Developmental regulation of the human embryonic beta-like globin gene is mediated by synergistic interactions among multiple tissue- and stage-specific elements

Induction of basic helix-loop-helix protein-containing complexes during erythroid differentiation

The involvement of basic helix-loop-helix (bHLH) transcription factors in erythroid differentiation and development has been established by forced expression of the proteins TAL1 and Id1 in cultured cell lines and by targeted disruption of the mouse TAL1 gene. To better understand the mechanism by which bHLH proteins regulate erythropoiesis, we have investigated HLH protein-DNA interactions in mouse erythroleukemia (MEL) cells before and during chemically induced differentiation. Three bHLH (E-box) binding activities were found to be induced in nuclei from differentiating MEL cells. Using specific antisera, we have demonstrated that these complexes are dimers of TAL1 and ubiquitous E proteins. Similar complexes were detected in nuclear extracts from a human erythroid cell line, K562, and from mouse fetal liver. All three bHLH complexes were disrupted in vitro by Id1, a dominant-negative HLH protein that we and others have previously shown to antagonize MEL cell differentiation. During differentiation of an Id1-overexpressing MEL cell line, induction of a complex containing TAL1 and E2A was not only blocked but reduced below the levels seen in undifferentiating cells. These observations are consistent with the idea that TAL1 and Id1 have opposing effects on erythroid differentiation and that the level of TAL1/E2A heterodimer and/or another E protein-containing complex may influence the decision of a cell to terminally differentiate.

Developmental regulation of the vertebrate globin multigene family

"Hemoglobin switching," or the sequential expression of globin genes in erythroid cells during development, has provided an important paradigm for tissue- and stage-specific gene regulation. Over the past decade, regulatory DNA sequences and transcription factors involved in controlling the expression of individual globin genes in erythroid cells have been identified. The picture that has emerged indicates that gene proximal control elements collaborate with a "locus control region" located far upstream - probably via a DNA looping mechanism - to ensure that each gene is turned on only in erythroid cells and at the appropriate time during development. Interactions among the various regulatory sequences are thought to be mediated and stabilized by an array of tissue-specific and ubiquitous proteins. Chromatin structure plays a critical but still poorly understood role in this process.

The modern primitives: applying new technological approaches to explore the biology of the earliest red blood cells

One of the most critical stages in mammalian embryogenesis is the independent production of the embryo's own circulating, functional red blood cells. Correspondingly, erythrocytes are the first cell type to become functionally mature during embryogenesis. Failure to achieve this invariably leads to in utero lethality. The recent application of technologies such as transcriptome analysis, flow cytometry, mutant embryo analysis, and transgenic fluorescent gene expression reporter systems has shed new light on the distinct erythroid lineages that arise early in development. Here, I will describe the similarities and differences between the distinct erythroid populations that must form for the embryo to survive. While much of the focus of this review will be the poorly understood primitive erythroid lineage, a discussion of other erythroid and hematopoietic lineages, as well as the cell types making up the different niches that give rise to these lineages, is essential for presenting an appropriate developmental context of these cells.

Analysis of primitive erythroid cell proliferation and enucleation using a cyan fluorescent reporter in transgenic mice

Primitive erythropoiesis is a vital process for mammalian embryonic development. Here we report the generation and characterization of a new transgenic mouse line that expresses a histone H2B-CFP fusion protein in the nuclei of primitive erythroid cells. We demonstrate the potential of this ε-globin-histone H2B-CFP line for multicolor imaging and flow cytometry analysis. The ε-globin-H2B-CFP line was used to analyze the cell cycle distribution and proliferation of CFP-expressing primitive erythroblasts from E8.5-E13.5. We also evaluated phagocytosis of extruded CFP-positive nuclei by macrophages in fetal liver and placenta. The ε-globin-H2B-CFP transgenic mouse line adds to the available tools for studying the development of the primitive erythroid lineage.

