A homeodomain protein binds to gamma-globin gene regulatory sequences

Downstream targets of HOXB4 in a cell line model of primitive hematopoietic progenitor cells

Enforced expression of the homeobox transcription factor HOXB4 has been shown to enhance hematopoietic stem cell self-renewal and expansion ex vivo and in vivo. To investigate the downstream targets of HOXB4 in hematopoietic progenitor cells, HOXB4 was constitutively overexpressed in the primitive hematopoietic progenitor cell line EML. Two genome-wide analytical techniques were used: RNA expression profiling using microarrays and chromatin immunoprecipitation (ChIP)-chip. RNA expression profiling revealed that 465 gene transcripts were differentially expressed in KLS (c-Kit(+), Lin(-), Sca-1(+))-EML cells that overexpressed HOXB4 (KLS-EML-HOXB4) compared with control KLS-EML cells that were transduced with vector alone. In particular, erythroid-specific gene transcripts were observed to be highly down-regulated in KLS-EML-HOXB4 cells. ChIP-chip analysis revealed that the promoter region for 1910 genes, such as CD34, Sox4, and B220, were occupied by HOXB4 in KLS-EML-HOXB4 cells. Side-by-side comparison of the ChIP-chip and RNA expression profiling datasets provided correlative information and identified Gp49a and Laptm4b as candidate "stemness-related" genes. Both genes were highly ranked in both dataset lists and have been previously shown to be preferentially expressed in hematopoietic stem cells and down-regulated in mature hematopoietic cells, thus making them attractive candidates for future functional studies in hematopoietic cells.

HOXBES2: a novel epididymal HOXB2 homeoprotein and its domain-specific association with spermatozoa

The sperm from the testis acquires complete fertilizing ability and forward progressive motility following its transit through the epididymis. Acquisition of these characteristics results from the modification of the sperm proteome following interactions with epididymal secretions. In our attempts to identify epididymis-specific sperm plasma membrane proteins, a partial 2.83-kb clone was identified by immunoscreening a monkey epididymal cDNA library with an agglutinating monoclonal antibody raised against washed human spermatozoa. The sequence of the 2.83-kb clone exhibited homology to the region between 1 and 1097 bp of the homeobox gene, Hoxb2. This sequence was found to be species conserved, as revealed by RT-PCR analysis. To obtain a full-length clone of the sequence, 5' RACE-PCR (rapid amplification of cDNA ends PCR) was carried out using rat epididymal RNA as the template. It resulted in a full-length 1.657-kb cDNA encoding a 32.9-kDa putative protein. The protein designated HOXBES2 exhibited homology to the conserved 61-amino acid homeodomain region of the HOXB2 homeoprotein. However, characteristic differences were noted in its amino and carboxyl termini compared with HOXB2. A putative 30-kDa protein was detected in the tissue extracts from adult rat epididymis and caudal spermatozoa, and a 37-kDa protein was detected in the rat embryo when probed with a polyclonal antibody against HOXB2 protein. Multiple tissue Western blot and immunohistochemical analysis further indicated its expression in the cytoplasm of the principal and basal epithelial cells, with maximal expression in the distal epididymal segments. Northern blot analysis detected a single approximately 2.5-kb transcript from the adult epididymis. Indirect immunofluorescence localized the protein to the acrosome, midpiece, and equatorial segments of rat caudal and ejaculated human and monkey spermatozoa, respectively. In conclusion, we have identified and characterized a novel epididymal homeoprotein different from HOXB2 protein and hereafter referred to as HOXBES2, (HOXB2 homeodomain containing epididymis-specific sperm protein) with a probable role in fertilization.

