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PubMed2005

Allele-specific transcription of fetal genes in primary erythroid cell cultures from Lepore and deltabeta degrees thalassemia patients.

OBJECTIVE: Autonomous gene silencing and gene competition by globin promoters for locus control region (LCR) function have been proposed as mechanisms in developmental regulation of beta-like genes. deltabeta degrees thalassemias are syndromes presenting an increased production of fetal hemoglobin in adult life; the majority of them are due to various deletions in beta-globin gene cluster. We studied samples from double heterozygotes for beta-thalassemia and for Lepore or Sicilian deltabeta degrees deletions, both lacking beta-promoter sequence. Our goal was to address the question of whether the allele carrying the deltabeta degrees deletion is responsible for high level of fetal hemoglobin (HbF) production. PATIENTS AND METHODS: We analyzed the globin gene transcription in human erythroid cell cultures from peripheral blood stem cells, using primary transcript in situ hybridization. We performed primary erythroid cultures from patients with the following genotypes: Lepore/beta degrees 39, Sicilian deltabeta degrees /beta degrees 39, and, as controls, two thalassemia patients with nondeletional mutations (IVS1,6/IVS1,6; IVS1,6/beta degrees 39), and one normal individual. RESULTS: The cells where it is possible to unambiguously assign gamma genes transcription in cis with the deletion (gamma:beta) are strongly represented with respect to the nine other combinations of gamma and beta hybridization signals. These cells are at least nine times more represented than those expressing the gamma allele in trans to the deletion. CONCLUSION: The allele-specific transcription of fetal genes in cis with the deletion is favored in both deletional genotypes. The absence of the adult promoter may influence LCR recruitment by fetal promoter, supporting the hypothesis that competition mechanism and gene silencing can coexist in regulating human globin gene transcription.

Alleles↗
PubMed2005

The lambda5-VpreB1 locus--a model system for studying gene regulation during early B cell development.

The lambda5 and VpreB genes encode the components of the surrogate light-chain, which forms part of the pre-B cell receptor. In mouse, the lambda5 and VpreB1 genes of mouse are closely linked and coordinately regulated by a locus control region (LCR). Activation of the genes in pro-B cells depends on the combined effects of early B cell factor (EBF) and the E2A factors E12 and E47. Silencing of lambda5 expression in mature B cells occurs through the action of Ikaros on the gene promoter where it may compete for binding of EBF and initiate the formation of a silent chromatin structure.

Animals↗
PubMed2003

Identification and characterization of mechanistically distinct inducers of gamma-globin transcription.

Inhibition of HbS polymerization is a major target for therapeutic approaches in sickle cell anemia. Toward this goal, initial efforts at pharmacological elevation of fetal hemoglobin (HbF) has shown therapeutic efficacy. In order to identify well-tolerated, novel agents that induce HbF in patients, we developed a high-throughput screening approach based on induction of gamma-globin gene expression in erythroid cells. We measured gamma-globin transcription in K562 cells transfected with either gamma promoter elements fused with the locus control region hypersensitivity site 2 and luciferase reporter gene (HS2 gamma) or a beta-yeast artificial chromosome in which the luciferase reporter gene was recombined into the gamma-globin coding sequences (gamma YAC). Corresponding pharmacological increases in HbF protein were confirmed in both K562 cells and in human primary erythroid progenitor cells. Approximately 186,000 defined chemicals and fungal extracts were evaluated for their ability to increase gamma gene transcription in either HS2 gamma or gamma YAC models. Eleven distinct classes of compounds were identified, the majority of which were active within 24-48 hr. The short chain hydroxamate-containing class generally exhibited delayed maximal activity, which continued to increase transcription up to 120 hr. The cyclic tetrapeptide OSI-2040 and the hydroxamates were shown to have histone deacetylase inhibitory activity. In primary hematopoietic progenitor cell cultures, OSI-2040 increased HbF by 4.5-fold at a concentration of only 40 nM, comparable to the effects of hydroxyurea at 100 microM. This screening methodology successfully identifies active compounds for further mechanistic and preclinical evaluation as potential therapeutic agents for sickle cell anemia.

Anemia, Sickle Cell↗
PubMed2003

Genomic domains and regulatory elements operating at the domain level.

