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PubMed2006

Differential binding of erythroid Krupple-like factor to embryonic/fetal globin gene promoters during development.

The competition model for beta-like globin gene switching during development predicts that differential binding of transcription factors to globin gene promoters and/or proximal enhancers regulate the competitive interactions of globin gene family members with the powerful locus control region (LCR). Direct interactions of individual genes with the LCR are essential for high level expression in erythroid cells. In this paper, we have demonstrated, by chromatin immunoprecipitation, that erythroid-Krupple-like factor (EKLF) binds to embryonic/fetal globin gene promoters in primitive (but not in definitive) erythroid cells. EKLF binds strongly to adult globin gene promoters and to LCR sequences HS4, HS3, HS2, and HS1 in both primitive and definitive erythroid cells. Trimethylation of histone H3K4 and H3K27 at the embryonic/fetal and adult globin gene promoters is equivalent in definitive cells; therefore, the differential binding of EKLF to these promoters does not appear to result from changes in chromatin configuration. Interestingly, the level of EKLF in definitive cells is 3-fold higher than the level in primitive cells. These results suggest that temporal-specific changes in EKLF abundance result in differential binding of this essential erythroid transcription factor to embryonic/fetal globin gene promoters during development and that these changes in EKLF binding specificity mediate the competitive interactions of globin gene family members with the LCR.

Animals↗
PubMed1998

Reversal of lethal alpha- and beta-thalassemias in mice by expression of human embryonic globins.

Genetic mutations that block alpha- or beta-globin gene expression in humans can result in severe and frequently lethal thalassemic phenotypes. Homozygous inactivation of the endogenous alpha- or beta-globin genes in mice results in corresponding thalassemic syndromes that are uniformly fatal in utero. In the current study, we show that the viability of these mice can be rescued by expression of human embryonic zeta- and -globins, respectively. The capacity of embryonic globins to fully substitute for their adult globin homologues is further demonstrated by showing that zeta- and -globins reverse the hemolytic anemia and abnormal erythrocyte morphology of mice with nonlethal forms of alpha- and beta-thalassemia. These results illustrate the potential therapeutic utility of embryonic globins as substitutes for deficient adult globins in thalassemic individuals. Moreover, the capacity of embryonic globins to functionally replace their adult homologues brings into question the physiologic basis for globin gene switching.

Animals↗
PubMed2000

Sex in the wormcounting and compensating X-chromosome dose.

The nematode Caenorhabditis elegans counts its X chromosomes to determine sex and to activate the process of dosage compensation, which ensures that males (XO) and hermaphrodites (XX) express equal levels of most X-chromosome products. The number of X chromosomes is communicated by a set of X-linked genes called X-signal elements, which repress the master sex-determination switch gene xol-1 via two distinct, dose-dependent molecular mechanisms in XX embryos. X-chromosome gene dosage is compensated by a specialized protein complex that includes evolutionarily conserved components of mitotic and meiotic machinery. This complex assembles on both X chromosomes of hermaphrodites to repress transcription by half. The recruitment of chromosome segregation proteins to the new task of regulating X-chromosome-wide gene expression points to the evolutionary origin of nematode dosage compensation.

Animals↗
PubMed2006

Conservative inheritance of newly synthesized DNA in double-strand break-induced gene conversion.

To distinguish among possible mechanisms of repair of a double-strand break (DSB) by gene conversion in budding yeast, Saccharomyces cerevisiae, we employed isotope density transfer to analyze budding yeast mating type (MAT) gene switching in G2/M-arrested cells. Both of the newly synthesized DNA strands created during gene conversion are found at the repaired locus, leaving the donor unchanged. These results support suggestions that mitotic DSBs are primarily repaired by a synthesis-dependent strand-annealing mechanism. We also show that the proportion of crossing-over associated with DSB-induced ectopic recombination is not affected by the presence of nonhomologous sequences at one or both ends of the DSB or the presence of additional sequences that must be copied from the donor.

Conserved Sequence↗
PubMed1994

Distinct negative regulatory mechanisms involved in the repression of human embryonic epsilon- and fetal G gamma-globin genes in transgenic mice.

