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At least 541 records · Page 30Linked to original sources
PubMed1986

Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster.

We find DNA fragments attached to the nuclear scaffold (SARs) both 5' and 3' of three Drosophila genes, defining looped domains ranging from 4.5 to 13 kb. For the two-promoter-containing gene Adh (alcohol dehydrogenase), we find two upstream and two downstream SARs. For Sgs-4, the 5' SAR covers 866 bp immediately upstream of the transcript, and in the case of fushi tarazu, the 5' SAR is found on a small fragment 4.8 kb upstream of the start of transcription. These four upstream scaffold-attached fragments comap with enhancer-like regulatory sequences. Sequence analysis of five upstream SARs reveals clusters of sequences closely related to the cleavage consensus of topoisomerase II, several copies of a specific 10 bp A-rich sequence (AATAAATCAAA), and another 10 bp T-rich stretch.

Alcohol Dehydrogenase↗
PubMed1986

Cloning of a major developmentally regulated gene expressed in mature females of Schistosoma mansoni.

A cDNA library constructed from RNA isolated from adult Schistosoma mansoni has been screened by differential hybridization to identify clones corresponding to genes highly expressed by female worms. Several such cDNAs encoding the same highly abundant mRNA species were identified. Studies with one of these (pSF10) which contained a 500 base pair insert demonstrated that this gene was not expressed in immature females or eggs and encoded a polypeptide of approximately 35 000 daltons. Quantitation of the levels of RNA showed that 10% of the total RNA of female parasites was homologous to pSF10. A single gene corresponding to pSF10 was identified in Southern blotting experiments using adult worm DNA. The cloning of this gene will facilitate study of the molecular and genetic events controlling female schistosome maturation.

Animals↗
PubMed1993

A developmentally regulated gene of Echinococcus granulosus codes for a 15.5-kilodalton polypeptide related to fatty acid binding proteins.

A stage-specific expressed gene has been isolated from a cDNA expression library of Echinococcus granulosus protoscolices. The isolated clone contains the complete coding sequence. The corresponding protein (EgDf1) has a molecular weight of 15.5 kDa and is expressed at the tegumental level in the protoscolices, being undetectable in the germinal layer of the metacestode. This protein shares an important homology with a family of low-molecular weight proteins involved in the binding of hydrophobic ligands. This family includes a protein of Schistosoma mansoni (Sm 14) that has immunoprotective activity in rodents. Histochemical and metabolic data already reported for E. granulosus suggest that EgDf1 could be a molecular marker for early events in the process of protoscolex differentiation.

Amino Acid Sequence↗
PubMed1992

Identification of a developmentally regulated gene in the mouse central nervous system which encodes a novel proline rich protein.

A full length cDNA whose corresponding mRNA is down-regulated during the mouse embryonic brain development was isolated. The cDNA contains a single long open reading frame which could encode a protein with relative molecular mass of 41 kDa. The predicted gene product contains long stretches of prolines towards the NH2-terminus, followed by a leucine/proline rich region. The cDNA probe detected a number of mRNA species in Northern blot analysis. The reverse transcriptase-polymerase chain reaction analysis of mRNA from adult mouse tissues indicated that heart and testis expressed this gene (named NDPP-1) at relatively high levels, while lower levels of mRNA were detected in a number of other tissues. Expression of NDPP-1 was also detected in embryonic carcinoma and pheochromocytoma cell lines, but not in fibroblasts. The cDNA hybridized to genomic DNA from several vertebrates species in Southern blot analysis indicating interspecies conservation of this gene. The interesting pattern of expression of the NDPP-1 gene during mouse brain development and the structure of its putative protein product indicate that this gene may play an important biological role in the development of mouse central nervous system.

Animals↗
PubMed1994

The use of arbitrary primers and the RADES method for the rapid identification of developmentally regulated genes in trypanosomes.

Biological processes, such as the cell-division cycle, differentiation and development, are driven by changes in gene expression. Short oligodeoxyribonucleotide primers (10-mers) of arbitrary sequence are currently used in the polymerase chain reaction (PCR) to generate genomic fingerprints (RAPDs) for the characterisation and differentiation of organisms and for mapping loci of interest. Since the products of such reactions are generally less than 1 kb in size, the use of arbitrary primers on cDNA should generate RAPDs which are characteristic of expressed genes. To assess this possibility, two model systems were employed; one in which actively dividing Trypanosoma brucei brucei bloodstream forms differentiate to non-dividing forms, and the second in which non-dividing metacyclic forms of T. congolense differentiate to actively dividing bloodstream forms. In the technique herein, mRNA from each differentiated form was reverse transcribed into cDNA which was then used as the template in the PCR. The resultant products were examined by agarose-gel electrophoresis. As few as 10(3) trypanosomes were sufficient for the generation of a RAPD print after first amplifying the total cDNA through exploitation of the fixed 3' and 5' ends of trypanosome nuclear mRNAs. Differences in RAPD patterns between the differentiated forms examined were mainly due to differences in gene expression. The technique can rapidly identify genes expressed at very low levels and which are up- or down-regulated in the different forms examined. PCR products of interest are easily purified from the agarose gels for direct cloning and complete sequence determination due to their relatively small size (0.1-1 kb).

