Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genes, Developmental”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 919 records · Page 51Linked to original sources

Isolation of unknown genes from human bone marrow by differential screening and single-pass cDNA sequence determination.

A cDNA sequencing project was initiated to characterize gene expression in human bone marrow and develop strategies to isolate novel genes. Forty-eight random DNAs from total human bone marrow were subjected to single-pass DNA sequence analysis to determine a limited complexity of mRNAs expressed in the bone marrow. Overall, 8 cDNAs (17%) showed no similarity to known sequences. Information from DNA sequence analysis was used to develop a differential prescreen to subtract unwanted cDNAs and to enrich for unknown cDNAs. Forty-eight cDNAs that were negative with a complex probe were subject to single-pass DNA sequence determination. Of these prescreened cDNAs, the number of unknown sequences increased to 23 (48%). Unknown cDNAs were also characterized by RNA expression analysis using 25 different human leukemic cell lines. Of 13 unknown cDNAs tested, 10 were expressed in all cell types tested and 3 revealed a hematopoietic lineage-restricted expression pattern. Interestingly, while a total of only 96 bone marrow cDNAs were sequenced, 31 of these cDNAs represent sequences from unknown genes and 12 showed significant similarities to sequences in the data bases. One cDNA revealed a significant similarity to a serine/threonine-protein kinase at the amino acid level (56% identity for 123 amino acids) and may represent a previously unknown kinase. Differential screening techniques coupled with single-pass cDNA sequence analysis may prove to be a powerful and simple technique to examine developmental gene expression.

Amino Acid Sequence↗

Evolution of developmental mechanisms in nematodes.

The recent findings that key developmental genes are conserved across animal phyla have led to descriptions of evolutionary change in development based on the recruitment of these few molecules. This approach, however, encounters problems in assigning homology across long evolutionary distances. By contrast, reproducibility of the cell lineage of free-living soil nematodes (order Rhabditida) and conservation of larval blast cells across nematode species permit evolutionary comparisons of developmental mechanisms among nematodes at the cellular level. Such comparative studies uncover an unexpected flexibility of developmental mechanisms: Large evolutionary differences have been described between invariant and noninvariant lineages, in the cellular mechanisms specifying a given cell (for instance, the gonadal anchor cell), in the subcellular events leading to asymmetric divisions (for instance, the first division of the egg), and in redundant networks of cell interactions (for instance, those specifying the centered pattern of vulva precursor fates). Interestingly, redundancy of developmental mechanisms favored by selective pressure allows in turn for evolution of these mechanisms. Such evolutionary changes in developmental mechanisms specifying cell fates can occur in the absence of obvious morphological change, which rather correlates with evolution of cell fates per se: death, division, migration, and differentiation (for instance, in the reduction of the posterior gonadal arm in monodelphic species or in change in vulva position).

Animals↗

Established epigenetic modifications determine the expression of developmentally regulated globin genes in somatic cell hybrids.

Somatic cell hybrids generated from transgenic mouse cells have been used to examine the developmental regulation of human gamma-to-beta-globin gene switching. In hybrids between mouse erythroleukemia (MEL) cells and transgenic erythroblasts taken at various stages of development, there was regulated expression of the human fetal gamma and adult beta genes, reproducing the in vivo pattern prior to fusion. Hybrids formed from embryonic blood cells produced predominantly gamma mRNA, whereas beta gene expression was observed in adult hybrids and a complete range of intermediate patterns was found in fetal liver hybrids. The adult environment of the MEL cells, therefore, did not appear to influence selective transcription from this gene complex. Irradiation of the embryonic erythroid cells prior to fusion resulted in hybrids containing only small fragments of donor chromosomes, but the pattern of gene expression did not differ from that of unirradiated hybrids. This finding suggests that continued expression of trans-acting factors from the donor erythroblasts is not necessary for continued expression of the human gamma gene in MEL cells. These results contrast with the lack of developmental regulation of the cluster after transfection of naked DNA into MEL cells and suggest that epigenetic processes established during normal development result in the gene cluster adopting a developmental stage-specific, stable conformation which is maintained through multiple rounds of replication and transcription in the MEL cell hybrids. On prolonged culture, hybrids that initially expressed only the gamma transgene switched to beta gene expression. The time period of switching, from approximately 10 to > 40 weeks, was similar to that seen previously in human fetal erythroblast x MEL cell hybrids but in this case bore no relationship to the time of in vivo switching. It seems unlikely, therefore, that switching in these hybrids is regulated by a developmental clock.