A current model for human beta-globin gene switching proposes that the stage-specific activation of embryonic and fetal globin genes requires the interaction of the beta-globin locus control region with proximal promoter elements. Subsequent repression in fetal and adult stages likely involves negative regulatory promoter elements and factors. To begin addressing these negative regulatory mechanisms, the regulation of human fetal G gamma-globin promoter fused to the SV40 T antigen gene was analyzed in transgenic mice. The results showed correct developmental expression in erythroid tissue, but lower levels of expression were also detected in non-erythroid tissue. Thus, the 5'-flanking G gamma-globin promoter sequence contains stage-specific erythroid elements but is lacking nonerythroid-specific negative elements. In contrast, the human embryonic epsilon-globin gene was only expressed in nonerythroid tissue of transgenic embryos, suggesting the presence of an erythroid-specific negative element(s). With the locus control region, complete repression of epsilon-globin RNA in fetal liver was observed in epsilon-globin genes without the previously characterized silencer, suggesting the presence of additional negative elements. Overall, this transgenic study suggests that distinct negative regulatory mechanisms function in the repression of embryonic and fetal globin genes.

Animals↗
PubMed2001

Interpretation of X chromosome dose at Sex-lethal requires non-E-box sites for the basic helix-loop-helix proteins SISB and daughterless.

For Drosophila melanogaster flies, sexual fate is determined by the X chromosome number. The basic helix-loop-helix protein product of the X-linked sisterlessB (sisB or scute) gene is a key indicator of the X dose and functions to activate the switch gene Sex-lethal (Sxl) in female (XX), but not in male (XY), embryos. Zygotically expressed sisB and maternal daughterless (da) proteins are known to form heterodimers that bind E-box sites and activate transcription. We examined SISB-Da binding at Sxl by using footprinting and gel mobility shift assays and found that SISB-Da binds numerous clustered sites in the establishment promoter Sxl(Pe). Surprisingly, most SISB-Da sites at Sxl(Pe) differ from the canonical CANNTG E-box motif. These noncanonical sites have 6-bp CA(G/C)CCG and 7-bp CA(G/C)CTTG cores and exhibit a range of binding affinities. We show that the noncanonical sites can mediate SISB-Da-activated transcription in cell culture. P-element transformation experiments show that these noncanonical sites are essential for Sxl(Pe) activity in embryos. Together with previous deletion analysis, the data suggest that the number, affinity, and position of SISB-Da sites may all be important for the operation of the Sxl(Pe) switch. Comparisons with other dose-sensitive promoters suggest that threshold responses to diverse biological signals have common molecular mechanisms, with important variations tailored to suit particular functional requirements.

Amino Acid Motifs↗
PubMed1987

Immunoglobulin heavy chain switch region recombination within a retroviral vector in murine pre-B cells.

We have employed a retroviral vector, ZN(Smu/S gamma 2b)tk1, as a substrate for detecting the presence of immunoglobulin heavy chain constant region (CH) gene switch (S) recombination activity in murine pre-B cells. ZN(Smu/S gamma 2b)tk1 contains a neomycin (neo) resistance gene in addition to the herpes simplex virus thymidine kinase (Htk) gene which is positioned between murine Smu and S gamma 2b sequences. Stable acquisition of the ZN(Smu/S gamma 2b)tk1 vector was selected in G-418 and switch region recombination within these proviruses was selected by resistance to the drug bromodeoxyuridine (BUdR). Fluctuation analyses of ZN(Smu/S gamma 2b)tk1 infected 18-8tk- and 38B9tk- pre-B lines revealed Htk gene inactivations with apparent frequencies of 5 X 10(-5) and 1 X 10(-5) events/cell/generation, respectively, while G-418 resistant Ltk- fibroblasts lost the HTK phenotype at an apparent rate of 4 X 10(-8). Southern blot analysis demonstrated that switch recombination caused the deletion of the Htk gene in all pre-B clones examined while the loss of Htk in Ltk- clones was not mediated by S region recombination. In 21 out of 24 pre-B clones, the recombinations involved the tandemly repetitive portions of the Smu and S gamma 2b sequences. These results demonstrate that the CH gene S region segments inserted into ZN(Smu/S gamma 2b)tk1 are sufficient for B-cell-specific recombination/deletion within the S region tandem repeats.

Animals↗
PubMed1985

The Sex-lethal gene of Drosophila: DNA alterations associated with sex-specific lethal mutations.

