Biomedical subjects

Y T Ip

Publications and source records attributed to Y T Ip.

31 records · Page 2Linked to original sources

PubMed1994

Molecular genetics of Drosophila immunity.

Insects resist bacterial infections through the induction of both cellular and humoral immune responses. The cellular response involves the mobilization of hemocytes, whereas the humoral response utilizes antibacterial peptides that are synthesized in the fat bodies and secreted into the circulating hemolymph. Recent studies suggest that the induction of the humoral response involves Rel-containing regulatory proteins, Dif and dorsal, which are related to mammalian NF-kappa B. These regulatory proteins function as sequence-specific transcription factors that induce the expression of immunity genes, including cecropin and diptericin. In mammals, NF-kappa B has been implicated in both lymphocyte differentiation and the acute-phase response. The finding that insect and mammalian immunity involve related transcription factors offers the promise that genetic studies in Drosophila might lead to the identification of novel components mediating mammalian immunity.

Animals↗

PubMed1994

Neurogenic expression of snail is controlled by separable CNS and PNS promoter elements.

The Drosophila snail (sna) gene is first expressed in cells giving rise to mesoderm and is required for mesoderm formation. sna is subsequently expressed in the developing nervous system. sna expression during neurogenesis evolves from segmentally repeated neuroectodermal domains to a pan-neural pattern. We have identified a 2.8 kb regulatory region of the sna promoter that drives LacZ expression in a faithful neuronal pattern. Deletion analysis of this region indicates that the pan-neural element is composed of separable CNS and PNS components. This finding is unexpected since all known genes controlling early neurogenesis, including the proneural genes (i.e. da and AS-C), are expressed in both the CNS and PNS. We also show that expression of sna during neurogenesis is largely independent of the proneural genes da and AS-C. The separate control of CNS and PNS sna expression and independence of proneural gene regulation add to a growing body of evidence that current genetic models of neurogenesis are substantially incomplete.

Animals↗

PubMed1993

Dif, a dorsal-related gene that mediates an immune response in Drosophila.

There are striking parallels between the regulation of gene expression along the dorsoventral (DV) axis of Drosophila embryos and lymphoid-restricted expression in the mammalian immune system. Both depend on regulatory factors containing rel domains (dorsal and NF-kappa B) that are controlled at the level of nuclear transport. A novel Rel-containing gene in Drosophila, Dif (dorsal-related immunity factor), provides a potential link between these seemingly disparate processes. Although Dif maps close to dorsal, it does not appear to participate in DV patterning, but instead mediates an immune response in Drosophila larvae. Dif is normally localized in the cytoplasm of the larval fat body, but quickly accumulates in the nucleus upon bacterial infection or injury. Evidence is presented that once in the nucleus, Dif binds to kappa B-like sequence motifs present in promoter regions of immunity genes. These results suggest that mammalian and insect immunity share a common evolutionary origin.

Adipose Tissue↗

PubMed1992

dorsal-twist interactions establish snail expression in the presumptive mesoderm of the Drosophila embryo.

The first step in the differentiation of the Drosophila mesoderm is the activation of two regulatory genes, twist (twi) and snail (sna), in ventral regions of early embryos. sna is a transcriptional repressor that is uniformly expressed throughout the presumptive mesoderm. Its sharp lateral limits help to establish the boundary between the mesoderm and neuroectoderm. Genetic studies suggest that sna is a target of the dorsal (dl) morphogen, and this interaction provides a model for determining how a morphogen gradient establishes a sharp, on/off threshold response. We present evidence that dl and twi directly activate sna expression. Site-directed mutagenesis of dl- and twi-binding sites within defined regions of the sna promoter suggest that the two proteins (containing the Rel and helix-loop-helix domains, respectively) function multiplicatively to ensure strong, uniform expression of sna, particularly in ventral-lateral regions where there are diminishing amounts of dl. These results are consistent with the possibility that the sharp sna borders are formed by multiplying the shallow dl gradient and the steeper twi gradient.

Animals↗

PubMed1992

The dorsal gradient morphogen regulates stripes of rhomboid expression in the presumptive neuroectoderm of the Drosophila embryo.

rhomboid (rho) encodes a putative transmembrane receptor that is required for the differentiation of the ventral epidermis. It is initially expressed before the completion of cellularization in lateral stripes within the presumptive neuroectoderm. Here, we present evidence that the maternal morphogen dorsal (dl) acts in concert with basic helix-loop-helix (b-HLH) proteins, possibly including twist (twi), to activate rho in both lateral and ventral regions. Expression is blocked in ventral regions (the presumptive mesoderm) by snail (sna), which is also a direct target of the dl morphogen. A 300-bp region of the rho promoter (the NEE), which is sufficient for neuroectoderm expression, contains a cluster of dl and b-HLH activator sites that are closely linked to sna repressor sites. Mutations in these binding sites cause genetically predicted changes in the levels and limits of rho expression. In particular, the disruption of sna-binding sites causes a derepression of the pattern throughout ventral regions, providing evidence that sna is directly responsible for establishing the mesoderm/neuroectoderm boundary before gastrulation. The tight linkage of activator and repressor sites in the rho NEE is similar to the arrangement of binding sites observed in the even-skipped stripe 2 element, which is regulated by bicoid (bcd). This suggests that the dl and bcd morphogens use a similar mechanism to make stripes in the Drosophila embryo.