β -thalassaemia-87 C→G: relationship of the Hb F modulation and polymorphisms in compound heterozygous patients

A clinical, haematological, biochemical and molecular study was carried out in 17 patients affected with thalassaemia intermedia, who were compound heterozygotes for the beta-thalassaemia mutation beta-87 C-->G to determine the genetic basis of their clinical heterogeneity. The beta-87 was found associated with haplotype VIII (beta-87/VIII) or V (beta-87/V). The 10 patients with the beta-87/VIII showed milder clinical conditions, with significantly higher levels of haemoglobin (Hb) (9.8 +/- 1.1 g/dl vs. 8.5 +/- 1.3 g/dl) and fetal haemoglobin (Hb F) (6.2 +/- 1.5 g/dl vs. 2.6 +/- 1.5 g/dl; P = 0.0034) and higher synthesis of (G)gamma ((G)gamma/(Total)gamma 69.4 +/- 2.6% vs. 42.8 +/- 16.2%; P = 0.0042) than the seven patients with the beta-87/V. The beta-87/VIII showed a configuration of rare polymorphisms in the 5' sub-haplotype, which have been reported to exert an increasing effect on Hb F. They were "T"-158 (G)gamma-globin gene, T-A-G in pre-(G)gamma framework, (TG)(11)(CG)(3) in the (G)gamma-IVS2, (AT)(9)N(12)(AT)(10) in LCR-HS2; in contrast, the haplotype V had, respectively, "C", T-G-A (TG)(19)(CG)(2)CACG in the (G)gamma-IVS2, and (AT)(10)N(12)(AT)(11). In all patients the beta-87 was associated with the (AT)(9)T(5) motif 5' beta-globin gene with increased affinity for the BP-1 protein, and with the (TG)(13) in the (A)gamma-IVS2. The high increase of the Hb F, mostly of the (G)gamma-type, strongly suggests the hypothesis that the 'T'-158 (G)gamma plays a principal role and that the other polymorphisms could exert a cooperative role in the modulation of Hb F in patients with erythropoietic stress.

BP1, a homeodomain-containing isoform of DLX4, represses the beta-globin gene

In earlier studies we identified a putative repressor of the human beta-globin gene, termed beta protein 1 (BP1), which binds to two silencer DNA sequences upstream of the adult human beta-globin gene and to a negative control region upstream of the adult delta-globin gene. Further studies demonstrated an inverse correlation between the binding affinity of the BP1 protein for the distal beta-globin silencer sequence and the severity of sickle cell anemia, suggesting a possible role for BP1 in determining the production of hemoglobin S. We have now cloned a cDNA expressing the BP1 protein. Sequencing revealed that BP1 is a member of the homeobox gene family and belongs to the subfamily called Distal-less (DLX), genes important in early development. Further analysis showed that BP1 is an isoform of DLX4. BP1 protein has repressor function towards the beta-globin promoter, acting through the two beta-globin DNA silencers, demonstrated in transient transfection assays. Strong BP1 expression is restricted to placenta and kidney tissue, with no expression in 48 other human tissues. BP1 exhibits regulated expression in the human erythroid cell line MB-02, where its expression decreases upon induction of the beta-globin gene. BP1 is thus the first member of the DLX family with known DNA binding sites and a function in globin gene regulation.

Nucleotide variation regulates the level of enhancement by hypersensitive site 2 of the beta-globin locus control region

The beta-globin locus control region hypersensitive site 2 (HS2) enhancer possesses a unique property for stimulating high-level globin gene expression. Although the deletion of cis-acting motifs influences the level of enhancement conferred by HS2, there is controversy on whether polymorphism of the same elements contributes to variation of the fetal hemoglobin (HbF) level among patients with sickle cell anemia. We analyzed reporter gene activity of constructs containing variant HS2 enhancers derived from beta(S) chromosomes to directly test the effect of polymorphism on enhancer activity. Constructs containing four enhancer variants linked to an identical gamma-globin promoter showed markedly different levels of reporter gene activity. Juxtaposition of HS2 derived from the Asian and Senegal chromosomes, which are associated with similarly high levels of HbF, to cognate sequence extending to -1500 of the (G)gamma globin gene showed significantly different levels of reporter gene activity. Our findings indicate that nucleotide variation regulates the level of enhancement conferred by HS2; however, the reporter activities showed no correlation with the level of Hb F associated with the common beta(S) chromosomes.

