arrays

We have identified a large family of U1 RNA genes in Xenopus laevis that encodes two distinct species of U1 RNA. These genes are expressed primarily at the onset of transcription in the 4,000-cell embryo (D. J. Forbes, M. W. Kirschner, D. Caput, J. E. Dahlberg, and E. Lund, Cell 38:681-689, 1984). The two types of embryonic U1 RNA genes are interspersed and are organized in large tandem arrays. The basic 1.9-kilobase repeating unit contains a single copy of each of the embryonic genes and is reiterated ca. 500-fold per haploid genome. This repetitive U1 DNA accounts for more than 90% of all U1 DNA in X. laevis. In addition to this major family, there exist several minor families of dispersed U1 RNA genes, which presumably encode the oocyte and somatic species of X. laevis U1 RNA. Although the embryonic genes are normally inactive in stage VI oocytes, they are expressed when cloned copies are injected into oocyte nuclei.

scholarly journals Coiled Bodies Preferentially Associate with U4, U11, and U12 Small Nuclear RNA Genes in Interphase HeLa Cells but Not with U6 and U7 Genes

1999 ◽  
Vol 10 (5) ◽  
pp. 1653-1663 ◽  
Author(s):  
Erica Y. Jacobs ◽  
Mark R. Frey ◽  
Wei Wu ◽  
Thomas C. Ingledue ◽  
Thomas C. Gebuhr ◽  
...  
Keyword(s):  
Single Gene ◽  
Single Copy ◽  
Small Nuclear Rna ◽  
Structural Morphology ◽  
Functional Roles ◽  
Coiled Bodies ◽  
Small Nuclear Rnas ◽  
Bona Fide ◽  
Nascent Transcripts ◽  
Rna Genes

Coiled bodies (CBs) are nuclear organelles involved in the metabolism of small nuclear RNAs (snRNAs) and histone messages. Their structural morphology and molecular composition have been conserved from plants to animals. CBs preferentially and specifically associate with genes that encode U1, U2, and U3 snRNAs as well as the cell cycle–regulated histone loci. A common link among these previously identified CB-associated genes is that they are either clustered or tandemly repeated in the human genome. In an effort to identify additional loci that associate with CBs, we have isolated and mapped the chromosomal locations of genomic clones corresponding to bona fide U4, U6, U7, U11, and U12 snRNA loci. Unlike the clustered U1 and U2 genes, each of these loci encode a single gene, with the exception of the U4 clone, which contains two genes. We next examined the association of these snRNA genes with CBs and found that they colocalized less frequently than their multicopy counterparts. To differentiate a lower level of preferential association from random colocalization, we developed a theoretical model of random colocalization, which yielded expected values for χ2tests against the experimental data. Certain single-copy snRNA genes (U4, U11, and U12) but not controls were found to significantly (p < 0.000001) associate with CBs. Recent evidence indicates that the interactions between CBs and genes are mediated by nascent transcripts. Taken together, these new results suggest that CB association may be substantially augmented by the increased transcriptional capacity of clustered genes. Possible functional roles for the observed interactions of CBs with snRNA genes are discussed.

Activation of dorsal development by contact between the cortical dorsal determinant and the equatorial core cytoplasm in eggs of Xenopus laevis

Development ◽  
1997 ◽  
Vol 124 (8) ◽  
pp. 1543-1551 ◽  
Author(s):  
H. Kageura
Keyword(s):  
Xenopus Laevis ◽  
Dorsal Side ◽  
Equatorial Region ◽  
Normal Embryo ◽  
Dorsal Region ◽  
The Core ◽  
Dorsal Axis ◽  
The Future ◽  
Vegetal Pole ◽  
Cell Embryo

In eggs of Xenopus laevis, dorsal development is activated on the future dorsal side by cortical rotation, after fertilization. The immediate effect of cortical rotation is probably the transport of a dorsal determinant from the vegetal pole to the equatorial region on the future dorsal side. However, the identity and action of the dorsal determinant remain problematic. In the present experiments, individual isolated cortices from various regions of the unfertilized eggs and embryos were implanted into one of several positions of a recipient 8-cell embryo. The incidence of secondary axes was used not only to locate the cortical dorsal determinant at different times but also to locate the region of the core competent to respond to the dorsal determinant. The dorsal axis-inducing activity of the cortex occurred around the vegetal pole of the unfertilized egg. During cortical rotation, it shifted from there to a wide dorsal region. This is apparently the first evidence for the presence of a dorsal determinant in the egg cortex. The competence of the core of the 8-cell embryo was distributed in the form of gradient with the highest responsiveness at the equator. These results suggest that, in the normal embryo, dorsal development is activated by contact between the cortical dorsal determinant and the equatorial core cytoplasm, brought together through cortical rotation.