Animals↗

PubMed1992

The bicoid and dorsal morphogens use a similar strategy to make stripes in the Drosophila embryo.

The anterior-posterior (A-P) and dorsal-ventral (D-V) axes of the early Drosophila embryo are established by two key maternal morphogens: bicoid (bcd) and dorsal (dl), respectively. The bcd protein is expressed in a broad concentration gradient along the A-P axis, with peak levels present at the anterior pole, while dl is expressed in a gradient along the D-V axis with peak levels along the ventral surface. The two morphogens are unrelated and their gradients are formed by distinct processes. Nonetheless, we have obtained evidence that they generate sharp on/off stripes of target gene expression through a similar mechanism. Both morphogens establish overlapping patterns of transcriptional activators and repressors in the early embryo. The activators and repressors bind to closely linked sites within short (300 to 500 bp) target promoter elements that have the properties of on/off switches. The activators act in concert with the morphogen to define a broad region where target genes can be initiated. Borders of target gene expression are established by the repressors, resulting in the formation of stripes.

Animals↗

PubMed1991

Establishment of the mesoderm-neuroectoderm boundary in the Drosophila embryo.

A gradient of the maternal morphogen dorsal establishes asymmetric patterns of gene expression along the dorsal-ventral axis of early embryos and activates the regulatory genes twist and snail, which are responsible for the differentiation of the ventral mesoderm. Expression of snail is restricted to the presumptive mesoderm, and the sharp lateral limits of this expression help to define the mesoderm-neuroectoderm boundary by repressing the expression of regulatory genes that are responsible for the differentiation of the neuroectoderm. The snail gene encodes a zinc finger protein, and neuroectodermal genes that are normally restricted to ventral-lateral regions of early embryos are expressed throughout ventral regions of snail- mutants. The formation of the sharp snail border involves dosage-sensitive interactions between dorsal and twist, which encode regulatory proteins that are related to the mammalian transcription factors NF-kB and MyoD, respectively.

Animals↗

PubMed1991

The dorsal morphogen is a sequence-specific DNA-binding protein that interacts with a long-range repression element in Drosophila.

A gradient of the maternal morphogen dorsal (dl) establishes dorsal-ventral (D-V) polarity in the early Drosophila embryo. The dl concentration gradient is initiated by regulated nuclear transport, and only protein that enters nuclei is active in the D-V patterning process. Here we show that dl is a DNA-binding protein that specifically interacts with distal sequences of the zerknüllt (zen) promoter, one of the genetic targets of the morphogen. These zen sequences have the properties of a silencer element and can act over long distances to repress the expression of a heterologous promoter. The dl protein recognizes a sequence motif similar to that of the mammalian transcriptional activator NF-kappa B, which was shown to contain extensive homology with dl and the oncoprotein rel. We present evidence that the DNA-binding activity of the dl protein is mediated by the region of homology (the rel domain) conserved in the rel and NF-kappa B proteins.

Animals↗

PubMed1991

The dorsal morphogen gradient regulates the mesoderm determinant twist in early Drosophila embryos.

A gradient of the maternal morphogen dorsal (dl) initiates the differentiation of various tissues along the dorsal-ventral axis of early Drosophila embryos. dl is a sequence-specific DNA-binding protein that is related to the mammalian regulatory factor NF-kappa B. Previous studies suggest that dl can function as a transcriptional repressor. To determine how dl functions as an activator we have examined the promoter of the mesoderm determinant gene twist (twi). Genetic studies suggest that peak levels of dl protein in ventral regions of early embryos initiate twi expression. Using a combination of promoter fusion-P-transformation assays, and in vitro DNA-binding assays coupled with site-directed mutagenesis, we establish a direct link between dl-binding sites and twi expression in the early embryo. We also present evidence that the dorsal-ventral limits of twi expression depend on the number and affinity of dl-binding sites present in its promoter. A comparison of twi with a second dl target gene, zen, suggests a correlation between the affinities of dl-binding sites and response to different thresholds of dl morphogen.

Animals↗

PubMed1990

Interaction of a liver-specific factor with an enhancer 4.8 kilobases upstream of the phosphoenolpyruvate carboxykinase gene.