The gammaPE complex contains both SATB1 and HOXB2 and has positive and negative roles in human gamma-globin gene regulation

A large nuclear protein complex, termed gammaPE (for gamma-globin promoter and enhancer binding factor), binds to five sites located 5' and 3' of the human y-globin gene. Two proteins, SATB1 (special A-T-rich binding protein 1) and HOXB2, can bind to yPE binding sites. SATB1 binds to nuclear matrix-attachment sites, and HOXB2 is a homeodomain protein important in neural development that is also expressed during erythropoiesis. The present work showed that antisera directed against either SATB1 or HOXB2 reacted specifically with the entire gammaPE complex in electrophoretic mobility shift assays (EMSAs), suggesting that the two proteins can bind to the gammaPE binding site simultaneously. When SATB1 or HOXB2 was expressed in vitro, they could bind independently to gammaPE binding sites in EMSA. Interestingly, the proteins expressed in vitro competed effectively with each other for the gammaPE binding site, suggesting that this may occur under certain conditions in vivo. Transient cotransfections of a HOXB2 cDNA and a y-globin-luciferase reporter gene construct into cells expressing SATB1 suggested that SATB1 has a positive and HOXB2 a negative regulatory effect on transcription. Taking into account their potentially opposing effects and binding activities, SATB1 and HOXB2 may modulate the amount of gamma-globin mRNA expressed during development and differentiation.

Physiology and molecular genetics of multidrug resistance in Entamoeba histolytica

Entamoeba histolytica presents the evolutionarily conserved multidrug-resistance (MDR) phenotype, discovered in mammalian cells. MDR cells overexpress the membrane P-glycoprotein, which excludes unrelated drugs from the cytoplasm. E. histolytica mutants exhibit cross-resistance to unrelated drugs, which are pumped out from the cytoplasm. In drug-resistant trophozoites, the constitutively expressed EhPg1 gene appears to be up-regulated by a C/EBP-like factor and a multiprotein complex that were not found in drug-sensitive trophozoites. The drug-induced EhPgp5 gene, on the other hand, appears to be up-regulated by AP-1 and HOX factors. Here we review the main physiological and molecular facts of the MDR phenotype in E. histolytica. Copyright 1999 Harcourt Publishers Ltd.

Localisation of cis regulatory elements at the beta-globin locus: analysis of hybrid haplotype chromosomes

Several cis elements at the beta-globin gene cluster and the upstream locus control region (LCR) have been implicated in modulation of fetal haemoglobin (Hb F) level in beta-globin disorders. To determine the role of elements at the LCR and the beta-globin gene cluster on HbF level among sickle cell anaemia (SCA) patients, hybrid haplotype betaS chromosomes exhibiting variation in the association of alleles of LCR hypersensitive site 2 (HS2) and the beta-globin gene cluster restriction fragment length polymorphosim (RFLP) haplotypes were identified in an unselected population of 100 patients. On 15 chromosomes the polymorphic HS2 short tandem repeat(TA)xN10-12(TA)y containing a Hox2 binding motif differed from that typically associated with the corresponding beta-globin gene cluster RFLP haplotype. Among patients homozygous for the Benin RFLP haplotype, in whom one chromosome carried the (TA)9N10(TA)10 allele, no effect on HbF level was observed. Polymorphism of the pre-Ggamma framework, an enhancer located 25 kb downstream of HS2 localised the breakpoint for each of these 'hybrid' haplotype chromosomes upstream of this element. Previously described hybrid haplotype chromosomes with the (TA)9N10(TA)10 HS2 allele associated with raised HbF by contrast arise by recombination 1 kb downstream of the pre-Ggamma framework. This study suggests that variability in HbF level associated with polymorphisn of the HS2 enhancer depend on downstream determinant (s) in tight linkage disequilibrium with HS2. The pre-Ggamma framework is the only known polymorphic cis-active determinant in this region.