Animals↗

Expression pattern of an axolotl floor plate-specific fork head gene reflects early developmental differences between frogs and salamanders.

Gastrulation is one of the most important stages of animal development and, as such, tends to be remarkably conserved. Therefore it is interesting to see that the two amphibian species, Xenopus laevis (frog) and Ambystoma mexicanum (axolotl), are different in the arrangement of cell types just before and during gastrulation. In Xenopus, the cells that will form dorsal mesoderm are located deep in the dorsal marginal zone, while in the axolotl, these are on the surface of the embryo. In this study we investigated whether homologous genes known to be involved in the formation of dorsal structures show a different pattern of expression in these two species. For this purpose, we isolated a fork head gene (AxFKH 1) from the axolotl, which is likely to be the homologue of the Xenopus fork head gene, XFKH 1 (Pintallavis, XFD-1). We find that AxFKH 1 and XFH 1 have a similar pattern of expression, but there are some important differences. In early gastrulae, transcripts are detected in the organizer region of both species. In late gastrulae, the transcripts in Xenopus are located in both the superficial and deep layers, but they are only found in the superficial layer of axolotl embryos. During neurulation, XFKH 1 is expressed in notochord and neural floor plate, whereas AxFKH 1 is expressed in the neural floor plate only. We propose that the differences in expression pattern of these two genes are due to a difference in formation of dorsal structures between these two species. Furthermore, the expression pattern of these two genes early in gastrulation is consistent with the idea that at least some of the neural floor plate cells are already determined at this time.

Ambystoma mexicanum↗

Role of HOXA7 to HOXA13 and PBX1 genes in various forms of MRKH syndrome (congenital absence of uterus and vagina).

The Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome refers to the congenital absence or severe hypoplasia of the female genital tract, often described as uterovaginal aplasia which is the prime feature of the syndrome. It is the second cause of primary amenorrhea after gonadal dysgenesis and occurs in approximately 1 in 4500 women. Aetiology of this syndrome remains poorly understood. Frequent association of other malformations with the MRKH syndrome, involving kidneys, skeleton and ears, suggests the involvement of major developmental genes such as those of the HOX family. Indeed mammalian HOX genes are well known for their crucial role during embryogenesis, particularly in axial skeleton, hindbrain and limb development. More recently, their involvement in organogenesis has been demonstrated notably during urogenital differentiation. Although null mutations of HOX genes in animal models do not lead to MRKH-like phenotypes, dominant mutations in their coding sequences or aberrant expression due to mutated regulatory regions could well account for it. Sequence analysis of coding regions of HOX candidate genes and of PBX1, a likely HOX cofactor during Müllerian duct differentiation and kidney morphogenesis, did not reveal any mutation in patients showing various forms of MRKH syndrome. This tends to show that HOX genes are not involved in MRKH syndrome. However it does not exclude that other mechanisms leading to HOX dysfunction may account for the syndrome.

Abnormalities, Multiple↗

Expression of the Streptomyces aureofaciens glyceraldehyde-3-phosphate dehydrogenase gene (gap) is developmentally regulated and induced by glucose.

In previous experiments, the Streptomyces aureofaciens gap gene encoding glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified. To investigate expression of the gene, S1 nuclease mapping and Northern blot hybridization were performed using RNA prepared from S. aureofaciens cultivated under various conditions. These studies suggested monocistronic organization and developmental regulation of the gene. A single promoter, gap-P, was identified upstream of the gap coding region. In cultures grown on solid medium in the absence of glucose, its transcription was induced at the time of aerial mycelium formation. In addition, gap transcription was also induced in substrate mycelium by glucose. A promoter-bearing DNA fragment was inserted into two promoter-probe vectors, to give expression patterns consistent with the results of direct RNA analysis.

Amino Acid Sequence↗

A cytological approach to the ordering of events in gene activation using the Sgs-4 locus of Drosophila melanogaster.