Animals↗
PubMed1994

Differential repair of UV damage in a developmentally regulated gene of Dictyostelium discoideum.

The repair of cyclobutane pyrimidine dimers was measured under non-replicating conditions in a 2054-bp fragment of a cAMP-inducible cysteine proteinase (CP2) gene in D. discoideum. Overall genomic repair was unaffected by cAMP. The removal of dimers from CP2 in the wild-type NP2 cells as quantified using T4 endonuclease V was independent of transcription and was the same as in the overall genome. In a UV-sensitive radC mutant in which the rate of overall dimer removal was previously shown to be reduced, the initial rate of dimer removal in the uninduced CP2 gene (-cAMP) was 3-fold lower compared to the induced gene (+cAMP), in which repair was identical to that for the induced and uninduced states of NP2. D. discoideum may have two pathways for repairing dimers. One, effective in the wild-type strain but of reduced efficiency in radC repairs dimers equally well independent of transcription and at about the same rate as in the overall genome. A second pathway, retained in radC, repairs dimers more slowly in the overall genome and in the uninduced CP2 gene while undergoing the wild-type rate of repair in the transcriptionally active gene. Hence radC has reduced ability to repair transcriptionally inactive DNA, a defect similar to that of xeroderma pigmentosum group C.

Animals↗
PubMed2004

Expression profiling of the Leishmania life cycle: cDNA arrays identify developmentally regulated genes present but not annotated in the genome.

As genomic sequencing of Leishmania nears completion, functional analyses that provide a global genetic perspective on biological processes are important. Despite polycistronic transcription, RNA transcript abundance can be measured using microarrays. To provide a resource to evaluate cDNA arrays, we undertook 5' expressed sequence tag analysis of 2183 full-length randomly selected cDNAs from Leishmania major promastigote (days 3, 7, 10 of culture in vitro), and lesion-derived amastigote libraries. PCR-amplified inserts from 1830 of these cDNA representing 1001 unique genes were spotted onto microarrays, and compared internally with PCR-amplified open reading frames (ORFs) from 904 genes representing 842 unique genes annotated in the L. major genome. Microarrays were screened with RNA from procyclic, metacyclic and amastigote populations of L. major. Redundant clones on the array gave highly reproducible results, providing confidence in identification of stage-specific gene expression. Four hundred and thirty unique (i.e. non-redundant) stage-specific genes were identified. A higher percentage of stage-specific gene expression was observed in amastigotes ( approximately 35%) compared to metacyclics ( approximately 12%) for both cDNAs and ORFs, but cDNAs provided a richer source of regulated genes than currently annotated ORFs from the Leishmania genome. In mapping cDNAs onto the Leishmania genome, we noted that approximately 42% aligned to regions not recognised as genes using current predictive annotation tools. These genes are highly represented in our stage-specific genes, and therefore represent important drug targets and vaccine candidates. Careful annotation of cDNAs onto the Leishmania genome will be important before producing the next generation of oligonucleotide arrays based on annotated genes of the genomic sequencing project.

Animals↗
PubMed2005

Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes.

Sequence conservation has been used to find genes and to pinpoint functional non-coding sequences such as transcriptional regulatory elements. In this article, we analysed the conservation of 104 experimentally validated murine enhancer sequences between the mouse and zebrafish genomes. Surprisingly, only 10.5% of the mouse enhancers have homologues in zebrafish. All of the genes with conserved cis-elements have regulatory functions during embryonic development, perhaps reflecting substantial structural constraints on the integration of spatio-temporal signalling cues during the formation of the vertebrate body.

Animals↗
PubMed2000

Alterations of expression of developmentally important genes in preimplantation bovine embryos by in vitro culture conditions: implications for subsequent development.