Genomic DNA encoding Sex-lethal, a developmental switch gene in Drosophila melanogaster that regulates sex determination and dosage compensation has been isolated. Wild-type DNA sequence organization of the gene has been compared at the restriction level with those of 17 female-specific, loss-of-function and five male-specific, gain-of-function mutant alleles. DNA lesions associated with 12 of these mutations delimit an 11 kb DNA region that is necessary for proper Sex-lethal function in females. Males who are deleted for this region are both viable and fertile. Loss-of-function alleles are associated with gross DNA alterations as well as true point mutations; the former are located throughout the region. In contrast, all five gain-of-function alleles are associated with DNA insertions that are clustered within a 1 kb portion of the Sxl gene region.

Alleles↗
PubMed1994

A regulatory system for use in gene transfer.

We recently have demonstrated that a C-terminal deletion mutant of the human progesterone receptor (hPRB891) fails to bind to progesterone but can bind RU 486 (Mifepristone) and other progesterone antagonists. Most significantly, this mutant receptor activates transcription of a reporter gene containing the progesterone response element in the presence of these antagonists. Taking advantage of this finding and the modular nature of functional domains of steroid receptors, we constructed a chimeric regulator (pGL-VP) by fusing the ligand-binding domain of human progesterone receptor hPRB891 to the yeast transcriptional activator GAL4 DNA-binding domain and the herpes simplex virus protein VP16 activation domain. We demonstrated that this chimeric regulator activates target genes containing the GAL4-binding sites in transient transfection assays in response to RU 486. In addition, this regulatory system has been validated by ex vivo transplantation of a stable cell line containing both the regulator and a reporter gene into rats. The dosage of RU 486 used is significantly lower than that required for antagonizing progesterone action. The gene-switch system reported here represents a regulatory system, which could be applicable for gene-transfer studies involving animals, as well as humans, in which the delivered gene(s) can be specifically turned on/off in response to an exogenous compound.

Animals↗
PubMed2001

The Tet-On system in transgenic mice: inhibition of the mouse pdx-1 gene activity by antisense RNA expression in pancreatic beta-cells.

To elucidate the function of pancreas duodenal homeobox 1 (PDX-1; insulin promoter factor 1/somatostatin transcription factor 1/islet duodenum homeobox 1/insulin upstream factor 1) in differentiated beta-cells of adult animals we generated transgenic mice using the Tet-On system. Inducible expression of an antisense RNA should down-regulate the PDX-1 protein. The selective and continuous inhibition of PDX-1 gene expression should impair the expression of PDX-1 dependent beta-cell specific genes. A gene switch such as the Tet-On system provides a powerful tool to analyze eukaryotic gene expression and function in transgenic mice. The original Tet system contained two transcriptional units, transactivator and target of control, on two plasmids. We combined the two transcriptional units on a single DNA molecule. The transactivator was placed under control of the mouse insulin promoter. The tet responsive element, driving the gene of interest, was inserted further down-stream into the same vector. The tet regulatory system in this approach permitted a tissue-specific and a doxycycline-inducible control of PDX-1 expression in transgenic mice. The expression of glucose transporter 2 and glucokinase was markedly reduced in dox-treated transgenic mice. In contrast, the number of insulin- and amylin-expressing cells was only slightly decreased, whereas the expression of glucagon was increased distinctly in islets of these mice. Furthermore, the exposure to doxycycline resulted in a progressive impairment of glucose tolerance. The characterization of our transgenic mouse model demonstrates the suitability of the Tet-On system for analyzing physiological consequences emerging from a stepwise decrease in a given protein. Using this system we confirmed the essential role of PDX-1 in pancreatic islets and demonstrated that an antisense-mediated PDX-1 deficiency provokes a beta-cell dysfunction.

Amyloid↗
PubMed1999

The primary sex determination signal of Caenorhabditis elegans.

An X chromosome counting process determines sex in Caenorhabditis elegans. The dose of X chromosomes is translated into sexual fate by a set of X-linked genes that together control the activity of the sex-determination and dosage-compensation switch gene, xol-1. The double dose of X elements in XX animals represses xol-1 expression, promoting the hermaphrodite fate, while the single dose of X elements in XO animals permits high xol-1 expression, promoting the male fate. Previous work has revealed at least four signal elements that repress xol-1 expression at two levels, transcriptional and post-transcriptional. The two molecularly characterized elements include an RNA binding protein and a nuclear hormone receptor homolog. Here we explore the roles of the two mechanisms of xol-1 repression and further investigate how the combined dose of X signal elements ensures correct, sex-specific expression of xol-1. By studying the effects of increases and decreases in X signal element dose on male and hermaphrodite fate, we demonstrate that signal elements repress xol-1 cumulatively, such that full repression of xol-1 in XX animals results from the combined effect of individual elements. Complete transformation from the hermaphrodite to the male fate requires a decrease in the dose of all four elements, from two copies to one. We show that both mechanisms of xol-1 repression are essential and act synergistically to keep xol-1 levels low in XX animals. However, increasing repression by one mechanism can compensate for loss of the other, demonstrating that each mechanism can exert significant xol-1 repression on its own. Finally, we present evidence suggesting that xol-1 activity can be set at intermediate levels in response to an intermediate X signal.