The polytene chromosomes of Drosophila strains that differ in the synthesis of the major salivary gland glue protein sgs-4 were examined by indirect immunofluorescence using antisera to several nonhistone chromosomal proteins. The Oregon-R X chromosome, which produces sgs-4 messenger RNA, showed a strong fluorescent band at locus 3C11-12 when stained with anti-RNA polymerase II, whereas the null mutant Berkeley 1 failed to exhibit fluorescence at that locus. The presence of another antigen (Band 2), normally associated with developmentally active loci, was clearly evident at locus 3C11-12 of both transcriptionally competent and null strains, indicating that the association of Band 2 antigen with the chromatin is an event independent of RNA polymerase II binding. Antibodies directed against Drosophila topoisomerase I stained 3C11-12 in the Sgs-4+ (wild-type) strain brightly, but gave significantly less staining in the null strain. This indicates that the high concentrations of topoisomerase I seen at active loci are closely associated with the transcriptional event. In some of these analyses, we have made use of flies heterozygous for the wild-type and null alleles in order to make internally controlled comparisons. The results suggest that this type of analysis will enable conclusions to be drawn concerning the interdependence and order of action of chromosomal proteins involved in developmental gene activation.

Alleles↗

Two separable functional domains in the sigma-subunit of RNA polymerase in Bacillus subtilis?

The sigma-subunit of RNA polymerase is responsible for promoter recognition in prokaryotes [(1969) Nature 221, 43-46]. Alterations in the sigma-subunit are thought to be involved in controlling 'global' changes in gene expression, such as those involved in differentiation in the spore-forming bacterium Bacillus subtilis [(1981) Cell 25, 582-584]. Stragier et al. [(1985) FEBS Lett. 195, 3-11] have proposed that sigma-factors are composed of two domains: a C-terminal domain involved in promoter recognition and an N-terminal domain involved in interactions with RNA polymerase. We have sequenced another developmental gene from B. subtilis, spoIIIC, and the strong homology of its predicted product suggests that it too may be a sigma-factor. However, the spoIIIC product is small and lacks completely the conserved N-terminal domain of the sigma-subunits. I propose that the product of the spoIIIC gene may carry out the DNA-recognition functions of a sigma-factor but that it probably requires an auxiliary factor to interact with core RNA polymerase.

Amino Acid Sequence↗

High level class II trans-activator induction does not occur with transient activation of the IFN-gamma signaling pathway.

Gene activation in early development is highly dependent on precise concentrations of trans-acting factors for the activation of different genes at differing points in the embryo. Thus, not only is the presence or absence of a particular trans-activator or repressor relevant in determining gene activation, but also the concentration of the regulatory protein must be above or below a certain threshold for proper gene regulation. Signaling pathways in somatic cells are thought to represent cascades of on/off switches, mediated most commonly by phosphorylation. Here we demonstrate a quantitative mechanism for regulating the level of a component of the IFN-gamma signaling pathway that in effect represents the differential sensitivities of STAT1, IFN-regulatory factor-1, and class II trans-activator (CIITA) to IFN-gamma. Unlike developmental gene regulation, in which specificity of gene activation is a function of regulatory protein concentrations, specificity of gene activation in the IFN-gamma signaling pathway is regulated by the duration of the activation of the primary IFN-gamma-regulatory protein, STAT1. This result most likely explains previously reported data indicating that a minimum amount of IFN-gamma is required for MHC class II gene activation despite the fact that the level of the IFN-gamma-inducible factor directly required for MHC class II induction, CIITA, directly correlates with the level of MHC class II expression. The induction of a high level of CIITA is dependent on sustained IFN-gamma signaling. The possible implications of this result for tumorigenesis are discussed.

Cell Line, Transformed↗

A histidine protein kinase homologue required for regulation of bacterial cell division and differentiation.