Recent advances in molecular technology and in vitro production of bovine embryos have enabled studies of gene transcription in preimplantation embryos. On the basis of knowledge of the sequence of the selected gene, various modifications of Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) technology have been employed. Several lines of evidence in mouse and cattle indicate that expression patterns of genes from in vitro-produced embryos are not necessarily representative of those of in vivo embryos. An important gene that has been found to be expressed by in vivo-derived bovine blastocysts, but not in their in vitro-produced counterparts, is the Connexin43 gene that is crucial for maintenance of compaction. The bovine leukemia inhibitory factor (bLIF) and LIF-receptor-beta (LR-beta) genes were expressed by in vitro-produced embryos, but not in their in vivo counterparts. The heat shock protein gene 70.1 (Hsp 70.1) was upregulated by blastocysts produced in vitro compared to in vivo embryos, while the glucose transporter-1 mRNA (Glut-1) was downregulated by morulae produced in vitro as compared to in vivo-derived morulae. Furthermore, mRNA expression levels of a set of "marker genes" were shown to be affected by the presence or absence of serum in the culture medium. Most embryos grown under serum-free conditions had higher mRNA abundances than those cultured in serum-enriched medium. It is hypothesized that persistent alterations of the normal gene expression patterns may be responsible for the large offspring syndrome that is observed in approximately one third of the calves resulting from the transfer of in vitro-produced embryos. A primary candidate for such deviations may be an altered methylation pattern that can either lead to silencing or induction of a specific gene. Messenger RNA phenotyping of genes essential in early development provides a useful tool to assess the normality of the produced embryos and a tool to optimize in vitro culture conditions for bovine embryos.

Animals↗
PubMed1999

The fork head transcription factor Fkh5/Mf3 is a developmental marker gene for superior colliculus layers and derivatives of the hindbrain somatic afferent zone.

Fork head-5 (Fkh5; also known as Mf3 and TWH) is a transcription factor of the winged helix family. As part of an extended project to understand the function of this protein in the developing mouse brain, in the present work we have used Fkh5/Mf3 expression as a marker to study the development of the midbrain and hindbrain. In the midbrain, Fkh5/Mf3 is expressed in the superior colliculus, in the ventricular layer of the inferior colliculus and in the isthmus. In the superior colliculus, Fkh5/Mf3 is expressed by cells of layers 4a and 4c since early in development. In the hindbrain, Fkh5/Mf3 is a longitudinal marker (as opposed to a transverse or rhombomeric one), since it labels nuclei belonging to the somatic afferent zone (ventral cochlear nucleus, cuneate and external cuneate nuclei, principal and spinal nuclei of the trigeminal). In addition, Fkh5/Mf3 is expressed by the developing endopiriform nucleus and by the olivary pretectal nucleus. The results suggest that Fkh5/Mf3 has an early role in the lamination of the tectum and in the longitudinal differentiation of the hindbrain.

Afferent Pathways↗
PubMed1985

mRNA stabilization controls the expression of a class of developmentally regulated genes in Dictyostelium discoideum.

During the development of Dictyostelium discoideum, several thousand new mRNA species appear in the cytoplasm after the cells have formed stable aggregates. Here we show that six of these late mRNAs, corresponding to six clones randomly chosen from a genomic library, are synthesized from the very beginning of development at a rate comparable to that observed late in development but that transcripts do not accumulate until after aggregation. The early- and late-synthesized mRNAs are identical in size and compete with each other for hybridization to the genomic clones. The early-synthesized mRNAs do not accumulate in the cytoplasm in the preaggregation stage because they are very unstable. Their stability, estimated from the kinetics of incorporation during continuous labeling with (32)P, increases by perhaps an order of magnitude in the postaggregation stage. We conclude that mRNA stabilization is the major controlling factor of the expression of these genes.

Journal Article↗
PubMed1993

Type 2X-myosin heavy chain is coded by a muscle fiber type-specific and developmentally regulated gene.

We have previously reported the identification of a distinct myosin heavy chain (MyHC) isoform in a major subpopulation of rat skeletal muscle fibers, referred to as 2X fibers (Schiaffino, S., L. Gorza, S. Sartore, L. Saggin, M. Vianello, K. Gundersen, and T. Lømo. 1989. J. Muscle Res. Cell Motil. 10:197-205). However, it was not known whether 2X-MyHC is the product of posttranslational modification of other MyHCs or is coded by a distinct mRNA. We report here the isolation and characterization of cDNAs coding a MyHC isoform that is expressed in type 2X skeletal muscle fibers. 2X-MyHC transcripts differ from other MyHC transcripts in their restriction map and 3' end sequence and are thus derived from a distinct gene. In situ hybridization analyses show that 2X-MyHC transcripts are expressed at high levels in the diaphragm and fast hindlimb muscles and can be coexpressed either with 2B- or 2A-MyHC transcripts in a number of fibers. At the single fiber level the distribution of each MyHC mRNA closely matches that of the corresponding protein, determined by specific antibodies on serial sections. In hindlimb muscles 2X-, 2A-, and 2B-MyHC transcripts are first detected by postnatal day 2-5 and display from the earliest stages a distinct pattern of distribution in different muscles and different fibers. The emergence of type 2 MyHC isoforms thus defines a distinct neonatal phase of fiber type differentiation during muscle development. The functional significance of MyHC isoforms is discussed with particular reference to the velocity of shortening of skeletal muscle fibers.

