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PubMed1995

Developmental variability of metallothionein Mtn gene expression in the species of the Drosophila melanogaster subgroup.

Developmental expression of the Drosophila melanogaster metallothionein Mtn gene has been analysed. Transcripts of this gene accumulate during the vitellogenic phase of oogenesis in a ring of follicular cells at the oocyte-nurse cell margin and in the follicular cells surrounding the oocyte. There is also strong expression of the Mtn gene during the second half of embryogenesis in hemocytes, the endoderm midgut, and Malpighian tubules. A banded expression pattern is observed transiently in the midgut at stage 13. The two Mtn alleles, Mtn and Mtn, show quantitative differences in their expression patterns. Copper intoxication of flies does not induce ectopic expression of the Mtn gene, but rather leads to over-expression of the gene in the structures where it is normally transcribed. Mtn transcription is not altered in homozygous mutants of four genes (lab, wg, dpp, bap) known to be involved in midgut morphogenesis. Expression of Mtn has been also studied in six other species of the melanogaster subgroup. This analysis demonstrates that regulation of Mtn gene transcription has changed during evolution of the Drosophila lineage. For example, Mtn is expressed specifically in the Malpighian tubules of D. melanogaster, while in D. mauritiana and D. sechellia the amnioserosa is a specific location of expression. Nonetheless, expression of Mtn in the midgut is common to the seven species, suggesting a basic role for the MTN protein during embryogenesis in this organ, possibly in the release of metallic ions from vitellogenins. In contrast, two genes also expressed in the embryonic midgut, lab and dFRA, display identical patterns in all species of the melanogaster subgroup. The diversity of Mtn patterns in closely related Drosophila species exemplifies the rapid evolution of a gene regulatory system.

Alleles↗
PubMed1989

Developmental distribution of RNA and protein products of the Drosophila alpha-tubulin gene family.

The developmental pattern of gene expression of the Drosophila melanogaster alpha-tubulin family has been examined in detail at both the mRNA and protein levels. Northern data from 16 stages of development have been quantified to produce estimates of pool sizes of each of the alpha-tubulin transcripts through development. The in situ pattern of alpha 67C RNA localization in developing oocytes and early embryos has also been determined. At the protein level, two of the three previously unidentified products of alpha-tubulin genes (alpha 67C and alpha 85E) have been identified. Evidence that protein from the fourth gene comigrates with the ubiquitously expressed alpha 84B is presented. In addition to the primary translational products of the alpha-tubulin genes, an elaborate series of post-translationally modified alpha-tubulins has been resolved. The developmental profiles of both synthesis and accumulation of these alpha-tubulin proteins are described.

Animals↗
PubMed2006

Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: alternative structures, developmental expression, and biophysical variations.

We describe the regulated transcriptome of CACNA1G, a human gene for T-type Ca(v)3.1 calcium channels that is subject to extensive alternative RNA splicing. Fifteen sites of transcript variation include 2 alternative 5'-UTR promoter sites, 2 alternative 3'-UTR polyadenylation sites, and 11 sites of alternative splicing within the open reading frame. A survey of 1580 fetal and adult human brain full-length complementary DNAs reveals a family of 30 distinct transcripts, including multiple functional forms that vary in expression with development. Statistical analyses of fetal and adult transcript populations reveal patterns of linkages among intramolecular splice site configurations that change dramatically with development. A shift from nearly independent, biased splicing in fetal transcripts to strongly concerted splicing in adult transcripts suggests progressive activation of multiple "programs" of splicing regulation that reorganize molecular structures in differentiating cells. Patch-clamp studies of nine selected variants help relate splicing regulation to permutations of the gating parameters most likely to modify T-channel physiology in expressing neurons. Gating behavior reflects combinatorial interactions between variable domains so that molecular phenotype depends on ensembles of coselected domains, consistent with the observed emergence of concerted splicing during development. We conclude that the structural gene and networks of splicing regulatory factors define an integrated system for the phenotypic variation of Ca(v)3.1 biophysics during nervous system development.

Alternative Splicing↗
PubMed1999

Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle- and developmentally regulated promoter.