Animals↗
PubMed2003

Cellular context of coregulator and adaptor proteins regulates human adenovirus 5 early region 1A-dependent gene activation by the thyroid hormone receptor.

In mammalian cells, the human adenovirus type 5 early region 1A (E1A) oncoprotein functions as a thyroid hormone (TH)-dependent activator of the thyroid hormone receptor (TR). Interestingly, in the cellular context of the yeast Saccharomyces cerevisiae, E1A acts as a TR-specific constitutive coactivator that is down-regulated by TH. TH reduces the interaction of E1A with the TR in yeast but not HeLa cells. The N-terminal 82 amino acids of E1A are sufficient for coactivation in yeast and residues 4-29 are essential. In yeast, expression of the nuclear receptor corepressor (N-CoR) could down-regulate constitutive transcriptional activation of the TR by E1A, whereas expression of the glucocorticoid receptor interacting protein 1 (GRIP-1) coactivator reconstituted the E1A-induced pattern of enhanced TH-dependent gene activation by TR observed in mammalian cells. We further show that the mating type switching gene (SWI)/sucrose nonfermenting (SNF) gene chromatin remodeling complex is required for both TH/GRIP-1- and E1A-dependent coactivator function, whereas the general control nonrepressed protein (GCN5)/alteration/deficiency in activation protein (ADA2) components of the SPT, ADA, GCN5, acetylation (SAGA) transcriptional adaptor complex are required for TH/GRIP-1, but not E1A-dependent activation of the TR. Taken together, these studies demonstrate that the novel TR-specific coactivator function of E1A in yeast depends on the SWI/SNF chromatin remodeling complex and can be further influenced by changes in the cellular complement of transcriptional coregulatory proteins.

Adenovirus E1A Proteins↗
PubMed1982

T cell regulation of immunoglobulin class expression in the antibody response to trinitrophenyl-ficoll. Evidence for T cell enhancement of the immunoglobulin class switch.

In the absence of T cells, B cells were found to respond to the type 2 T-independent (TI-2) antigen, trinitrophenyl (TNP)-Ficoll, with a characteristic hierarchy of IgM and IgG subclass Ab production which directly correlated with 5' to 3' Igh-C gene order, i.e., IgM greater tha IgG3 greater than IgG1 greater than IgG2b greater than IgG2a. This was evident when immune serum Ab titers were analyzed, when in vitro secretion of antibody from immune cells was measured and when TNP-Ficoll-stimulated clones in a splenic focus assay were analyzed for isotype production. T cells were found to cause a preferential relative increase in the amount of IgG2a antibody produced to TNP-Ficoll. The T cell responsible was present in anti-IgM neonatally suppressed mice and was needed early in the response, i.e., on the day of immunization or earlier. T cells were found to increase the frequency of TNP-Ficoll-responsive B cell clones that produced IgG2a in the splenic focus assay. The great majority of these IgG2a-positive clones also produced IgM and all or nearly all of the IgG isotypes whose genes are encoded 5' to the Igh-gamma 2a gene. The data are discussed in terms to T cell enhancement of IgG2a Ab synthesis being mediated through T cell enhancement of the Igh-C gene switching mechanism within TNP-Ficoll-responsive B cell clones. Thus, isotypes encoded by genes on the 3' end of the Igh-gamma gene complex, which in the absence of T cells have a low probability of being switched to, are the most influenced by T cell help.

Animals↗
PubMed1999

Biological clocks.

Circadian rhythms describe biological phenomena that oscillate with an approximately 24-hour cycle. These rhythms include blood pressure, body temperature, hormone levels, the number of immune cells in blood, and the sleep-wake cycle. In this paper, we will focus on common genes between species that are responsible for determining the circadian behavior, especially some transcription factors (i.e., switch genes) that serve to regulate many circadian rhythm genes. The intent of this summary is to introduce the common molecular mechanism of biological clocks between flies and humans and then to describe the research from three laboratories that was presented in the session.