Differentiation in the dimorphic bacterium Caulobacter crescentus results from a sequence of discontinuous, stage-specific events that leads to the production of a stalked cell and a new motile swarmer cell after each asymmetric cell division. As reported previously, pseudoreversion analysis of mutations in the pleiotropic developmental gene pleC identified three cell division genes: divJ, divK, and divL. We show here that one of these genes, divJ, encodes a predicted protein of 596 residues with an extensive hydrophobic N-terminal region and a C-terminal domain containing all of the invariant residues found in the family of bacterial histidine protein kinases. Our results also show that divJ is discontinuously transcribed early in the swarmer cell cycle during a period that coincides with the G1 to S transition. We propose that the DivJ protein is one member of a signal transduction pathway regulating the cell cycle and differentiation in Caulobacter and that protein modification by phosphorylation may play a central role in coupling developmental events to progress through the cell division cycle.

Amino Acid Sequence↗

Gene regulation during dedifferentiation in Dictyostelium discoideum.

During development of Dictyostelium discoideum, cells acquire the capacity to rapidly recapitulate morphogenesis. Therefore, when cells at the loose aggregate stage are disaggregated and challenged to reaggregate, they do so in a tenth of the original time. If loose aggregate cells are disaggregated and resuspended in buffered dextrose solution (erasure medium), they retain the capacity of rapid recapitulation for 80 min, then completely lose this capacity in a single, synchronous step referred to as the "erasure event." The erasure event sets in motion a program of dedifferentiation during which cells lose developmentally acquired characteristics at different times. The erasure event is inhibited by the addition of 10(-4) M cAMP to erasure medium. The synthesis of 33 growth-associated polypeptides, the synthesis of 53 development-associated polypeptides, and the level of 2 development-associated RNAs have been monitored during the erasure program and in cultures inhibited from erasing by the addition of 10(-4) M cAMP. Growth-associated polypeptides begin to be resynthesized and development-associated polypeptides exhibit dramatic decreases in rate of synthesis at different times throughout the first 240 min in erasure medium. Inhibiting the erasure event with cAMP has no major effect in the resynthesis of the majority of growth-associated polypeptides. Only one growth-associated polypeptide, V28, is completely inhibited by cAMP, suggesting that it may play a role in the erasure process. In contrast, inhibiting the erasure event with cAMP has a marked effect on the synthesis of development-associated polypeptides, causing a dramatic reduction in the rate at which synthesis decreases for 6 polypeptides, and completely inhibits the decrease in the synthetic rate of 8 polypeptides. The two development-associated RNAs, 16G1 and 10C3, exhibit two distinctly different patterns of loss during erasure, but in both cases cAMP added at time zero of the erasure process dramatically retards or inhibits loss. In addition, when cAMP is added just prior to the erasure event, it inhibits the erasure event and stimulates a rapid increase in the level of 16G1 RNA back to the developmental level. The level of 16G1 RNA then remains at this level for at least 400 min. When cAMP is added after the erasure event, it causes a low, transient increase in the level of 16G1 RNA. These results are considered both in relation to the program of erasure, and in relation to the role of cAMP in the expression of developmental genes during the forward program of development.

Cell Differentiation↗

Identification of a unique cAMP-response element in the gene encoding the cell adhesion molecule gp80 in Dictyostelium discoideum.

Extracellular cAMP serves as a chemoattractant as well as a signal which regulates gene expression during development of Dictyostelium discoideum. The cell adhesion molecule gp80 is expressed at the aggregation stage, between 6 and 10 h of development, and is known to be under cAMP regulation. Transcription of the gp80 gene is first turned on at a low, basal level at the preaggregation stage and is then greatly augmented by pulses of low levels of cAMP at the aggregation stage. Using cloned cDNA sequences, we have isolated genomic DNA fragments encompassing the gp80 gene. The gp80 gene has a single open reading frame, with multiple transcription start sites located downstream from a putative TATA box. Several short, repeated sequences in the upstream sequence have also been identified. The cloned 1.3-kilobase upstream DNA was sufficient to confer proper temporal and cAMP regulation on a gp80 minigene reporter in Dictyostelium cells. Deletional analysis of this 5'-flanking DNA led to the mapping of a cAMP-response element (CRE) in the gp80 gene to sequences between -306 and -289 base pairs upstream of the translational start site. Present within this region is a sequence we refer to as box 1 (TGGTGTG). The gp80 box 1-CRE binds specifically to a protein present in nuclear extracts, but binding is abolished when mutations are introduced in the box 1 sequence. The gp80 box 1-CRE shows little sequence homology to CREs of late developmental genes and the expression of gp80 may involve a distinct signal transduction pathway.