Gene activation in eukaryotes requires chromatin remodeling complexes like Swi/Snf and histone acetylases like SAGA. How these factors are recruited to promoters is not yet understood. Using CHIP, we measured recruitment of Swi/Snf, SAGA, the repressor Ash1p, and transcription factors Swi5p and SBF to the HO endonuclease promoter as cells progress through the yeast cell cycle. Swi5p's entry into nuclei at the end of anaphase recruits Swi/Snf, which then recruits SAGA. These two factors then facilitate SBF's binding. Ash1p, which only accumulates in daughter cell nuclei, binds to HO soon after Swi5p and aborts recruitment of Swi/Snf, SAGA, and SBF. Swi5p remains at HO for only 5 min. Swi/Snf's and SAGA's subsequent persistence at HO is self sustaining and constitutes an "epigenetic memory" of HO's transient interaction with Swi5p.

Acetyltransferases↗
PubMed1986

Analysis of the DNase I-hypersensitive site of a developmentally regulated 25-kDa protein gene of Sarcophaga peregrina.

Change in chromatin structure of a developmentally regulated gene of Sarcophaga peregrina (flesh fly) during development was investigated. This gene (25-kDa protein gene) was specifically activated in the fat body, but not the hemocytes of larvae in the middle of the third instar. The mRNA level in the fat body decreased thereafter, reaching one-fifth of the maximum level in the late third instar to early pupal stage. In the chromatin of fat body nuclei, a DNase I-hypersensitive site was found about 300 base pairs upstream from the transcription initiation site of the 25-kDa protein gene. This DNase I-hypersensitive site appeared before activation of the 25-kDa protein gene, and it was conserved until the late third instar, but disappeared in the early pupal stage. Since activity of the 25-kDa protein gene decreases significantly in the early pupal stage, it is likely that disappearance of this DNase I-hypersensitive site coincides with inactivation of the 25-kDa protein gene.

Animals↗
PubMed1994

Identification of a fetal exon in the human fast troponin T gene.

A developmentally regulated exon has been identified in the 5'-alternatively spliced region of the human fast Troponin T (TnT) gene. Expressed in fetal (but not adult) muscle, this exon is homologous with the fetal exons recently described in the rabbit and rat fast TnT genes. They all exhibit a split codon organization and encode a highly acidic peptide. To determine if the splicing pathways, including the human fetal exon, are also conserved, we defined the major TnT splicing patterns in fetal muscle. They generate fetal TnT 1, fetal TnT 3, and TnT1f, and TnT3f, species previously described in rabbit and rat skeletal muscles.

Alternative Splicing↗
PubMed1992

Fluorescence-activated sorting of totipotent embryonic stem cells expressing developmentally regulated lacZ fusion genes.

Murine embryonic stem (ES) cells were infected with a retrovirus promoter trap vector, and clones expressing lacZ fusion genes (LacZ+) were isolated by fluorescence-activated cell sorting (FACS). Of 12 fusion genes tested, 1 was repressed when ES cells were allowed to differentiate in vitro. Two of three lacZ fusion genes tested were passed into the germ line, indicating that FACS does not significantly affect stem cell totipotency. The pattern of lacZ expression observed in vivo was consistent with that seen in vitro. Both fusion genes were expressed in preimplantation blastulas. However, a fusion gene whose expression was unaffected by in vitro differentiation was ubiquitously expressed in day-10 embryos, while the other, which showed regulated expression in vitro, was restricted to cells located along the posterior neural fold, the optic chiasm, and within the fourth ventricle. These results demonstrate the utility of using promoter trap vectors in conjunction with fluorescence sorting to disrupt developmentally regulated genes in mice.

Animals↗
PubMed1995

Tissue-specific and developmental regulation of a gene encoding a low molecular weight sulfur-rich protein in soybean seeds.

A gene corresponding to a cDNA clone, SE60, encoding a low molecular weight sulfur-rich protein in soybean seeds was isolated from a soybean genomic library and characterized at the nucleotide level. The SE60 gene is interrupted by an intervening sequence of 694 bp in size. The 5' flanking region of the gene contained various regulatory sequences such as the RY repeat and CACA elements found in other seed protein genes of legumes. The SE60 gene encoded a preprotein of 75 amino acids, having a signal sequence of 28 amino acids at the N-terminus. The mature protein of 47 amino acids was basic and cysteine-rich. Northern blot analysis suggested that the SE60 gene is expressed in a tissue-specific and developmentally regulated manner during soybean seed development. The SE60 genes form a small multigene family composed of about four members in the soybean genome.