The study of sequence configuration and functional impact of the (AC)n(AT)xTy motif in human beta-globin gene promoter

In this report we examine the (AC)n(AT)xTy motif residing -530 bp 5' upstream of the beta-globin gene in Chinese thalassaemic patients. This motif is a putative binding site for a repressor protein, termed beta protein 1 (BP1) (Berg et al., Nucleic Acids Res 1989;17:8833-8852). Variations in the (AC)n(AT)xTy repeats affect the binding affinity of BP1, thereby altering the expression of the beta-globin gene. Eight different configurations of this repeat motif are identified in our population of Chinese beta-thalassaemia patients. A (AC)3(AT)7T5 motif was identified among these thalassaemia patients and its influence in beta-globin gene expression was studied using stable transfection assay in murine erythroleukemia (MEL) cells. Our data demonstrated that the (AC)3(AT)7T5 motif has a moderately strong repressor effect on the expression of the cis-linked beta-globin gene. The high affinity of BP1 for this motif may result in the suppression of the transcription of the beta-globin gene (Berg et al., Am J Hematol 1991;36:42-47). We postulate that silencer elements in the beta-globin promoter play an important role in modifying the clinical presentation of the disease.

Maturation and enucleation of primitive erythroblasts during mouse embryogenesis is accompanied by changes in cell-surface antigen expression

Primitive erythroblasts (EryPs) are the first hematopoietic cell type to form during mammalian embryogenesis and emerge within the blood islands of the yolk sac. Large, nucleated EryPs begin to circulate around midgestation, when connections between yolk sac and embryonic vasculature mature. Two to 3 days later, small cells of the definitive erythroid lineage (EryD) begin to differentiate within the fetal liver and rapidly outnumber EryPs in the circulation. The development and maturation of EryPs remain poorly defined. Our analysis of embryonic blood at different stages reveals a stepwise developmental progression within the EryP lineage from E9.5 to E12.5. Thereafter, EryDs are also present in the bloodstream, and the 2 lineages are not easily distinguished. We have generated a transgenic mouse line in which the human epsilon-globin gene promoter drives expression of green fluorescent protein exclusively within the EryP lineage. Here, we have used this line to characterize changes in cell morphology and surface-marker expression as EryPs mature and to track EryP numbers and enucleation throughout gestation. This study identifies previously unrecognized synchronous developmental stages leading to the maturation of EryPs in the mouse embryo. Unexpectedly, we find that EryPs are a stable cell population that persists through the end of gestation.

Investigations of a human embryonic globin gene silencing element using YAC transgenic mice

A silencing element has been previously located upstream of the human epsilon-globin gene promoter using transient assays and transgenic mice carrying plasmid constructs in which the element has been deleted or its transcriptional motifs have been mutated. To investigate whether this element functions in the context of the whole beta-globin locus, we analyzed epsilon-globin gene expression in transgenic mice carrying a deletion of the silencing element in the context of a 213-kilobase human beta-globin yeast artificial chromosome (beta-YAC). epsilon-Globin gene expression was measured during embryonic and fetal development and in adult mice. epsilon-mRNA levels in embryonic cells in Day 12 blood were as high as those measured in wild-type beta-YAC controls, indicating that the deletion does not affect epsilon gene promoter function. epsilon-Globin gene expression was confined to the embryonic cells, indicating that deletion of this silencing element did not affect epsilon-globin developmental expression in the context of the beta-YAC. These results suggest that in the context of the whole beta-globin locus, other proximal and upstream epsilon gene promoter elements as well as competition by the downstream globin genes contribute to the silencing of the epsilon-globin gene in the cells of definitive erythropoiesis.

Transcriptional potentials of the beta-like globin genes at different developmental stages in transgenic mice and hemoglobin switching

Developmental-stage-specific regulation and physiological levels of expression of the globin genes can be recaptured in transgenic mice carrying a YAC/BAC- or cosmid-based construct. By contrast, proper developmental regulation and high-level expression cannot be achieved coordinately in transgenic mice carrying a more manipulated construct, such as a plasmid-based globin gene construct. These differences provide us an opportunity to define the requirements for a developmentally regulated, high-level expression of the globin genes in vivo. To achieve this, as a first step, we studied maximum transcriptional potentials of the beta-globin genes at various stages of development. microLCR-enhanced expression of the epsilon-, gamma-, and beta-globin genes driven by their minimal promoters was estimated and compared with that in betaYAC transgenic mice. Quantitative measurements of steady state mRNA levels of the epsilon-, gamma-, and beta-globin genes showed that the microLCR was able to enhance expression of each beta-like globin gene to levels similar to those in the betaYAC mice. Moreover, transcriptional potentials of each globin gene were unchanged during the entire course of development. These observations indicate that the highest level of expression of the globin genes can be achieved in both embryonic and definitive erythropoiesis regardless of developmental specificity of the genes. This finding implies that transcription suppression is the major mechanism of the developmental specificity of the expression of the beta-like globin genes.