Amino Acid Sequence↗

A sporulation-induced sigma-like regulatory protein from B. subtilis.

We have isolated a sigma-like regulatory protein termed sigma 29 whose synthesis or association with Bacillus subtilis RNA polymerase was induced during spore formation. sigma 29 is a sporulation-specific component of RNA polymerase as it was absent in enzyme from an early-blocked sporulation mutant (SpoOA). We have demonstrated specific RNA synthesis by sigma 29-RNA polymerase using as a DNA template a cloned cluster of vegetative and sporulation genes from the purA-cysA region of the B. subtilis chromosome. The pattern of gene recognition by sigma 29-RNA polymerase was distinct from that observed for RNA polymerases containing sigma 55 or sigma 37, species of sigma factor that are present in vegetative cells of B. subtilis. A reconstitution experiment in which purified sigma 29 was added to core RNA polymerase demonstrates that sigma 29 was directly responsible for the altered transcriptional specificity of sporulation RNA polymerase. We propose that sigma 29 is a regulatory protein that controls developmental gene transcription at an early stage of spore formation.

Bacillus subtilis↗

A locus for autosomal recessive congenital microphthalmia maps to chromosome 14q32.

Congenital microphthalmia (CMIC) (OMIM 309700) may occur in isolation or in association with a variety of systemic malformations. Isolated CMIC may be inherited as an autosomal dominant, an autosomal recessive, or an X-linked trait. On the basis of a whole-genome linkage analysis, we have mapped the first locus for isolated CMIC, in a five-generation consanguineous family with autosomal recessive inheritance, to chromosome 14q32. All affected individuals in this family have bilateral CMIC. Linkage analysis gave a maximum two-point LOD score of 3.55 for the marker D14S65. Surrounding this marker is a region of homozygosity of 7.3 cM, between the markers D14S987 and D14S267, within which the disease gene is predicted to lie. The genes for several eye-specific transcription factors are located on human chromosome 14q and in the syntenic region of mouse chromosome 12. However, both CHX10 (14q24.3), mutations of which give rise to CMIC in mouse models, and OTX2 (14q21-22) can be excluded as candidates for autosomal recessive congenital microphthalmia (arCMIC), since they map outside the critical disease region defined by recombination events. This suggests that arCMIC is caused by defects in a novel developmental gene that may be important or even essential in eye development.

Animals↗

Two histone fold proteins, CHRAC-14 and CHRAC-16, are developmentally regulated subunits of chromatin accessibility complex (CHRAC).

The ISWI ATPase of Drosophila is a molecular engine that can drive a range of nucleosome remodelling reactions in vitro. ISWI is important for cell viability, developmental gene expression and chromosome structure. It interacts with other proteins to form several distinct nucleosome remodelling machines. The chromatin accessibility complex (CHRAC) is a biochemical entity containing ISWI in association with several other proteins. Here we report on the identification of the two smallest CHRAC subunits, CHRAC-14 and CHRAC-16. They contain histone fold domains most closely related to those found in sequence-specific transcription factors NF-YB and NF-YC, respectively. CHRAC-14 and CHRAC-16 interact directly with each other as well as with ISWI, and are associated with functionally active CHRAC. The developmental expression profiles of both subunits suggest specialized roles in chromatin remodelling reactions in the early embryo for both histone fold subunits.

Adenosine Triphosphatases↗

Oligosaccharide signaling in plants. Specificity of oligouronide-enhanced plasma membrane protein phosphorylation.