The sequencing of the complete genomes of several organisms, including humans, has so far not contributed much to our understanding of the mechanisms regulating gene expression in the course of realization of developmental programs. In this so-called "postgenomic" era, we still do not understand how (if at all) the long-range organization of the genome is related to its function. The domain hypothesis of the eukaryotic genome organization postulates that the genome is subdivided into a number of semiindependent functional units (domains) that may include one or several functionally related genes, with these domains having well-defined borders, and operate under the control of special (domain-level) regulatory systems. This hypothesis was extensively discussed in the literature over the past 15 years. Yet it is still unclear whether the hypothesis is valid or not. There is evidence both supporting and questioning this hypothesis. The most conclusive data supporting the domain hypothesis come from studies of avian and mammalian beta-globin domains. In this review we will critically discuss the present state of the studies on these and other genomic domains, paying special attention to the domain-level regulatory systems known as locus control regions (LCRs). Based on this discussion, we will try to reevaluate the domain hypothesis of the organization of the eukaryotic genome.

Animals↗
PubMed2003

Effect of the Emu IgH enhancer on expression of a GFP reporter gene in transfected B cells and transgenic mice.

Transgenic mice were generated to identify the first B cell maturation stage showing expression of an immunoglobulin transcriptional enhancer element (Emu)-green fluorescent protein (GFP) transgene, and to check the ability of the Emu element to behave as a locus control region. Flow cytometry experiments indicated that stably transfected 18-81 cells (a murine pre-B cell line) and A20 cells (a murine IgM(+) B cell line) maintained a constant GFP expression for several months in culture. Contrasting with in vitro results, flow cytometry experiments did not highlight GFP(+) B cells in spleen and bone marrow of Emu-GFP transgenic mice and no GFP transcripts were detected by Northern blot and reverse transcriptase polymerase chain reaction analysis. In transgenic mice, the lack of GFP expression seemed related to transgene DNA methylation occurring within all organs. Our results show dramatic differences for expression of the Emu-GFP transgene in vitro and in vivo. Despite that Emu was reported to efficiently control the in vivo expression of other associated transgenes, it is not sufficient to sustain GFP expression in transgenic mice and to counteract developmental silencing programs that occur in the embryo.

Animals↗
PubMed2003

Rapid in vivo isolation of gene expression elements using an HSV amplicon system.

Short-lived gene expression elements (GEE) represent currently a significant obstacle for gene therapy. To identify GEE such as promoters, enhancers, locus control regions, or insulators, useful for long-term or tissue-specific gene therapy, we developed a GEE trapping strategy in which any sequence can be screened for activity in vivo and the expressing clones can be rapidly isolated. Test sequences are introduced into a herpesvirus (HSV) amplicon vector that expresses green fluorescent protein (GFP) only if the insert has GEE function. The plasmid amplicons can be packaged and used to transduce either cultured cells or any tissue or organ in vivo. Single cell suspensions can then be prepared and GFP positive cells isolated by FACS. After sorting, the plasmid amplicons can be isolated and reintroduced into bacteria, cloning the GEE for further characterization. The CMV promoter was used to demonstrate the utility of the system. The amplicon vector was packaged into herpesvirus virions and transduced into Vero cells, confirming the vector can be packaged. After injection into rat eyes, the packaged amplicon virions were capable of transducing cells and the GFP expressing plasmid amplicons were recovered from rat eye tissues by single cell isolation followed by FACS. This novel amplicon system should prove valuable in identifying and characterizing GEE for use in gene therapy.

Animals↗
PubMed1999

LXIII Cold Spring Harbor Symposium on Quantitative Biology: Mechanisms of Transcription, 3-8 June 1998.

A new perspective is emerging in the transcription field towards understanding gene regulation not only at its most fundamental level but also in the context of chromatin, nuclear compartmentalization, and physiological processes. This direction is being fueled by several key observations. Among them is the discovery of multi-protein complexes whose components reveal a link between gene activity, nuclear structure, and cellular signaling pathways. This information will no doubt be extended by identifying expanded regulatory circuitry using the microchip oligonucleotide array technology. In addition to elucidating the regulatory consequences of these intricate connections, another frontier will be to analyze gene expression within chromosomes. This requires deciphering the mechanism of action of a variety of DNA elements that create a genetic domain such as locus control regions, distal enhancers, insulators, silencers, and matrix attachment regions. Hopefully, with the development of new assays these elements can be as rigorously defined as promoters have been. We can also look forward to capturing critical transcriptional processes by increasingly refined structural analyses. Thus, the scope of problems being addressed in gene regulation has been greatly expanded and the opportunity exists to answer very sophisticated questions in the future.

Archaea↗
PubMed2000

Stable and unstable transgene integration sites in the human genome: extinction of the Green Fluorescent Protein transgene in K562 cells.