Molecular regulation of embryonic hematopoiesis and vascular development: a novel pathway

In all vertebrate animals, the first blood and vascular endothelial cells are formed during gastrulation, a process in which the mesoderm of the embryo is induced and then patterned by molecules whose identity is still largely unknown. Clusters of developing blood cells surrounded by a layer of endothelial cells comprise the "blood islands" and form in the visceral yolk sac, external to the developing embryo proper. Despite the identification of genes, such as Flk1, SCL/tal-1, Cbfa2/Runx1/AML1, and CD34, that are expressed during the induction of primitive hematopoiesis and vasculogenesis, the early molecular and cellular events involved in these processes are not well understood. Recent work has demonstrated that extracellular signals secreted by a layer of visceral endoderm surrounding the embryo are essential for the initiation of these events. A member of the Hedgehog family of signaling molecules is produced by visceral endoderm and is required for formation of blood and endothelial cells in explant cultures. Hedgehog proteins also stimulate proliferation of definitive hematopoietic stem/progenitor cells. Therefore, these findings may have important medical implications for regulating hematopoiesis and vascular development for therapeutic purposes and for the development of new sources of hematopoietic stem cells for transplantation and as targets for gene therapy.

Induction of embryonic hematopoietic and endothelial stem/progenitor cells by hedgehog-mediated signals

Blood and vascular endothelial cells form in all vertebrates during gastrulation, a process in which the mesoderm of the embryo is induced and then patterned by molecules whose identity is still largely unknown. Blood islands' of primitive hematopoietic cell clusters surrounded by a layer of endothelial cells form in the yolk sac, external to the developing embryo proper. These lineages arise from a layer of extraembryonic mesoderm that is closely apposed with a layer of primitive (visceral) endoderm. Despite the identification of genes such as Flk1, SCL/tal-1, Cbfa2/Runx1/AML1 and CD34 that are expressed during the induction of primitive hematopoiesis and vasculogenesis, the early molecular and cellular events involved in these processes are not well understood. Recent work has demonstrated that extracellular signals secreted by visceral endoderm surrounding the embryo are essential for the initiation of these events. A member of the Hedgehog family of signaling molecules (Indian hedgehog) is produced by visceral endoderm, can induce formation of blood and endothelial cells in explant cultures and can reprogram prospective neurectoderm along hematopoietic and endothelial cell lineages. Hedgehog proteins also stimulate proliferation of definitive hematopoietic stem/progenitor cells. These findings may have important implications for regulating hematopoiesis and vascular development for therapeutic purposes in humans and for the development of new sources of stem cells for transplantation and gene therapy.

Indian hedgehog activates hematopoiesis and vasculogenesis and can respecify prospective neurectodermal cell fate in the mouse embryo

During gastrulation in the mouse, mesoderm is induced and patterned by secreted signaling molecules, giving rise first to primitive erythroblasts and vascular endothelial cells. We have demonstrated previously that development of these lineages requires a signal(s) secreted from the adjacent primitive endoderm. We now show that Indian hedgehog (Ihh) is a primitive endoderm-secreted signal that alone is sufficient to induce formation of hematopoietic and endothelial cells. Strikingly, as seen with primitive endoderm, Ihh can respecify prospective neural ectoderm (anterior epiblast) along hematopoietic and endothelial (posterior) lineages. Downstream targets of the hedgehog signaling pathway (the genes encoding patched, smoothened and Gli1) are upregulated in anterior epiblasts cultured in the presence of Ihh protein, as is Bmp4, which may mediate the effects of Ihh. Blocking Ihh function in primitive endoderm inhibits activation of hematopoiesis and vasculogenesis in the adjacent epiblast, suggesting that Ihh is an endogenous signal that plays a key role in the development of the earliest hemato-vascular system. To our knowledge, these are the earliest functions for a hedgehog protein in post-implantation development in the mouse embryo.