Amino Acid Sequence↗
PubMed1984

Developmental genetics of the 2E-F region of the Drosophila X chromosome: a region rich in "developmentally important" genes.

We have analyzed the 2E1-3A1 area of the X chromosome with special attention to loci related to embryogenesis. Published maps indicate that this chromosomal segment contains ten bands. Our genetic analysis has identified 11 complementation groups: one recessive visible (prune), two female steriles and eight lethals. One of the female sterile loci is fs(1)k10 for which homozygous females produce both egg chambers and embryos with a dorsalized morphology. The second female sterile is the paternally rescuable fs(1)pecanex in which unrescued embryos have a hypertrophic nervous system. Of the eight lethal complementation groups two are recessive embryonic lethals: hemizygous giant (gt) embryos possess segmental defects, and hemizygous crooked neck (crn) embryos exhibit a twisted phenotype. Analysis of these mutations in the female germ line indicates that gt does not show a maternal effect, whereas normal activity of crn is required for germ cell viability. Analysis of the maternal effect in germ line clones of the remaining six recessive lethal complementation groups indicates that four are required for germ cell viability and one produces ambiguous results for survival of the germ cells. The remaining, l(1)pole hole, is a recessive early pupal lethal in which embryos derived from germ line clones and lacking wild-type gene activity exhibit the "torso" or "pole hole" phenotype.

Alleles↗
PubMed1986

Functional, developmentally expressed genes for mouse U1a and U1b snRNAs contain both conserved and non-conserved transcription signals.

Four genes that encode mouse U1a1, U1b2 and U1b6 snRNAs have been isolated from a mouse genomic DNA library. They all appear to be functional U1 genes since they are accurately transcribed into full length, capped snRNAs upon injection into Xenopus oocytes. A mouse pseudogene that is not transcribed in Xenopus oocytes was also isolated from the mouse genomic library. DNA sequence analysis of the 5' and 3' flanking regions of the functional genes revealed the presence of three highly conserved sequence elements that have been shown to be required for transcription initiation or 3' end formation in other U1 genes. Each of these U1 RNA genes also contains non-conserved sequences in the 5' flanking region that could function in their controlled expression during development.

Animals↗
PubMed1986

Homologies of nucleotide sequences in the 5'-end regions of two developmentally regulated genes of Sarcophaga peregrina.

In the previous paper we demonstrated that the storage protein gene and 25-kDa protein gene are expressed sequentially in the fat body of middle third-instar Sarcophaga peregrina larvae. In this paper, we showed that the expressions of these two genes are regulated at the transcriptional level, and searched for homologous nucleotide sequences in the two genes in the vicinity of their 5'-ends, assuming that these two genes are regulated by a common mechanism. We selected 9 homologous sequences and found that most of them were distributed in two clusters located between positions -400 and +1. We identified an SV40 enhancer core segment-like sequence in the nontranslated region of the first exons of both genes, which might explain the efficient transcriptions of these two genes.

Animals↗
PubMed1992

A negative transcriptional control region of a developmentally-regulated gene co-localizes with the origin of replication of an endogenous plasmid in Dictyostelium.

The endogenous nuclear plasmid Ddp1 from the wild-type Dictyostelium discoideum strain NC4 has been cloned, its origin of replication has been localized, and plasmid-encoded genes have been mapped that are preferentially expressed during growth or development. Here we present an analysis of the regulation of the Ddp1-encoded gene d5, which, in wild-type cells, is expressed only during the multicellular stages of development. In this study, we show that sequences 3' to the d5 coding region are required to suppress constitutive expression of d5 from aberrant transcriptional start sites and that this regulatory region acts at a distance and in an orientation-independent manner. The cis-acting negative regulatory element(s) necessary for repression of aberrant d5 expression is either very tightly linked or identical to sequences required for extrachromosomal replication, such that all 3' deletions that cause constitutive d5 expression result in the integration of the plasmid into the D. discoideum genome. Placing d5 (without the 3' regions containing the Ddp1 origin) on an extrachromosomal vector based on another endogenous plasmid (Ddp2) did not restore proper transcriptional regulation, suggesting that an extrachromosomal environment alone is not sufficient to confer proper transcriptional regulation to d5.

Animals↗