In gene transfer experiments including gene therapy studies, expression of the integrated transgenes in host cells often declines with time. The molecular basis of this phenomenon is not clearly understood. We have used the Green Fluorescent Protein (GFP) gene as both a selectable marker and a reporter to study long-term transgene integration and expression in K562 cells. Cells transfected with plasmids containing the GFP gene coupled to the HS2 or HS3 enhancer of the human beta-globin Locus Control Region (LCR) or the cytomegalovirus (CMV) enhancer were sorted by either fluorescence-activated-cell-sorting (FACS) alone or FACS combined with drug selection based on a co-integrated drug resistance gene. The two groups of selected cells were subsequently cultured for long periods up to 250 cell generations. Comparison of long-term GFP transgene integration and expression in these two groups of cells revealed that the K562 genome contains two types of transgene integration sites: i) abundant unstable sites that permit transcription but not long-term integration of the transgenes and thus eliminate the transgenes in 60-250 cell generations and ii) rare stable sites that permit both efficient transcription and long-term stable integration of the transgenes for at least 200 cell generations. Our results indicate that extinction of GFP expression with time is due at least in part to elimination of the gene from the host genome and not entirely to transcriptional silencing of the gene. However, long-term, stable expression of the transgene can be achieved in cells containing the transgene integrated into the rare, stable host sites.

Binding Sites↗
PubMed2003

Chromosome-based vectors for gene therapy.

Currently used vectors in human gene therapy suffer from a number of limitations with respect to safety and reproducibility. There is increasing agreement that the ideal vector for gene therapy should be completely based on chromosomal elements and behave as an independent functional unit after integration into the genome or when retained as an episome. In this review we will first discuss the chromosomal elements, such as enhancers, locus control regions, boundary elements, insulators and scaffold- or matrix-attachment regions, involved in the hierarchic regulation of mammalian gene expression and replication. These elements have been used to design vectors that behave as artificial domains when integrating into the genome. We then discuss recent progress in the use of mammalian artificial chromosomes and small circular non-viral vectors for their use as expression systems in mammalian cells.

Animals↗
PubMed2000

Stable and full rescue of the pigmentation in a medaka albino mutant by transfer of a 17 kb genomic clone containing the medaka tyrosinase gene.

In the medaka Oryzias latipes, several albino strains have mutations in the tyrosinase gene that have been fully characterized at the molecular level. A genomic clone from wild-type medaka containing the 5 kb tyrosinase gene with its five exons, 10 kb of upstream sequences and 2 kb downstream sequences was introduced into fertilized eggs from a tyrosinase-negative albino strain. We show that the injection of this genomic clone predominantly conferred mosaic expression ending before the hatching stage. A minority of juveniles retained a variable number of pigmented cells, including four individuals keeping one pigmented eye through adulthood. Two of these could be mated, and one of these transmitted the transgene resulting in complete rescue of pigmentation to 16% of its offspring. The resulting transgenic line harbors a single copy of the wild-type tyrosinase gene and all fish are wild-type with respect to pigmentation. These experiments suggest that the tyrosinase genomic clone, or a future shorter version of it, can be used in fish to routinely detect transgenic lines. The apparent faithful and systematic expression of the tyrosinase transgene is most probably due to the presence of a locus control region (LCR) in the injected clone.

Albinism↗
PubMed1994

Chromatin domains as potential units of eukaryotic gene function.

Many current models for eukaryotic gene activation and regulation postulate that higher order chromatin structures act as major modulators of gene function. Genetic evidence suggests that nucleosomes and more specifically targeted proteins, such as Polycomb in Drosophila and SIR3 in Saccharomyces cerevisiae, are involved in creating repressive chromatin structures. In addition, the discovery of locus control regions in vertebrates suggests that the primary information for gene activation can reside entirely in specific combinations of transcription factor binding sites. Difficulties associated with experimental design and interpretation make the investigation of whether domains have discrete functional boundaries problematic, and the concept of the chromatin domain as an integrated structural and functional unit remains to be established.

Animals↗
PubMed2003

Sequential recruitment of HAT and SWI/SNF components to condensed chromatin by VP16.