Transcriptional analysis of the EhPgp5 promoter of Entamoeba histolytica multidrug-resistant mutant

We report here the cloning and transcriptional characterization of the EhPgp5 multidrug resistance gene promoter isolated from the drug-resistant clone C2 of Entamoeba histolytica. The EhPgp5 promoter has the TATA-like motif at -31 base pairs; transcription initiates three nucleotides upstream from the ATG in trophozoites grown in 225 microM emetine (clone C2(225)), whereas in those grown without the drug (clone C2) a product with no open reading frame was detected. The promoter was active in transfected clone C2 trophozoites, its activity increased when trophozoites were cultured in 40 microM emetine, while it was turned off in the drug-sensitive clone A. The first -235 base pair kept full promoter activity, suggesting that it has important drug responsive elements. Gel shift assays detected the complex Ib in clone C2, which was augmented in clone C2(225). Competition experiments suggested that complex Ib may be constituted by HOX and AP-1 like factors in clone C2, whereas in clone C2(225), complex Ib was only competed by the HOX sequence. Complexes Ie, detected in clones A and C2 but not in C2(225), and Ia, present in all clones, were competed by the TATA box oligonucleotide. Our results suggest that proteins forming complexes Ib and Ie may be participating in the regulation of the EhPgp5 gene expression.

Transcriptional analysis of the EhPgp1 promoter of Entamoeba histolytica multidrug-resistant mutant

We present here the cloning and characterization of the EhPgp1 multidrug resistance gene promoter isolated from the Entamoeba histolytica drug-resistant mutant clone C2. The EhPgp1 promoter lacks the typical TATA box and the transcriptional initiation sequences described for other E. histolytica promoters. The major transcription initiation site of the EhPgp1 gene was located at the ATG start codon. The EhPgp1 core promoter located within the first 244 base pairs showed a higher chloramphenicol acetyltransferase expression in the transfected trophozoites of clone C2 than in those of the sensitive clone A. Gel shift assays revealed three specific DNA-protein complexes (Ia, IIa, and IIIc) using nuclear extracts from clone C2, whereas three main complexes (If, IIf, and IIg) were limited to clone A. Competition assays suggested the presence of C/EBP-like and OCT-like proteins in complexes Ia and IIa, respectively, probably involved in the expression of the EhPgp1 gene, whereas complex IIIc was competed by GATA-1, C/EBP, OCT, and HOX oligonucleotides. Thus, differential DNA-protein complexes may be formed by transcriptional factors involved in the regulation of the EhPgp1 gene expression.

Hox homeobox genes as regulators of normal and leukemic hematopoiesis

Hox genes, first recognized for their role in embryonic development, may also play lineage-specific functions in a variety of somatic tissues including the hematopoietic system. Expression of these transcription factors has been demonstrated both in normal and leukemic human and hematopoietic cells, suggesting functional roles in hematopoietic cell growth and differentiation. Several recent studies have shown that Hox proteins are involved in controlling proliferation of primitive bone marrow cells and also in altering differentiation of myeloid as well as lymphoid progenitors, alterations that also can contribute to leukemic transformation. Hox genes, together with their upstream regulators and downstream target genes, may play key roles in fundamental processes controlling hematopoietic stem cell properties.

Modulatory subdomains of the HS2 enhancer differentially regulate enhancer activity in erythroid cells at different developmental stages

The HS2 enhancer in the locus control region of human beta-like globin genes displays developmental-stage-independent enhancer function. The mechanism by which it regulates the transcription of the globin genes in erythroid cells throughout development is not fully understood. In this paper we dissect the HS2 enhancer into an enhancer core and five modulatory subdomains M1 to M5. The enhancer core possesses developmental-stage-independent enhancer activity. The modulatory subdomains by themselves do not possess such enhancer activity, but they apparently respond to environmental signals and modulate enhancer core activity in a developmental-stage specific manner. M1 located 5' of the core strongly stimulates core activity in K562 cells at the embryonic stage. M2 and M3 located 3' of the core strongly stimulate core activity in MEL cells at the adult stage. Moreover, M3 suppresses core activity at the embryonic stage and exhibits an adult-stage-selector activity. These findings indicate that the apparent developmental-stage-independence of the HS2 enhancer is a result of multiple interactions between the core and the modulatory subdomains located both near and far from the core.