A negative cis-element regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control region

The core of DNase hypersensitive site (HS) 2 from the beta-globin locus control region is a potent enhancer of globin gene expression. Although it has been considered to contain only positive cis-regulatory sequences, our study of the enhancement conferred by segments of HS2 in erythroid cells reveals a novel negative element. Individual cis-regulatory elements from HS2 such as E boxes or Maf-response elements produced as great or greater enhancement than the intact core in mouse erythroleukemia (MEL) cells, indicating the presence of negative elements within HS2. A deletion series through HS2 revealed negative elements at the 5' and 3' ends of the core. Analysis of constructs with and without the 5' negative element showed that the effect is exerted on the promoters of globin genes expressed at embryonic, fetal, or adult stages. The negative effect was observed in bipotential human cells (K562 and human erythroleukemia (HEL) cells), proerythroblastic mouse (MEL) cells, and normal adult human erythroid cells. The novel negative element also functions after stable integration into MEL chromosomes. Smaller deletions at the 5' end of the HS2 core map the negative element within a 20-base pair region containing two conserved sequences.

Expression, purification, and characterization of human hemoglobins Gower-1 (zeta(2)epsilon(2)), Gower-2 (alpha(2)epsilon(2)), and Portland-2 (zeta(2)beta(2)) assembled in complex transgenic-knockout mice

Embryonic zeta- and epsilon-globin subunits assemble with each other and with adult alpha- and beta-globin subunits into hemoglobin heterotetramers in both primitive and definitive erythrocytes. The properties of these hemoglobins-Hbs Gower-1 (zeta(2)epsilon(2)), Gower-2 (alpha(2)epsilon(2)), and Portland-2 (zeta(2)beta(2))-have been incompletely described as they are difficult to obtain in quantity from either primary human tissue or conventional expression systems. The generation of complex transgenic-knockout mice that express these hemoglobins at levels between 24% and 70% is described, as are efficient methods for their purification from mouse hemolysates. Key physiological characteristics-including P(50), Hill coefficient, Bohr effect, and affinity for 2,3-BPG-were established for each of the 3 human hemoglobins. The stability of each hemoglobin in the face of mechanical, thermal, and chemical stresses was also determined. Analyses indicate that the zeta-for-alpha exchange distinguishing Hb Portland-2 and Hb A alters hemoglobin O(2)-transport capacity by increasing its P(50) and decreasing its Bohr effect. By comparison, the epsilon-for-beta exchange distinguishing Hb Gower-2 and Hb A has little impact on these same functional parameters. Hb Gower-1, assembled entirely from embryonic subunits, displays an elevated P(50) level, a reduced Bohr effect, and increased 2,3-BPG binding compared to Hb A. The data support the hypothesis that Hb Gower-2, assembled from reactivated epsilon globin in individuals with defined hemoglobinopathies and thalassemias, would serve as a physiologically acceptable substitute for deficient or dysfunctional Hb A. In addition, the unexpected properties of Hb Gower-1 call into question a common hypothesis for its primary role in embryonic development.

Functional effects of replacing human alpha- and beta-globins with their embryonic globin homologues in defined haemoglobin heterotetramers