Eukaryotic transcription initiation requires the complex dynamics of hundreds of proteins, many of which are found in large multisubunit complexes. Recent experiments have suggested stepwise recruitment of preassembled complexes, including chromatin remodeling, general transcription factor, mediator, and polymerase complexes, in which the actual order of recruitment may vary for different promoters. How do these complexes access target sequences contained within tightly condensed chromatin? While chromatin remodeling activities may facilitate the accessibility of large transcription and polymerase complexes to promoters, it is not known how they themselves are targeted within condensed chromatin. Gene activation in the context of condensed chromatin does occur. A yeast acidic activator, Gal4, can overcome heterochromatin gene silencing in Drosophila, and the addition of LCRs (locus control regions) to transgenes overcomes position effect silencing, even within centromeric chromatin. Here, we directly visualize the recruitment of HAT and SWI/SNF components after tethering the VP16 acidic activation domain within condensed chromatin. A recruitment delay of tens to hundreds of minutes for catalytic HAT subunits and SWI/SNF subunits, relative to other HAT and SWI/SNF components, suggests sequential recruitment/assembly of chromatin remodeling complexes within condensed chromatin.

Adaptor Proteins, Signal Transducing↗
PubMed1999

Inhibition of Rho at different stages of thymocyte development gives different perspectives on Rho function.

Development of thymocytes can be staged according to the levels of expression of the cell-surface markers CD4, CD8, CD44, CD25 and CD2. Thymocyte development is regulated by a complex signalling network [1], one component of which is the GTPase Rho. The bacterial enzyme C3 transferase from Clostridium botulinum selectively ADP-ribosylates Rho in its effector-binding domain and thereby abolishes its biological function [2,3]. To explore the function of Rho in thymocyte development, we previously used the proximal promoter of the gene encoding the Src-family kinase p56lck to make transgenic mice that selectively express C3 transferase in the thymus [4,6]. In these mice, which lack Rho function from the earliest thymocyte stages, thymocyte numbers are reduced by approximately 50- to 100-fold. Here, we describe transgenic mice that express C3 transferase under the control of the locus control region (LCR) of the CD2 gene; this regulatory element drives expression at a later stage of thymocyte development than the lck proximal promoter [7]. In these mice, thymocyte numbers were also reduced by 50- to 100-fold, but unlike the lck-C3 mice, in which the reduction predominantly results from defects in cell survival of CD25(+) thymocyte progenitors, the CD2-C3 transgenic mice had a pre-T-cell differentiation block at the CD25(+) stage after rearrangement of the T-cell receptor (TCR) beta chains. Analysis of CD2-C3 mice demonstrated that Rho acts as an intracellular switch for TCR beta selection, the critical thymic-differentiation checkpoint. These results show that Rho-mediated survival signals for CD25(+) pre-T cells are generated by the extracellular signals that act on earlier thymocyte precursors and also that temporal cell-type-specific elimination of Rho can reveal different functions of this GTPase in vivo.

ADP Ribose Transferases↗
PubMedDate not supplied

Autocrine stimulation by erythropoietin in transgenic mice results in erythroid proliferation without neoplastic transformation.

Erythropoietin (Epo) autocrine stimulation has been implicated in erythroleukemia. To develop a model of Epo autocrine stimulation, we made transgenic mice using a construct that linked the human Epo gene to an erythroid-specific regulatory element, designated 5'HS-2, from the human beta-globin locus control region. We hypothesized that Epo gene expression would be targeted to erythroid cells in these mice, resulting in autocrine stimulation of erythroid progenitor cell growth in culture, and that chronic autocrine Epo stimulation would result in erythroleukemia. Transgenic mice containing intact copies of the 5'HS-2Epo construction had elevated hematocrits, reticulocyte counts and serum Epo levels and marked splenic enlargement. Analysis of RNA isolated from organs of transgenic mice revealed constitutive Epo mRNA expression primarily in spleen, blood and bone marrow. RNA samples from anemic transgenic mice revealed Epo gene induction only in the liver. Marrow derived from 5'HS-2Epo mice grew BFU-E in the absence of exogenous Epo. Despite observation of up to 2 years, no mouse developed erythroleukemia, demonstrating that Epo autocrine stimulation alone is insufficient for progression to malignancy. These studies show that 5'HS-2 can be used to target Epo gene expression to erythroid tissue. These mice could provide a model system for studying autocrine growth regulation.

Animals↗
PubMed1998

The NF-E2 transcription factor.

NF-E2 belongs to the basic-leucine zipper family of dimeric transcription factors. It consists of a widely expressed 18 kDa subunit, related to chicken Maf proteins, and a tissue-restricted 45 kDa subunit, which contains a cnc domain. It is found almost exclusively in hematopoietic progenitors, and cells of the erythroid/mega/mast cell trilineage. NF-E2 is involved in regulation of globin gene transcription, acting through locus control regions (LCRs) upstream of the alpha and beta globin gene clusters. In addition, it is essential for normal platelet production. Targeted disruption of the gene encoding the 45 kDa subunit leads to severe thrombocytopenia but little if any defect in erythropoiesis, indicating that other molecules can substitute for p45 in red cell maturation in developing mice. However, retroviral integration within the p45 gene has been shown to disrupt erythroid differentiation in erythroleukemia cells; this suggests that p45 could, conceivably, be a target for pharmacologic interventions in patients with excess red cell production due to polycythemia vera.