Amino Acid Sequence↗
PubMed1988

Developmental regulation of embryonic genes in plants.

Somatic embryogenesis from cultured carrot cells progresses through successive morphogenetic stages termed globular, heart, and torpedo. To understand the molecular mechanisms underlying plant embryogenesis, we isolated two genes differentially expressed during embryo development. The expression of these two genes is associated with heart-stage embryogenesis. By altering the culture conditions and examining their expressions in a developmental variant cell line, we found that these genes were controlled by the developmental program of embryogenesis and were not directly regulated by 2,4-dichlorophenoxyacetic acid, the growth regulator that promotes unorganized growth of cultured cells and suppresses embryo morphogenesis. These genes are also expressed in carrot zygotic embryos but not in seedlings or mature plants.

Journal Article↗
PubMed1992

Light-independent developmental regulation of cab gene expression in Arabidopsis thaliana seedlings.

We found a transient increase in the amount of mRNA for four nuclear genes encoding chloroplast proteins during early development of Arabidopsis thaliana. This increase began soon after germination as cotyledons emerged from the seed coat; it occurred in total darkness and was not affected by external factors, such as gibberellins or light treatments used to stimulate germination. Three members of the cab gene family and the rbcS-1A gene exhibited this expression pattern. Because timing of the increase coincided with cotyledon emergence and because it occurred independently of external stimuli, we suggest that this increase represents developmental regulation of these genes. Further, 1.34 kilobases of the cab1 promoter was sufficient to confer this expression pattern on a reporter gene in transgenic Arabidopsis seedlings. The ability of the cab genes to respond to phytochrome preceded this developmental increase, showing that these two types of regulation are independent.

Base Sequence↗
PubMed2001

Genetic studies of mrp, a locus essential for cellular aggregation and sporulation of Myxococcus xanthus.

Under starvation conditions, Myxococcus xanthus undergoes a complex developmental process which includes cellular aggregation and sporulation. A transposon insertion mutant (the Tn5-Omega280 mutant) with defects in both aggregation and sporulation was analyzed in this study. The Tn5-Omega280 mutant was found to have a disrupted NtrC-like response regulator designated Myxococcus regulatory protein B (mrpB). Further sequencing analyses revealed a histidine kinase homolog (mrpA) immediately upstream of mrpB and a cyclic AMP receptor protein-like transcriptional regulator (mrpC) downstream of mrpB. In-frame deletion analyses revealed that both the mrpB and mrpC genes were required for cellular aggregation and sporulation but that only mrpA was required for sporulation only. Site-specific mutagenesis of the putative phosphorylation site of MrpB, D58, showed that a D58A mutation caused defects in both aggregation and sporulation but that a D58E mutation resulted in only a sporulation defect. Further genetic and molecular analyses with reporter genes and reverse transcription-PCR indicated that mrpA and mrpB are cotranscribed but that mrpC is transcribed independently and that all of these genes are developmentally regulated. In addition, MrpB is essential for transcription of mrpC and MrpC regulates its own transcription. These data indicate that Mrp proteins are important components required for M. xanthus development. The complicated interaction between Mrp proteins may play an important role in regulating developmental gene expression in M. xanthus.

Amino Acid Sequence↗
PubMed2006

Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster.

Polycomb group (PcG) proteins maintain transcriptional repression of developmentally important genes and have been implicated in cell proliferation and stem cell self-renewal. We used a genome-wide approach to map binding patterns of PcG proteins (Pc, esc and Sce) in Drosophila melanogaster Kc cells. We found that Pc associates with large genomic regions of up to approximately 150 kb in size, hereafter referred to as 'Pc domains'. Sce and esc accompany Pc in most of these domains. PcG-bound chromatin is trimethylated at histone H3 Lys27 and is generally transcriptionally silent. Furthermore, PcG proteins preferentially bind to developmental genes. Many of these encode transcriptional regulators and key components of signal transduction pathways, including Wingless, Hedgehog, Notch and Delta. We also identify several new putative functions of PcG proteins, such as in steroid hormone biosynthesis. These results highlight the extensive involvement of PcG proteins in the coordination of development through the formation of large repressive chromatin domains.