Regular arrangement of nucleosomes on 5S rRNA genes in Xenopus laevis

1983 ◽  
Vol 3 (4) ◽  
pp. 720-730
Author(s):  
D Young ◽  
D Carroll
Keyword(s):  
Xenopus Laevis ◽  
Chromatin Structure ◽  
Micrococcal Nuclease ◽  
Rrna Genes ◽  
Dna Repeats ◽  
5S Rna ◽  
5S Dna ◽  
Regular Arrangement ◽  
5S Rna Genes ◽  
Rna Genes

The chromatin structure of the oocyte-type 5S RNA genes in Xenopus laevis was investigated. Blot hybridization analysis of DNA from micrococcal nuclease digests of erythrocyte nuclei showed that 5S DNA has the same average nucleosome repeat length, 192 +/- 4 base pairs, as two Xenopus satellite DNAs and bulk erythrocyte chromatin. The positions of nuclease-sensitive regions in the 5S DNA repeats of purified DNA and chromatin from erythrocytes were mapped by using an indirect end-labeling technique. Although most of the sites cleaved in purified DNA were also cleaved in chromatin, the patterns of intensities were strikingly different in the two cases. In 5S chromatin, three nuclease-sensitive regions were spaced approximately a nucleosome length apart, suggesting a single, regular arrangement of nucleosomes on most of the 5S DNA repeats. The observed nucleosome locations are discussed with respect to nucleotide sequences known to be important for expression of 5S RNA. Because the preferred locations appear to be reestablished in each repeating unit, despite spacer length heterogeneity, we suggest that the regular chromatin structure reflects the presence of a sequence-specific DNA-binding component on inactive 5S RNA genes.

scholarly journals The pentose phosphate pathway in Trypanosoma cruzi: a potential target for the chemotherapy of Chagas disease

2007 ◽  
Vol 79 (4) ◽  
pp. 649-663 ◽  
Author(s):  
Mariana Igoillo-Esteve ◽  
Dante Maugeri ◽  
Ana L. Stern ◽  
Paula Beluardi ◽  
Juan J. Cazzulo
Keyword(s):  
Oxidative Stress ◽  
Trypanosoma Cruzi ◽  
Pentose Phosphate Pathway ◽  
Single Copy ◽  
Pentose Phosphate ◽  
Site Directed Mutagenesis ◽  
Haploid Genome ◽  
Salt Bridges ◽  
Phosphogluconate Dehydrogenase ◽  
Genes Encoding

Trypanosoma cruzi is highly sensitive to oxidative stress caused by reactive oxygen species. Trypanothione, the parasite's major protection against oxidative stress, is kept reduced by trypanothione reductase, using NADPH; the major source of the reduced coenzyme seems to be the pentose phosphate pathway. Its seven enzymes are present in the four major stages in the parasite's biological cycle; we have cloned and expressed them in Escherichia coli as active proteins. Glucose 6-phosphate dehydrogenase, which controls glucose flux through the pathway by its response to the NADP/NADPH ratio, is encoded by a number of genes per haploid genome, and is induced up to 46-fold by hydrogen peroxide in metacyclic trypomastigotes. The genes encoding 6-phosphogluconolactonase, 6-phosphogluconate dehydrogenase, transaldolase and transketolase are present in the CL Brener clone as a single copy per haploid genome. 6-phosphogluconate dehydrogenase is very unstable, but was stabilized introducing two salt bridges by site-directed mutagenesis. Ribose-5-phosphate isomerase belongs to Type B; genes encoding Type A enzymes, present in mammals, are absent. Ribulose-5-phosphate epimerase is encoded by two genes. The enzymes of the pathway have a major cytosolic component, although several of them have a secondary glycosomal localization, and also minor localizations in other organelles.