Animals↗
PubMedDate not supplied

Molecular genetics of color-vision deficiencies.

The normal X-chromosome-linked color-vision gene array is composed of a single long-wave-sensitive (L-) pigment gene followed by one or more middle-wave-sensitive (M-) pigment genes. The expression of these genes to form L- or M-cones is controlled by the proximal promoter and by the locus control region. The high degree of homology between the L- and M-pigment genes predisposed them to unequal recombination, leading to gene deletion or the formation of L/M hybrid genes that explain the majority of the common red-green color-vision deficiencies. Hybrid genes encode a variety of L-like or M-like pigments. Analysis of the gene order in arrays of normal and deutan subjects indicates that only the two most proximal genes of the array contribute to the color-vision phenotype. This is supported by the observation that only the first two genes of the array are expressed in the human retina. The severity of the color-vision defect is roughly related to the difference in absorption maxima (lambda(max)) between the photopigments encoded by the first two genes of the array. A single amino acid polymorphism (Ser180Ala) in the L pigment accounts for the subtle difference in normal color vision and influences the severity of red-green color-vision deficiency. Blue-cone monochromacy is a rare disorder that involves absence of L- and M-cone function. It is caused either by deletion of a critical region that regulates expression of the L/M gene array, or by mutations that inactivate the L- and M-pigment genes. Total color blindness is another rare disease that involves complete absence of all cone function. A number of mutants in the genes encoding the cone-specific alpha- and beta-subunits of the cGMP-gated cation channel as well as in the alpha-subunit of transducin have been implicated in this disorder.

Animals↗
PubMedDate not supplied

Characterization of a novel form of X-linked incomplete achromatopsia.

X-linked incomplete achromatopsia (XIA), also called blue-cone monochromacy (BCM), is a rare cone disorder that most commonly results either from one of two conditions. The first condition is a deletion of the locus control region (LCR) which is a critical DNA element that lies upstream of the L and M photopigment gene array on the X-chromosome and is necessary for expression of the photopigment genes. The second condition is an inactivating point mutation within the coding sequence of the remaining photopigment gene in an array from which all but one gene has been deleted. Many previous studies have concluded that affected individuals either have only rods and S-cones (Blackwell & Blackwell, 1957, 1961; Daw & Enoch, 1973; Hess et al., 1989) or have rods, S-cones, and another cone type that contains the rod pigment (Pokorny et al., 1970; Alpern et al., 1971). However, Smith et al. (1983) described individuals with XIA who had residual L-cone function. Here we report results for a subject with XIA who appears to have residual M-cone function. Genetic analysis revealed that he had apparently normal genes for M-cone photopigment thus leaving open the possibility that he has a contribution to vision based on expression of these genes at a very low level.

Adult↗
PubMedDate not supplied

Mutually exclusive expression of the L and M pigment genes in the human retinoblastoma cell line WERI: Resetting by cell division.

The key steps in the evolution of full trichromatic color vision in primates include duplication of the ancestral pigment gene to form the L and M pigment gene array on the X chromosome, mutually exclusive expression of the L and M pigment genes in cone photoreceptors, and formation of a retinal mosaic with randomly distributed L and M cones. Previous work using transgenic mice has indicated that a locus control region adjacent to this array of genes plays an important role in their mutually exclusive expression in respective cone cells (Smallwood et al., 2002). However, the mechanism by which this is accomplished is unknown. We searched for a cellular model system to investigate the mechanism of this mutually exclusive expression. We previously showed that the undifferentiated human retinoblastoma cell line WERI expresses L and M cone opsin but not rod opsin genes. We now show that WERI cells express the L and M pigment genes in a mutually exclusive manner, in that either L or M pigment mRNA is expressed in a single cell. Importantly, clonal analysis showed that single WERI cells that express either L or M generate, upon cell division produce, a mixed population of L- or M-expressing cells. These results indicate, first, that cell division resets L or M pigment gene expression, most likely due to disassembly and reassembly of LCR-promoter DNA-protein complexes during cell division. Second, a retinal mosaic with near-random distribution of L and M cones may have been generated automatically after duplication of the ancestral gene to form the L and M pigment genes. Third, determination of L and M cone identity may not require external molecular cues during differentiation, and is consistent with the idea that L and M cones are not intrinsically different.

Blotting, Northern↗