The in vitro phosphorylation by [gamma-32P]ATP of a 34-kDa plasma membrane-associated protein (pp34) from tomato and potato is strongly enhanced in the presence of alpha-1,4-D-polygalacturonic acid (PGA) fragments (Farmer, E. E., Pearce, G., and Ryan, C. A. (1989) Proc. Natl. Acad. Sci. U. S. A. 86, 1539-1542) that activate the expression of defensive and developmental genes in plant tissues. [gamma-35S]ATP, but not [gamma-35S]GTP, has now been found to strongly label pp34 in the presence of the PGA fragments. PGA-enhanced phosphorylation of pp34 is at one or more threonine residue(s) and therefore is the product of a serine/threonine kinase. alpha-1,4-L-Polyguluronic acid (PGU) enhances thiophosphorylation of pp34, but is less effective than PGA. beta-1,4-D-Polymannuronic acid (PMA) is inactive. In vivo synthesis of proteinase inhibitors in tomato leaves in response to PGA, PGU, and PMA parallels enhancing activities in in vitro phosphorylation assays. The minimum oligogalacturonide lengths that enhance in vitro thiophosphorylation of pp34 are about 14-15 residues, which are near the minimum sizes of uronides required to elicit a variety of localized defensive and developmental responses in plants. The lengths of biologically active galacturonic acid oligomers are of the same length that form strong intermolecular complexes in solution with Ca2+. Uronide-Ca2+ complexes are proposed to be the active molecular species that initiate the signal transduction pathways regulating uronide-responsive genes.

Adenosine Triphosphate↗

Structure and developmental expression of troponin I isoforms. cDNA clone analysis of avian cardiac troponin I mRNA.

We isolated avian (chicken and quail) cardiac troponin I (TnIcardiac) cDNA clones for studies of Tn-Icardiac protein structure/evolution and developmental gene regulation. Comparison of the cDNA-predicted avian TnIcardiac amino acid sequences with known TnI sequences indicated 1) that the presence of an N-terminal extension sequence carrying a dual protein kinase A phosphorylation target site and an adjacent proline-rich segment is an ancient cardiac-specific feature of TnI which has been conserved since the bird/mammal divergence, 2) that features of the near-N-terminal troponin C (TnC)-binding site sequence suggest isoform-specific adaptation of TnI and TnC, and 3) that the avian TnIcardiac internal actin/TnC-binding, actomyosin-inhibitory, domain shows significant sequence divergence from mammalian TnIcardiac sequences, including the absence of a protein kinase C target site which is a cardiac-specific feature of TnI in mammals. Use of the cDNA clones to probe TnIcardiac mRNA expression during striated muscle development showed active expression in cardiac muscle from early developmental times (day 4 in ovo), but not in embryonic or adult skeletal muscle or in embryonic skeletal muscle cell cultures. Transcriptional run-on analysis showed that the heart-specific expression of TnIcardiac mRNA in embryonic striated muscle reflects transcriptional control of TnIcardiac gene expression. In many other contractile protein gene families, genes encoding cardiac isoforms are expressed early in skeletal muscle development and are later repressed. Thus, the restriction of active TnIcardiac gene expression to the cardiac muscle cell lineage is an unusual expression pattern for cardiac contractile protein genes and indicates that diverse gene regulatory mechanisms direct the differential expression of cardiac and skeletal muscle isoforms in different muscle gene families.

Amino Acid Sequence↗

Structure of the specificity domain of the Dorsal homologue Gambif1 bound to DNA.

BACKGROUND: NF-kappa B/Rel transcription factors play important roles in immunity and development in mammals and insects. Their activity is regulated by their cellular localization, homo- and heterodimerization and association with other factors on their target gene promoters. Gambif1 from Anopheles gambiae is a member of the Rel family and a close homologue of the morphogen Dorsal, which establishes dorsoventral polarity in the Drosophila embryo. RESULTS: We present the crystal structure of the N-terminal specificity domain of Gambif1 bound to DNA. This first structure of an insect Rel protein-DNA complex shows that Gambif1 binds a GGG half-site element using a stack of three arginine sidechains. Differences in affinity to Dorsal binding sites in target gene promoters are predicted to arise from base changes in these GGG elements. An arginine that is conserved in class II Rel proteins (members of which contain a transcription activation domain) contacts the outermost guanines of the DNA site. This previously unseen specific contact contributes strongly to the DNA-binding affinity and might be responsible for differences in specificity between Rel proteins of class I and II. CONCLUSIONS: The Gambif1-DNA complex structure illustrates how differences in Dorsal affinity to binding sites in developmental gene promoters are achieved. Comparison with other Rel-DNA complex structures leads to a general model for DNA recognition by Rel proteins.

Amino Acid Sequence↗