A cytoplasmic determinant for dorsal axis formation in an early embryo of Xenopus laevis

Development ◽  
1990 ◽  
Vol 110 (4) ◽  
pp. 1051-1056 ◽  
Author(s):  
M. Yuge ◽  
Y. Kobayakawa ◽  
M. Fujisue ◽  
K. Yamana
Keyword(s):  
Xenopus Laevis ◽  
Direct Evidence ◽  
Early Embryo ◽  
Dorsal Side ◽  
Axis Formation ◽  
Secondary Axis ◽  
Dorsal Axis ◽  
Cell Embryo ◽  
Dorsal Cells ◽  
Cytoplasmic Determinant

In Xenopus laevis, dorsal cells that arise at the future dorsal side of an early cleaving embryo have already acquired the ability to cause axis formation. Since the distribution of cytoplasmic components is markedly heterogeneous in an egg and embryo, it has been supposed that the dorsal cells are endowed with the activity to form axial structures by inheriting a unique cytoplasmic component or components localized in the dorsal region of an egg or embryo. However, there has been no direct evidence for this. To examine the activity of the cytoplasm of dorsal cells, we injected cytoplasm (dorsal cytoplasm) from dorsal vegetal cells of a Xenopus 16-cell embryo into ventral vegetal cells of a simultaneous recipient. The cytoplasm caused secondary axis formation in 42% of recipients. Histological examination revealed that well-developed secondary axes included notochord, as well as a neural tube and somites. However, injection of cytoplasm of ventral vegetal cells never caused secondary axis and most recipients became normal tailbud embryos. Furthermore, about two-thirds of ventral isolated halves injected with dorsal cytoplasm formed axial structures. These results show that dorsal, but not ventral, cytoplasm contains the component or components responsible for axis formation. This can be the first step towards identifying the molecular basis of dorsal axis formation.

Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable sextuple mutant

1988 ◽  
Vol 8 (8) ◽  
pp. 3150-3159
Author(s):  
R Parker ◽  
T Simmons ◽  
E O Shuster ◽  
P G Siliciano ◽  
C Guthrie
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcriptional Start Site ◽  
Single Copy ◽  
Gene Replacement ◽  
Null Alleles ◽  
Wild Type ◽  
Small Nuclear Rnas ◽  
Apparent Correlation ◽  
Genes Encoding ◽  
Sm Antigen

Saccharomyces cerevisiae contains at least 24 distinct small nuclear RNAs (snRNAs), several of which are known to be essential for viability and to participate in the splicing of pre-mRNAs; the RNAs in this subset contain binding sites for the Sm antigen, a hallmark of metazoan snRNAs involved in mRNA processing. In contrast, we showed previously that the single-copy genes for three other snRNAs (snR3, snR4, and snR10) are not required for viability, although cells lacking snR10 are growth impaired at low temperature. None of these RNAs associates with the Sm antigen. To assess this apparent correlation, we cloned and sequenced the genes encoding three additional non-Sm snRNAs. Comparison of these genes with nine additional yeast snRNA genes revealed a highly conserved TATA box located 92 +/- 8 nucleotides 5' of the transcriptional start site. By using the technique of gene replacement with null alleles, each of these three single copy genes was shown to be completely dispensable. We constructed multiple mutants to test the hypothesis that, individually, each of these snRNAs is nonessential because the snRNAs play functionally overlapping roles. A mutant lacking five snRNAs (snR3, snR4, snR5, snR8, snR9) was indistinguishable from the wild type, and growth of the sextuple mutant was no more impaired than that in strains lacking only snR10. This widespread dispensability of snRNAs was completely unexpected and forces us to reconsider the possible roles of these ubiquitous RNAs.