Embryonic- and adult-stage globin subunits assemble into haemoglobin (Hb) heterotetramers that are expressed at low levels throughout human intrauterine development. These haemoglobins differ from adult Hb A (alpha2beta2) by the substitution of embryonic zeta for adult alpha globin (Hb zeta2beta2), or embryonic epsilon for adult beta globin (Hb alpha2epsilon2). Several key physiological properties of these 'semiembryonic' haemoglobins remain undefined, as ethical and methodological considerations have limited their availability from both human sources and conventional expression systems. The current study attempts to estimate how the physiological properties of semiembryonic and adult haemoglobins may differ, by determining whether the O2-binding characteristics of hybrid human/mouse haemoglobins change when human alpha- or beta-globin subunits are replaced by human embryonic zeta- or epsilon-globin subunits respectively. Each of the four human globins is expressed in transgenic mice that are nullizygous for either the endogenous mouse alpha- or beta-globin genes, resulting in the high-level expression of haemoglobins that can be studied either in situ in intact erythrocytes or in vitro. We showed that the exchange of human zeta-globin for human alpha-globin chains increased haemoglobin O2 affinity, both in the presence and in the absence of 2, 3-bisphosphoglycerate (2,3-BPG), and reduced the pH-dependent shift in its oxygen equilibrium curve (Bohr effect). By comparison, hybrid haemoglobins containing either human epsilon-globin or human beta-globin exhibited nearly identical O2-binding properties, both in situ and in vitro, regardless of 2,3-BPG levels or ambient pH. Neither the zeta-for-alpha nor the epsilon-for-beta substitutions substantially altered binding affinity for 2,3-BPG or cooperativity between globin subunits. These studies suggest that semiembryonic haemoglobins that assemble entirely from human subunits may exhibit properties that are similar to those of human Hb A.

Hematopoietic induction and respecification of A-P identity by visceral endoderm signaling in the mouse embryo

The anteroposterior axis of the developing embryo becomes morphologically apparent at the onset of gastrulation with the formation of the primitive streak. This structure, where the first mesodermal cells arise, marks the posterior aspect of the embryo. To examine the potential role of non-mesodermal signals in specifying posterior (hematopoietic and endothelial) cell fates in the mouse embryo, we have devised a transgenic explant culture system. We show that interactions between primitive endoderm and adjacent embryonic ectoderm or nascent mesoderm are required early in gastrulation for initiation of hematopoiesis and vasculogenesis. Surprisingly, primitive endoderm signals can respecify anterior (prospective neural) ectoderm to a posterior mesodermal fate, resulting in formation of blood and activation of endothelial markers. Reprogramming of anterior ectoderm does not require cell contact and is effected by stage-dependent, short-range, diffusible signal(s). Therefore, primitive endoderm signaling is a critical early determinant of hematopoietic and vascular development and plays a decisive role in anterior-posterior patterning during mouse embryogenesis.

Reversal of Lethal - and β-Thalassemias in Mice by Expression of Human Embryonic Globins

Genetic mutations that block - or β-globin gene expression in humans can result in severe and frequently lethal thalassemic phenotypes. Homozygous inactivation of the endogenous - or β-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 ζ- and -globins, respectively. The capacity of embryonic globins to fully substitute for their adult globin homologues is further demonstrated by showing that ζ- and -globins reverse the hemolytic anemia and abnormal erythrocyte morphology of mice with nonlethal forms of - and β-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.

© 1998 by The American Society of Hematology.

Reversal of Lethal - and β-Thalassemias in Mice by Expression of Human Embryonic Globins

Genetic mutations that block - or β-globin gene expression in humans can result in severe and frequently lethal thalassemic phenotypes. Homozygous inactivation of the endogenous - or β-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 ζ- and -globins, respectively. The capacity of embryonic globins to fully substitute for their adult globin homologues is further demonstrated by showing that ζ- and -globins reverse the hemolytic anemia and abnormal erythrocyte morphology of mice with nonlethal forms of - and β-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.

© 1998 by The American Society of Hematology.

The 5'-flanking cis-acting elements of the human epsilon-globin gene associates with the nuclear matrix and binds to the nuclear matrix proteins

The nuclear matrix attachment regions(MARs) and the binding nuclear matrix proteins in the 5'-flanking cis-acting elements of the human epsilon-globin gene have been examined. Using in vitro DNA-matrix binding assay, it has been shown that the positive stage-specific regulatory element (epsilon-PREII, -446 bp(-)-419 bp) upstream of this gene could specifically associate with the nuclear matrix from K562 cells, indicating that epsilon-PREII may be an erythroid-specific facultative MAR. In gel mobility shift assay and Southwestern blotting assay, an erythroid-specific nuclear matrix protein (epsilon-NMP kappa) in K562 cells has been revealed to bind to this positive regulatory element (epsilon-PREII). Furthermore, we demonstrated that the silencer (-392 bp(-)-177 bp) upstream of the human epsilon-globin gene could associate with the nuclear matrices from K562, HEL and Raji cells. In addition, the nuclear matrix proteins prepared from these three cell lines could also bind to this silencer, suggesting that this silencer element might be a constitutive nuclear matrix attachment region (constitutive MAR). Our results demonstrated that the nuclear matrix and nuclear matrix proteins might play an important role in the regulation of the human epsilon-globin gene expression.