Animals↗
PubMed2005

Developmental expression of clock genes in the Syrian hamster.

Transcription/translation feedback loops consisting of multiple clock genes are thought to be essential for circadian oscillations at cellular, tissue and organismal levels. We examined the developmental expressions of three clock genes (Bmal1, Cry1 and Per1) in the Syrian hamster to probe the oscillatory properties of the suprachiasmatic nucleus (SCN) over the first 4 days after the completion of SCN neurogenesis. Samples were taken at the dam's circadian times 6, 12, and 18 daily over 4 days in constant dim light and processed for in situ hybridization using 35S-labeled RNA probes. Collection times were based on the phases of Bmal1 and Per1 rhythms in adult SCN and on an observed difference in Per1 mRNA at CT6 and 18 on postnatal day 2. For the developmental study, sections from each brain were processed in parallel for the three genes. Bmal1 was prominently expressed in the fetal SCN while Per1 and Cry1 were only weakly expressed. Transcripts of all three genes showed higher abundance just after birth. At subsequent ages, Bmal1 showed a significant decrease, while Per1 continued to be greater than prenatal levels. Significant variation was detected across circadian times for Cry1, but no circadian variation was detected for Per1 and Bmal1. Molecular oscillations equivalent to those observed in adults were not present in the fetal SCN despite evidence for an entrainable pacemaker at that time. An absence of robust oscillations during early SCN development may in part explain the strong phase-setting effects of pharmacological agents on the fetal/neonatal clock.

ARNTL Transcription Factors↗
PubMed2004

Identification and integrative analysis of 28 novel genes specifically expressed and developmentally regulated in murine spermatogenic cells.

Mammalian spermatogenesis is a highly ordered process that occurs in mitotic, meiotic, and postmeiotic phases. The unique mechanisms responsible for this tightly regulated developmental process suggest the presence of an intrinsic genetic program composed of spermatogenic cell-specific genes. In this study, we analyzed the mouse round spermatid UniGene library currently containing 2124 gene-oriented transcript clusters, predicting that 467 of them are testis-specific genes, and systematically identified 28 novel genes with evident testis-specific expression by in silico and in vitro approaches. We analyzed these genes by Northern blot hybridization and cDNA cloning, demonstrating the presence of additional transcript sequences in five genes and multiple transcript isoforms in six genes. Genomic analysis revealed lack of human orthologues for 10 genes, implying a relationship between these genes and male reproduction unique to mouse. We found that all of the novel genes are expressed in developmentally regulated and stage-specific patterns, suggesting that they are primary regulators of male germ cell development. Using computational bioinformatics tools, we found that 20 gene products are potentially involved in various processes during spermatogenesis or fertilization. Taken together, we predict that over 20% of the genes from the round spermatid library are testis-specific, have discovered the 28 authentic, novel genes with probable spermatogenic cell-specific expression by the integrative approach, and provide new and thorough information about the novel genes by various in vitro and in silico analyses. Thus, the study establishes on a comprehensive scale a new basis for studies to uncover molecular mechanisms underlying the reproductive process.

Animals↗
PubMed1988

Developmental expression of the Drosophila zeste gene and localization of zeste protein on polytene chromosomes.

The expression of the zeste gene varies through the life cycle of the fly. Its transcription is most abundant in maternal RNA, declines to very low levels during larval growth, but rises again in late third instar larvae and pupae. Using transposons containing a zeste-lacZ gene, we found a corresponding variation in the tissue distribution of zeste from stage to stage. Nearly ubiquitous expression of the zeste-lacZ gene is found in late embryos and first instar larvae, but disappears almost completely except in brain and gonads by third instar larva. Shortly before pupation expression rises again in imaginal discs, Malpighian tubules, and salivary glands and again becomes nearly ubiquitous in pupae. zeste continues to be expressed in adult brain and gonads. We constructed flies carrying a zeste gene controlled by the heat shock promoter and studied the distribution of zeste protein in their polytene chromosomes as well as those of wild-type flies. Using affinity-purified anti-zeste antibodies, we find that wild-type salivary gland chromosomes contain about 60 strong bands of zeste immunofluorescence at specific cytological locations. After heat induction of larvae containing the hs-zeste gene, many hundreds of bands appear. These results suggest the involvement of zeste in the expression of a wide variety of genes at different developmental stages.