The role of HOX homeobox genes in normal and leukemic hematopoiesis

A sizable amount of new data points to a role for the HOX family of homeobox genes in hematopoiesis. Recent studies have demonstrated that HOXA and HOXB genes are expressed in human CD34+ cells, and are downregulated as cells leave the CD34+ compartment. In addition, expression of certain genes, including HOXB3 and HOXB4, is largely restricted to the long-term culture-initiating cell enriched pool, containing the putative stem cell population. Studies have also shown that HOX genes appear to be important for normal T lymphocyte and activated natural killer cell function. Overexpression of Hox-b4 in transplanted murine marrow cell results in a dramatic expansion of stem cells, while maintaining normal peripheral blood counts. In contrast, overexpression of Hox-a10 resulted in expansion of progenitor pools, accompanied by unique changes in the differentiation patterns of committed progenitors. Overexpression of Hox-a10 or Hox-b8 led to the development of myeloid leukemias, while animals transfected with marrow cells overexpressing Hox-b4 do not appear to develop malignancies. Blockade of HOX gene function using antisense oligonucleotides has revealed that several HOX genes appear to influence either myeloid or erythroid colony formation. Mice homozygous for a targeted disruption of the HOX-a9 gene show reduced numbers of granulocytes and lymphocytes, smaller spleens and thymuses, and reduced numbers of committed progenitors. These studies demonstrate that HOX homeobox genes play a role in both the early stem cell function as well as in later stages of hematopoietic differentiation, and that perturbations of HOX gene expression can be leukemogenic.

Modulation of the phenotypic diversity of sickle cell anemia

Sickle cell anemia is noted for being phenotypically heterogeneous. This suggests that there are genetic influences that moderate the effects of the sickle hemoglobin mutation. In this review I focus on genetically determined modulation of hemoglobin concentration and fetal hemoglobin levels. Each of these variables has important influences upon sickle hemoglobin polymerization and the resulting pathophysiology.

Two mutations in the locus control region hypersensitivity site-2 (5' HS-2) of haplotype 19 beta s chromosomes alter binding of trans-acting factors

There are five major haplotypes associated with sickle cell anemia (SS). Individuals homozygous for haplotypes 3 (Senegal) and 31 (Saudi Arabian) have high fetal hemoglobin (HbF) levels (15 to 30% of total hemoglobin) whereas individuals homozygous for haplotypes 17 (Cameroon), 19 (Benin), and 20 (Bantu) have low HbF levels (1 to 10%). We previously identified several point mutations in the LCR 5'HS-2 that were specific for haplotype 19 beta s chromosomes (compared to the GenBank HUMHBB reference sequence, T-->G at position 8580, A-->G at position 8598, and A-->T at position 9114). We postulated that one or more of these mutations may alter the binding of specific trans-acting factors and ultimately affect the expression of HbF in these sickle cell patients. We performed gel mobility shift assays using 32P-end-labeled double-stranded 19mers corresponding to each of the LCR 5'HS-2 normal (GenBank) and mutant sequences. Nuclear extracts prepared from HeLa and HEL cells were used in our experiments and neither the normal nor mutant sequence at position 8580 bound trans-acting factors in either nuclear extract. The 8598 mutant increased binding of Sp1; using purified protein and both nuclear extracts. HEL extracts were used to quantify the increase in Sp1 binding to the 8598 mutation and we found an increase in binding of 66 and 47%, respectively, in two shifted bands. The 9114 mutation sharply decreased binding of an unknown trans-acting factor by 74%. This factor was present in both HeLa and HEL nuclear extracts.