Animals↗
PubMed2001

A lesson from flex: consider the Y chromosome when assessing Drosophila sex-specific lethals.

Bhattacharya et al. (Bhattacharya, A., Sudha, S., Chandra, H. S. and Steward, R. (1999) Development 126, 5485-5493) reported that loss-of-function mutations in the flex (female-specific lethal on X) gene caused female-specific lethality because flex(+) acts as a positive regulator of the master switch gene Sex lethal (Sxl). Sxl is essential for female development. Key to their conclusion was the ability of flex mutations to suppress the male lethality caused by Sxl(M) mutations, which inappropriately activate Sxl female-specific expression. Here we report our contrary findings that flex mutations fail to suppress even the weakest Sxl(M )alleles, arguing against the proposed regulatory relationship between flex and Sxl. Instead we show that the lethal flex phenotype depends on the absence of a Y chromosome, not on the presence of two X chromosomes. flex lethality is caused by a defect in the functioning of the X-linked rDNA locus called bobbed, since this defect is complemented by the corresponding wild-type rDNA complex on the Y.

Abdomen↗
PubMed2006

Pathogen escape from host immunity by a genome program for antigenic variation.

The vector-borne bacterium Borrelia hermsii, a relapsing fever agent, switches gene expression of a surface protein between different antigenic variants, thereby causing sequential waves of immune escape within hosts and increasing the likelihood of transmission. Analogous programmed systems of antigenic variation occur in African trypanosomes and Plasmodium falciparum. In these examples, switch rates to individual variants differ over a wide range. We studied how B. hermsii determines switch rates in two experimental infections: one where variants were identified by specific antisera and one based on identification by DNA sequence. Unexpressed loci of variant antigens copy into a single expression site at rates determined by extragenic features of silent loci rather than similarity between coding sequences of variants at silent sites and the single expression site. Two elements, in particular, determine switch rates. One set of elements overlaps the 5' ends of the expressed gene and the silent loci; greater sequence identity between elements was associated with a higher switch rate. The second set of elements flanks the expression site on the 3' side and occurs at variable distances downstream from silent loci; the nearer an element to a silent locus, the greater the switch rate of that locus into the expression site. In combination, these two features of the genome provide a simple mechanism to modulate switch rate whereby silent loci form a hierarchy of switch rates into the expression site. Although the switching hierarchy causes changes in individual cells that are stochastic, ordering of variants within hosts is semipredictable.

Animals↗
PubMed1998

The interpretation of position in a morphogen gradient as revealed by occupancy of activin receptors.

Xenopus blastula cells activate different mesodermal genes as a concentration-dependent response to activin, which behaves like a morphogen. To understand how cells recognize morphogen concentration, we have bound naturally labeled activin to cells and related this to choice of gene activation. We find that the increasing occupancy of a single receptor type can cause cells to switch gene expression. Cells sense ligand concentration by the absolute number of occupied receptors per cell (100 and 300 molecules of bound activin induce Xbra and Xgsc, respectively, i.e., 2% and 6% of the total receptors) and not by a ratio of occupied to unoccupied receptors. The long duration of occupancy explains a previously described ratchet effect. Our results suggest a new concept of morphogen gradient formation and interpretation that is particularly well suited to the needs of early development.

Activin Receptors↗
PubMed1998

Frequent but biased class switch recombination in the S mu flanking regions.

Immunoglobulin (Ig) heavy chain class switch recombination occurs mainly by joining two switch (S) regions, segments of tandemly repeated DNA sequences that lie upstream of heavy chain constant region genes. The products of this recombination event are a chromosomal DNA joint and a 'looped-out' circular DNA joint. Although a previous study showed that 40% of chromosomal joints in the mu gene switch region (S mu) are found in the flanking regions of S mu, which do not contain typical S mu region repeats [1], other studies revealed that almost all recombination sites on looped-out circular DNA are found within S regions [2-4]. To resolve this discrepancy, we have isolated and sequenced 164 DNA fragments containing recombination joints from both chromosomal and looped-out DNA of a single cell line, the murine B lymphoma line CH12F3, which switches from IgM to IgA production with a high frequency upon cytokine stimulation [5]. The recombination sites were distributed almost evenly in the S mu region and its flanking regions, suggesting that the final joining of DNA ends may not necessarily take place in S regions. In contrast, there were few joining sites in the exon located 5' of the switch region (the I mu exon), suggesting that the 3' end of the I mu exon might be the upstream border of the recombination joint.

Animals↗