We have previously identified a series of five DNase-I hypersensitive (HS) sites within and around the rat phosphoenolpyruvate carboxykinase (PEPCK) gene. The far upstream region has now been sequenced, and the tissue-specific HS site has been mapped more precisely at 4,800 base pairs upstream of the transcription start site of the PEPCK gene. DNA fragments that include the HS site were cloned upstream of various promoters to test whether these regions modulate transcription of the chloramphenicol acetyltransferase reporter gene. Chloramphenicol acetyltransferase activity was enhanced when the DNA fragment encompassing the upstream HS site was linked to various lengths of the PEPCK promoter or to the heterologous simian virus 40 promoter. This upstream region in conjunction with the proximal promoter, which may contain a tissue-specific element, conferred maximum activation in H4IIE hepatoma cells, which express the endogenous PEPCK gene. When these experiments were performed in XC cells, in which the gene is not expressed, transcriptional activation by the upstream element was still significant. Evidence of a specific protein-DNA interaction, using DNA mobility shift and DNase I footprinting assays, was obtained only when using H4IIE cell nuclear extracts. Competition assay showed that the interacting factor may be similar or identical to the liver-specific factor HNF3. We suggest that this protein factor binds to DNA within the HS site and interacts with the proximal promoter region to control tissue-specific high-level expression of the PEPCK gene.

Animals↗

PubMed1990

Extinction of phosphoenolpyruvate carboxykinase gene expression is associated with loss of a specific chromatin-binding protein from a far upstream domain.

We have analyzed the chromatin structure of the phosphoenolpyruvate carboxykinase (PEPCK) gene in hepatoma x fibroblast hybrids with different extinction phenotypes. These hybrids included a karyotypically complete hybrid in which all liver gene activity was extinguished, a microcell hybrid that contained a single mouse chromosome 11 and in which PEPCK gene activity was decreased but inducible by cyclic AMP, and a segregant line that had lost all mouse chromosomes and in which the PEPCK gene was reexpressed. We found that only in the completely extinguished hybrid was PEPCK chromatin structure radically different from that in the parental hepatoma cells. In this hybrid, there was no evidence of any factors binding to the promoter or to the upstream hypersensitive site at -4800 base pairs. In the other cell lines, even when PEPCK gene transcription was low, the PEPCK chromatin showed characteristic structures typical of a transcriptionally competent gene, with hypersensitive sites at positions previously described. Loss of the upstream hypersensitive site was also shown to be correlated with the absence of a liver-specific protein factor that binds specifically to the upstream region.

Animals↗

PubMed1989

Hormonal regulation of phosphoenolpyruvate carboxykinase gene expression is mediated through modulation of an already disrupted chromatin structure.

We used indirect end labeling to identify a series of five hypersensitive (HS) sites in the phosphoenolpyruvate carboxykinase (PEPCK) gene in H4IIE rat hepatoma cells. These sites were found at -4800 base pairs (bp) (site A), at -1300 bp (site B), over a broad domain between -400 and -30 bp (site C), at +4650 bp (site D), and at +6200 bp (site E). Sites A to D were detected only in cells capable of expressing the PEPCK gene, whereas site E was present in all of the cells examined thus far. The HS sites were present in H4IIE cells even when transcriptional activity was reduced to a minimum by treatment with insulin. Stimulation of transcription by a cyclic AMP analog to a 40-fold increase over the insulin-repressed level did not affect the main features of the HS sites. Furthermore, increased transcription did not disrupt the nucleosomal arrangement of the coding region of the gene, nor did it affect the immediate 5' region (site C), which is always nucleosome-free. In HTC cells, a rat hepatoma line that is hormonally responsive but unable to synthesize PEPCK mRNA, the four expression-specific HS sites were totally absent. Our experimental results also showed that, although there is a general correlation between lack of DNA methylation and transcriptional competence of the PEPCK gene, the role, if any, of methylation in the regulation of PEPCK gene activity is likely to be exerted at very specific sites.

Animals↗

PubMed1988

The separation of transcriptionally engaged genes.

We have developed a method for the separation of transcriptionally engaged chromatin from inactive genes as well as from active genes which are not being transcribed. This approach is dependent upon the integrity of the growing transcript and is reflected in a significant decrease in the density of the chromatin during transcription. The decrease in density appears to be due to an association between the growing transcript and a large zone of lower density, possibly the nuclear matrix. These interactions are preserved after fixation of the nuclear material with formaldehyde. Hormonal induction of transcriptional activity causes a shift of the genetic material for the stimulated gene from the high density domain to the low density region. The vast majority of the polymerase II which is engaged with the chromosomal material is also found in this lower density zone. We find that most of the fast form of histone acetylation occurs on those histones which are associated with the active chromatin, further supporting the idea that this modification is involved in some way with the transcriptional process. The merits of this approach are discussed, as are the possibilities for its further exploitation.

Animals↗