Animals↗
PubMed1991

Isolation, characterization, and developmental expression of the rat peptide-YY gene.

In the present study we describe the isolation, structural characterization, and developmental expression of the gene encoding the intestinal hormone peptide-YY. Examination of the nucleotide sequence of the peptide-YY gene reveals that each of the four exons encodes a functional domain of its mRNA that is analogous to the corresponding exons of the genes encoding two closely related peptides neuropeptide-Y and pancreatic polypeptide. The highly conserved structural organization of the genes encoding this family of three peptides suggests that each gene arose from the duplication of a common ancestral gene. Developmental studies reveal that the peptide-YY gene exhibits a complex pattern of tissue-specific expression in the gastrointestinal tract. Unlike many gastrointestinal hormones, peptide-YY mRNA levels are highest before birth. The pancreas appears to be the major site of peptide-YY gene expression in the fetus, exceeding colonic expression by 7-fold. The abundance of peptide-YY mRNA in the pancreas declines rapidly after birth, in contrast to the colon, where mRNA levels are maintained throughout development into adulthood. Expression of the peptide-YY gene before birth antedates the presence of known enteral secretagogues for this hormone, suggesting alternate mechanisms that control its biosynthesis during development.

Amino Acid Sequence↗
PubMed2004

[Developmental changes of myoglobin gene expression in longissimus dorsi muscle of Erhualian and large white pigs].

In present study, the developmental patterns of myoglobin (MB) mRNA expression were compared between Erhualian and Large White boars, Gender difference was also examined in Erhualian pigs. Semi-quantitative RT-PCR was applied to determine the level of MB mRNA. Different developmental patterns were observed in two breeds of pigs. MB mRNA expression was low in both breeds at D3, while divergent trends were followed by different breed of pigs thereafter. No significant changes in MB mRNA expression were observed in Large White boars over the period of investigation, although a higher level was seen at D120. In Erhualian boars, however, the level of MB mRNA increased significantly (P<0.01) from D3 to D20 and stayed high consistently afterwards. As a result, Erhualian boars expressed higher level of MB mRNA in Longissimus Dorsi muscle compared with Large White boars on 20, 90, 120 and 180 days of age. Similar patterns of MB mRNA expression were found in both sexes of Erhualian pigs, except at D180, a remarkable decrease occurred to females (P<0.01), resulting in a significant (P<0.01) gender difference at D180 with higher level of MB mRNA expressed in Erhualian boars.

Animals↗
PubMed1998

Gene expression during mammalian meiosis.

The expression of a wide variety of genes is developmentally regulated during mammalian meiosis. Drawing mainly on studies in spermatogenesis, this review shows that some of these genes are transcribed exclusively in germ cells, while others are also transcribed in somatic cells. Some of the genes expressed exclusively in spermatogenic cells are unlike any expressed in somatic cells, while others are isologous to genes expressed in somatic cells and are in the same gene family. Some of the developmentally regulated genes also expressed in somatic cells produce spermatogenic cell-specific transcripts, while others produce transcripts that are apparently the same in somatic and germ cells. Possible answers to why so many genes have atypical patterns of expression during meiosis are that: (1) all cell types express certain genes that define their cell type and lineage, (2) spermatogenesis is a developmental process that progresses according to a genetic program directing the sequential and coordinate expression of specific genes, (3) some genes are expressed that encode proteins required for meiosis, (4) some genes are expressed that encode proteins not required until after meiosis, (5) some genes are expressed to compensate for other genes that become inactivated with X chromosome condensation, and (6) it has been suggested that regulation of gene expression becomes leaky during spermatogenesis due to changes in DNA organization, leading to production of irrelevant transcripts. However, it is largely unknown how extrinsic cues from the endocrine system and surrounding somatic cells interact with intrinsic mechanisms of germ cells to activate signal transduction processes regulating transcription during mammalian meiosis.

Animals↗