Nuclear factor binding sites in human beta globin IVS2

The second intron of the human beta globin gene (beta IVS2) has been previously identified as a region required for proper expression of beta globin. To further characterize this region, we have footprinted the entire beta IVS2 and have analyzed regions of interest by electrophoretic mobility shift assay. Through these studies we have identified four utilized binding sites for the erythroid regulatory factor GATA-1, two sites bound by general transcription factor Oct-1, two sites bound by the nuclear matrix attachment DNA binding protein special A-T-rich binding protein 1, and a site bound by a potential homeobox protein. Additionally, we have found several factors displaying temporal or tissue specificity by electrophoretic mobility shift assay, which may be potentially involved in the regulation of beta globin expression. These proteins are not supershifted by antibodies to factors important in erythroid regulation such as GATA-1, NFE-2, or YY1, or by antibodies against more general transcription factors.

Homeobox genes and the patterning of skin diseases

Fundamental to our understanding of skin diseases and their presentation is an understanding of the pattern of their development. When we have established the molecular basis of their development we will be in a much better position to control and treat such diseases. The homeobox genes are a family of regulatory proteins that influence pattern formation at many levels. Their presence in skin implicates them in this important role. It seems highly likely that they will be shown to be fundamental to the development of the patterns used in diagnosing skin diseases.

Erythroid regulatory elements

Erythroid differentiation leads to the production of red blood cells that contain a high level of hemoglobin. This level is mainly regulated by globin gene transcription during development and differentiation. Although numerous cis-acting sequences are involved in transcriptional activity of globin genes, combinations of three motifs, CCACC, SP1 and GATA represent the core elements of their regulatory sequences. These combinations are also found in promoters and/or enhancers of non-globin genes specifically expressed in the late stages of erythroid differentiation. The CCACC and SP1 sequences bind proteins that do not display erythrocytic specificity, and the GATA sequences bind a family of transacting factors recently cloned. The GATA family members are distinctive for a highly homologous DNA binding domain that exists in two zinc fingers reminiscent of those of the glucocorticoid receptor. None of the GATA family members displays only erythroid specificity, but gene disruption followed by rescue indicates that GATA-1 is necessary for terminal erythroid differentiation throughout development. The GATA/SP1 and GATA/CCACC associations are present in positive, negative or inducible regulatory sequences suggesting that other elements control the fine tuning of erythroid gene expression. NF-E2, which is a major transcriptional activator, members of the ets family which are implicated in the early stages of erythropoiesis and finally c-erbA which directly regulates a set of erythroid-specific genes are proteins that bind these latter regulatory motifs.

Identification of a novel vertebrate homeobox gene expressed in haematopoietic cells

This paper describes the characterisation of a novel chicken homeobox gene, Prh, whose encoded homeodomain sequence differs significantly from those of other factors which have been described. As expected, a portion of the encoded protein, containing the homeodomain, is capable of sequence-specific DNA-binding. Outside the homeodomain, Prh, possesses an N-terminal region extremely rich in proline residues and a C-terminal acidic portion, either of which may function as transcription regulatory domains. Since, among the chicken tissues tested, its transcription is restricted to haematopoietic cells, lung and liver, it may function in tissue-specific patterns of gene regulation. Human and murine Prh homologues have also been identified; so it is likely that such genes are a general feature of vertebrate genomes.

Fetal hemoglobin reactivation in baboon and man: a short perspective

Present concepts of the mechanism of reactivation of synthesis of fetal hemoglobin (HbF) in the adult under conditions of erythropoietic stress are briefly reviewed. Since HbF can be considered an effective natural antisickling agent, the reactivation of its synthesis in patients with sickle cell anemia as a desirable therapeutic goal has been extensively explored since the discovery in 1982 that 5-azacytidine increases HbF levels in the baboon. Hydroxyurea (HU) has become the most widely used agent, although its effectiveness in increasing HbF levels and the number of F cells is highly variable. Recent investigations are cited showing that other agents such as butyrate, and the addition of recombinant hemopoietic growth factors, such as erythropoietin and stem cell factor, especially in combination with HU, offer important therapeutic possibilities. Transacting nuclear proteins are briefly discussed as possibly having a future role in the efforts of stimulating gamma-chain synthesis.