Multiple epsilon-promoter elements participate in the developmental control of epsilon-globin genes in transgenic mice

To delineate the regulation of the human epsilon-globin gene, we investigated epsilon-gene expression during the development of transgenic mice carrying constructs with epsilon-promoter truncations linked to a micro-locus control region (microLCR). Expression levels were compared with those of microLCR epsilon mice carrying a 2 kilobase epsilon-promoter and betaYAC controls. epsilon mRNA in the embryonic cells of microLCR (-179)epsilon mice were as high as in microLCR epsilon mice suggesting that the proximal epsilon-promoter contains most elements required for epsilon-gene activation. epsilon mRNA in adult microLCR (-179) epsilon mice was significantly lower than in the embryonic cells indicating that elements involved in epsilon-gene silencing are contained in the proximal epsilon-promoter. Extension of the promoter sequence to -463 epsilon decreased epsilon-gene expression in the definitive erythroid cells, supporting previous evidence that the -179 to -463epsilon region contains an epsilon-gene silencer. However, the epsilon-gene of the microLCR(-463)epsilon mice was not silenced in the definitive cells of fetal and adult erythropoiesis indicating that additional silencing elements are located upstream of position -463epsilon. These results provide in vivo evidence that multiple elements of the distal as well as the proximal promoter contribute to epsilon-gene silencing.

Developmental control of epsilon- and gamma-globin genes

In the last few years there have been considerable advances in the understanding of the molecular control of globin genes during development. Several insights have been obtained with studies using transgenic mice. The 5' to 3' order of the genes in the beta locus, the proximity of the genes to the locus control region and the availability of transcriptional factors have been implicated in the developmental activation of globin genes. Globin genes are turned off by two general mechanisms, autonomous gene silencing involving sequences located in the proximal and distal promoters and competition between genes for interaction with the locus control region. The current understanding of the control of embryonic (epsilon) and fetal (gamma) globin genes is reviewed.

Multiple regulatory elements in the 5'-flanking sequence of the human epsilon-globin gene

We have previously reported, on the basis of transfection experiments, the existence of a silencer element in the 5'-flanking region of the human embryonic (epsilon) globin gene, located at -270 base pairs 5' to the cap site, which provides negative regulation for this gene. Experiments in transgenic mice suggest the physiological importance of this epsilon-globin silencer, but also suggest that down-regulation of epsilon-globin gene expression may involve other negative elements flanking the epsilon-globin gene. We have now extended the analysis of epsilon-globin gene regulation to include the flanking region spanning up to 6 kilobase pairs 5' to the locus control region using reporter gene constructs with deletion mutations and transient transfection assays. We have identified and characterized other strong negative regulatory regions, as well as several positive regions that affect transcription activation. The negative regulatory regions at -3 kilobase pairs (epsilonNRA-I and epsilonNRA-II), flanked by a positive control element, has a strong effect on the epsilon-globin promoter both in erythroid K562 and nonerythroid HeLa cells and contains several binding sites for transcription factor GATA-1, as evidenced from DNA-protein binding assays. The GATA-1 sites within epsilonNRA-II are directly needed for negative control. Both epsilonNRA-I and epsilonNRA-II are active on a heterologous promoter and hence appear to act as transcription silencers. Another negative control region located at -1.7 kilobase pairs (epsilonNRB) does not exhibit general silencer activity as epsilonNRB does not affect transcription activity when used in conjunction with an epsilon-globin minimal promoter. The negative effect of epsilonNRB is erythroid specific, but not stage-specific as it can repress transcription activity in both K562 erythroid cells as well as in primary cultures of adult erythroid cells. Phylogenetic DNA sequence comparisons with other primate and other mammalian species show unusual degree of flanking sequence homology for the epsilon-globin gene, including in several of the regions identified in these functional and DNA-protein binding analyses, providing alternate evidence for their potential importance. We suggest that the down-regulation of epsilon-globin gene expression as development progresses involves complex, cooperative interactions of these negative regulatory elements, epsilonNRA-I/epsilonNRA-II, epsilonNRB, the epsilon-globin silencer and probably other negative and positive elements in the 5'-flanking region of the epsilon-globin gene.

Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights

Locus control regions (LCRs) are cis-acting DNA segments needed for activation of an entire locus or gene cluster. They are operationally defined as DNA sequences needed to achieve a high level of gene expression regardless of the position of integration in transgenic mice or stably transfected cells. This review brings together the large amount of DNA sequence data from the beta-globin LCR with the vast amount of functional data obtained through the use of biochemical, cellular and transgenic experimental systems. Alignment of orthologous LCR sequences from five mammalian species locates numerous conserved regions, including previously identified cis-acting elements within the cores of nuclease hypersensitive sites (HSs) as well as conserved regions located between the HS cores. The distribution of these conserved sequences, combined with the effects of LCR fragments utilized in expression studies, shows that important sites are more widely distributed in the LCR than previously anticipated, especially in and around HS2 and HS3. We propose that the HS cores plus HS flanking DNAs comprise a 'unit' to which proteins bind and form an optimally functional structure. Multiple HS units (at least three: HS2, HS3 and HS4 cores plus flanking DNAs) together establish a chromatin structure that allows the proper developmental regulation of genes within the cluster.

Induction of erythroid gene expression by microcell fusion

The molecular events which underlie lineage commitment and differentiation in hematopoietic cells are still incompletely understood. Microcell fusion is a versatile technique which has been utilized in characterizing and mapping genes involved in tumor suppression, cell senescence, and certain aspects of differentiation. Microcell fusion has the potential to contribute to the understanding of hematopoietic differentiation; however, application of this technique is limited by the need to use adherent cells as microcell donors, by the need to tag candidate chromosomes with a selectable marker, and by the need for prolonged selection of fused cells prior to characterization of their phenotype. We developed a modified technique of microcell fusion using square wave electroporation, which allows higher efficiency fusion than polyethylene glycol fusion. By using cross-species fusion and species-specific PCR primers, we were able to detect new gene induction events 48 h after microcell fusion. To study erythroid gene expression, we fused microcells from human erythroid K562 cells to murine B-lymphoid SP-2 cells. We found that microcell fusion induced the nonerythroid recipient cells to express alpha-globin mRNA in a dose-dependent manner. They also expressed RNA for beta-globin, GATA-1, and NF-E2. In contrast, there was no expression of heart- or liver-specific genes. We conclude that microcells from erythroid cells contain all the information necessary to induce expression of multiple erythroid genes. Analysis of the components of the microcells responsible for this new gene induction may allow the characterization of cellular factors responsible for erythroid-specific gene expression.

Structure and function of the zeta-globin upstream regulatory element

The human zeta-globin promoter contains a strong positive regulatory element in the 5' flanking region, designated the zeta-globin upstream regulatory element (URE). In this study, we define the minimal sequences required for URE function and characterize the associated protein-DNA interactions. Deletion experiments show that the URE spans a 60 bp region located between 220 and 279 bp 5' to the transcription start site. Further subdivision of this region shows that multiple cis acting sequences are present. Electrophoretic mobility shift assays demonstrate that the erythroid transcription factor GATA-1 binds a site at -230, and Sp1 and an unidentified factor bind a CCACC site at -240. The unidentified CCACC factor is distinct from two other CCACC factors, EKLF and BKLF/TEF-2. A third complex contains a novel DNA-binding activity that interacts with a site in the -269 to -255 region, designated URE binding factor (URE-BF). This factor is present in K562 cells that express zeta-globin, but is absent in the OCIM1 cell line, a human erythroid cell line that does not express zeta-globin. URE-BF appears to interact with a GATA factor, since formation of the URE-BF complex can be prevented by the presence of unlabeled oligonucleotides containing GATA sites. Finally, increasing the distance from the -230 GATA site to the two upstream sites causes a progressive decrease in zeta-globin promoter activity. There is no indication of a requirement for GATA-1 to be on the same side of the DNA helix as the other upstream factors. These results show that zeta-globin promoter function is highly dependent on a 60 bp region to which at least three different factors bind. Two of these factors may represent DNA-binding proteins not previously identified as important for regulation of globin gene expression. It is likely that these factors interact physically to create a functional regulatory unit.