Regional specification within the mesoderm of early embryos of Xenopus laevis

Development ◽  
1987 ◽  
Vol 100 (2) ◽  
pp. 279-295 ◽  
Author(s):  
L. Dale ◽  
J.M. Slack
Keyword(s):  
Xenopus Laevis ◽  
Marginal Zone ◽  
Mesoderm Induction ◽  
Intermediate Type ◽  
Cell Stage ◽  
Early Embryos ◽  
Significant Difference ◽  
Cell Embryo ◽  
Single Blastomeres

We have further analysed the roles of mesoderm induction and dorsalization in the formation of a regionally specified mesoderm in early embryos of Xenopus laevis. First, we have examined the regional specificity of mesoderm induction by isolating single blastomeres from the vegetalmost tier of the 32-cell embryo and combining each with a lineage-labelled (FDA) animal blastomere tier. Whereas dorsovegetal (D1) blastomeres induce ‘dorsal-type’ mesoderm (notochord and muscle), laterovegetal and ventrovegetal blastomeres (D2–4) induce either ‘intermediate-type’ (muscle, mesothelium, mesenchyme and blood) or ‘ventral-type’ (mesothelium, mesenchyme and blood) mesoderm. No significant difference in inductive specificity between blastomeres D2, 3 and 4 could be detected. We also show that laterovegetal and ventrovegetal blastomeres from early cleavage stages can have a dorsal inductive potency partially activated by operative procedures, resulting in the induction of intermediate-type mesoderm. Second, we have determined the state of specification of ventral blastomeres by isolating and culturing them in vitro between the 4-cell stage and the early gastrula stage. The majority of isolates from the ventral half of the embryo gave extreme ventral types of differentiation at all stages tested. Although a minority of cases formed intermediate-type and dorsal-type mesoderms we believe these to result from either errors in our assessment of the prospective DV axis or from an enhancement, provoked by microsurgery, of some dorsal inductive specificity. The results of induction and isolation experiments suggest that only two states of specification exist in the mesoderm of the pregastrula embryo, a dorsal type and a ventral type. Finally we have made a comprehensive series of combinations between different regions of the marginal zone using FDA to distinguish the components. We show that, in combination with dorsal-type mesoderm, ventral-type mesoderm becomes dorsalized to the level of intermediate-type mesoderm. Dorsal-type mesoderm is not ventralized in these combinations. Dorsalizing activity is confined to a restricted sector of the dorsal marginal zone, it is wider than the prospective notochord and seems to be graded from a high point at the dorsal midline. The results of these experiments strengthen the case for the three-signal model proposed previously, i.e. dorsal and ventral mesoderm inductions followed by dorsalization, as the simplest explanation capable of accounting for regional specification within the mesoderm of early Xenopus embryos.

Differential order of replication of Xenopus laevis 5S RNA genes

1986 ◽  
Vol 6 (7) ◽  
pp. 2536-2542
Author(s):  
D R Guinta ◽  
L J Korn
Keyword(s):  
Xenopus Laevis ◽  
Rna Replication ◽  
S Phase ◽  
Cold Spring Harbor ◽  
5S Rna ◽  
Expression Model ◽  
Cold Spring ◽  
5S Rna Genes ◽  
Equilibrium Centrifugation ◽  
Rna Genes

In Xenopus laevis there are two multigene families of 5S RNA genes: the oocyte-type 5S RNA genes which are expressed only in oocytes and the somatic-type 5S RNA genes which are expressed throughout development. The Xenopus 5S RNA replication-expression model of Gottesfeld and Bloomer (Cell 28:781-791, 1982) and Wormington et al. (Cold Spring Harbor Symp. Quant. Biol. 47:879-884, 1983) predicts that the somatic-type 5S RNA genes replicate earlier in the cell cycle than do the oocyte-type genes. Hence, the somatic-type 5S RNA genes have a competitive advantage in binding the transcription factor TFIIIA in somatic cells and are thereby expressed to the exclusion of the oocyte-type genes. To test the replication-expression model, we determined the order of replication of the oocyte- and somatic-type 5S RNA genes. Xenopus cells were labeled with bromodeoxyuridine, stained for DNA content, and then sorted into fractions of S phase by using a fluorescence-activated cell sorter. The newly replicated DNA containing bromodeoxyuridine was separated from the lighter, unreplicated DNA by equilibrium centrifugation and was hybridized with DNA probes specific for the oocyte- and somatic-type 5S RNA genes. In this way we found that the somatic-type 5S RNA genes replicate early in S phase, whereas the oocyte-type 5S RNA genes replicate late in S phase, demonstrating a key aspect of the replication-expression model.

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