Role of DNA sequences outside the cores of DNase hypersensitive sites (HSs) in functions of the beta-globin locus control region. Domain opening and synergism between HS2 and HS3

The roles of each DNase hypersensitive site (HS), and the DNA sequences between them, in the activity of the locus control region of the mammalian beta-globin gene domain were examined by placing human and rabbit restriction fragments containing the cores of HS2, HS3, HS4, and HS5, along with varying amounts of flanking DNA, upstream of a hybrid epsilon-globin-luciferase reporter gene and testing for effects on expression both prior to and after integration into the chromosomes of K562 cells, a human erythroid cell line. Prior to integration, fragments containing HS2 enhanced expression to the greatest extent, and the modest enhancement by some fragments containing HS3 correlated with the presence of a well-conserved binding site for AP1/NFE2. The stronger effects of larger locus control region DNA fragments in clones of stably transfected cells indicates a role for sequences outside the HS cores after integration into the genome. The strong effect of a 1.9-kilobase HindIII fragment containing HS3 after, but not prior to, integration argues for the presence of a chromatin domain-opening activity. Use of a rabbit DNA fragment containing both HS2 and HS3 demonstrated a synergistic interaction between the two HSs when their natural context and spacing are preserved.

Chaining multiple-alignment blocks

We derive a time-efficient method for building a multiple alignment consisting of a highest-scoring chain of "blocks," i.e., short gap-free alignments. Besides executing faster than a general-purpose multiple-alignment program, the method may be particularly appropriate when discovery of blocks meeting a certain criterion is the main reason for aligning the sequences. Utility of the method is illustrated by locating a chain of "phylogenetic footprints" (specifically, exact matches of length 6 or more) in the 5'-flanking regions of six mammalian epsilon-globin genes.

Upstream regulatory region of the human embryonic beta-like globin gene, epsilon

The sequence of the human embryonic beta-like globin gene (epsilon) upstream regulatory region has been reported previously. In the course of our own work, we found a significant number of discrepancies between our sequence and the data base sequence, which we show here to contain large clusters of errors within functional epsilon-globin regulatory domains.

Reversibility of the differentiated state in somatic cells

Analysis of de novo gene activation in multinucleated heterokaryons has shown that the differentiated state, although stable, is not irreversible, and can be reprogrammed in the presence of appropriate combinations of trans-acting regulatory molecules. These properties have been exploited to design strategies for identifying novel regulators of cellular differentiation.

Positive and negative regulatory elements of the rabbit embryonic epsilon-globin gene revealed by an improved multiple alignment program and functional analysis

The epsilon-globin genes of mammals are expressed in early embryos, but are silenced during fetal and adult erythropoiesis. As a guide to defining the regulatory elements involved in this developmental switch, we have searched the sequences of epsilon-globin genes from different mammals for highly conserved segments. The search was facilitated by the development of a new program, called yama, to generate a multiple alignment of very long sequences using an improved scoring scheme. This allowed us to generate a multiple alignment of sequences from a more divergent group than previously analyzed, as demonstrated here for representatives of four mammalian orders. In parallel experiments, we constructed a series of deletion mutations in the 5' flank of the rabbit epsilon-globin gene and tested their effect on an epsilon-globin-luciferase hybrid reporter gene. These results show that 121 bp of 5' flank, containing CACC, CCAAT and ATA motifs, is sufficient for expression in erythroid K562 cells. Both positive and negative cis-acting control sequences are located between 218 and 394 bp 5' to the cap site, in a region previously proposed to be a silencer. The positive regulatory sequence contains conserved binding sites for the nuclear protein YY1 adjacent to another highly conserved sequence. The negative element contains a conserved sequence followed by a purine-rich segment. This analysis maps the upstream control sequences more precisely and points to a very complex regulatory scheme for this gene.