Regulation of human globin gene switching

Transcriptional Enhancers: Bridging the Genome and Phenome

Enhancers play a major role in animal development by modulating spatiotemporal expression of genes. They interact with sequence-specific transcriptional regulators in response to internal and external cues to bring about transcriptional changes, thus serving as the critical link between an organism's genome and its phenotypic traits. Deciphering the biology of enhancers is a key to understanding the genetic basis of common human diseases. Although a large number of candidate enhancers have been annotated through genome-wide analyses of chromatin accessibility, transcription factor binding, and histone modification in diverse cell types, efforts to characterize their biological roles in human diseases have only begun. Recent experiments have suggested a role for the three-dimensional chromatin architecture in regulation of gene expression by enhancers.

Pharmacological Induction of Fetal Hemoglobin Synthesis using Histone Deacetylase Inhibitors

A number of pharmacological agents are currently available for the induction of the fetal hemoglobin (Hb F) to treat the patients with sickle cell disease and beta-thalassemia. In the present review, we summarized the investigation and development of these Hb F-inducing agents and introduced histone deacetylase inhibitors as the new strategy to induce Hb F to treat the hemoglobin disorders

Fetal hemoglobin in sickle cell anemia: genetic determinants of response to hydroxyurea

The increase in fetal hemoglobin (HbF) in response to hydroxyurea (HU) varies among patients with sickle cell anemia. Twenty-nine candidate genes within loci previously reported to be linked to HbF level (6q22.3-q23.2, 8q11-q12 and Xp22.2-p22.3), involved in metabolism of HU and related to erythroid progenitor proliferation were studied in 137 sickle cell anemia patients treated with HU. Three-hundred and twenty tagging single nucleotide polymorphisms (SNPs) for genotyping were selected based on HapMap data. Multiple linear regression and the nonlinear regression Random Forest method were used to investigate the association between SNPs and the change in HbF level after 2 years of treatment with HU. Both methods revealed that SNPs in genes within the 6q22.3-23.2 and 8q11-q12 linkage peaks, and also the ARG2, FLT1, HAO2 and NOS1 genes were associated with the HbF response to HU. Polymorphisms in genes regulating HbF expression, HU metabolism and erythroid progenitor proliferation might modulate the patient response to HU.

Predicting clinical severity in sickle cell anaemia

The ability to predict the phenotype of an individual with sickle cell anaemia would allow a reliable prognosis and could guide therapeutic decision making. Some risk factors for individual disease complications are known but are insufficiently precise to use for prognostic purposes; predicting the global disease severity is not yet possible. Genetic association studies, which attempt to link gene polymorphisms with selected disease subphenotypes, may eventually provide useful methods of foretelling the likelihood of certain complications and allow better individualized treatment.

Role of NF-Y in in vivo regulation of the gamma-globin gene

The duplicated CCAAT box is required for gamma gene expression. We report here that the transcriptional factor NF-Y is recruited to the duplicated CCAAT box in vivo. A mutation of the duplicated CCAAT box that severely disrupts the NF-Y binding also reduces the accessibility level of the gamma gene promoter, affects the assembly of basal transcriptional machinery, and increases the recruitment of GATA-1 to the locus control region (LCR) and the proximal promoter and the recruitment of transcription cofactor CBP/p300 to the LCR. These findings suggest that recruitment of NF-Y to the duplicated CCAAT box plays a role in the chromatin opening of the gamma gene promoter as well as in the communication between the gamma gene promoter and the LCR.

Modulation of fetal hemoglobin in sickle cell anemia

A partial understanding of the pathophysiology of sickle cell disease has suggested one means of treatment-increasing the distribution and concentration of fetal hemoglobin in sickle erythrocytes. Although this can be accomplished clinically with drugs like hydroxyurea, a complete understanding of the molecular and cellular basis of fetal hemoglobin regulation may suggest new and better ways of attaining this goal.

Efficient studies of long-distance Bmp5 gene regulation using bacterial artificial chromosomes

The regulatory regions surrounding many genes may be large and difficult to study using standard transgenic approaches. Here we describe the use of bacterial artificial chromosome clones to rapidly survey hundreds of kilobases of DNA for potential regulatory sequences surrounding the mouse bone morphogenetic protein-5 (Bmp5) gene. Simple coinjection of large insert clones with lacZ reporter constructs recapitulates all of the sites of expression observed previously with numerous small constructs covering a large, complex regulatory region. The coinjection approach has made it possible to rapidly survey other regions of the Bmp5 gene for potential control elements, to confirm the location of several elements predicted from previous expression studies using regulatory mutations at the Bmp5 locus, to test whether Bmp5 control regions act similarly on endogenous and foreign promoters, and to show that Bmp5 control elements are capable of rescuing phenotypic effects of a Bmp5 deficiency. This rapid approach has identified new Bmp5 control regions responsible for controlling the development of specific anatomical structures in the vertebrate skeleton. A similar approach may be useful for studying complex control regions surrounding many other genes important in embryonic development and human disease.

Novel approaches to treatment of sickle cell anaemia

Sickle cell anaemia, a chronic and often debilitating disease, results from homozygosity for a single amino acid substitution in the beta-globin subunit of the haemoglobin molecule. Sickle haemoglobin (HbS), the product of this mutation, polymerises when deoxygenated, thus damaging the red blood cell and causing vaso-occlusive complications and haemolytic anaemia. Most cases of sickle cell anaemia are found in Africa. Until recently, treatment was directed at the management of disease complications. Patients with central nervous system events undergo exchange transfusions followed by chronic transfusion programmes. Patients with painful episodes, which result in many days missed from work and school are treated with narcotics and aggressive hydration. Novel therapy for sickle cell anaemia is designed to prevent complications through targeting disease mechanisms. Hydroxyurea is given to severely affected sickle cell anaemia patients in an attempt to prevent painful episodes, reduce hospital days, improve the patients' overall quality of life, and perhaps to prevent or provide some degree of end-organ damage stabilisation. Other novel therapies, such as bone marrow transplantation and gene therapy, pursue a cure. For these novel therapies to be effective on a global basis they must be amenable to underdeveloped and poorer countries of the world.

Induction of globin synthesis in K562 cells is associated with differential expression of transcription factor genes

Globin gene switching may be mediated by proteins expressed during different stages of development. Their identification may clarify the mechanisms of the conversion from fetal to adult globin production and lead to new approaches to reversing or retarding the gamma- to beta-globin gene switch. To explore this hypothesis, K562 erythroleukemia cells were induced to differentiate with 1.25, 2.5, and 5 mM sodium butyrate and gene expression was studied after 24, 48, and 72 h. Erythroid differentiation was verified by benzidine staining and by measuring the activity of a transduced A gamma-globin gene promoter linked to a luciferase reporter gene. Using differential display polymerase chain reaction (PCR), total mRNA extracted from induced cells at each time point of induction was reverse transcribed in the presence of A, G, and C anchored primers and 16 arbitrary primers, calculated to amplify approximately 50% of expressed genes. Amplified mRNAs from induced and uninduced cells were separated in polyacrylamide gels and compared. More than 110 cDNA fragments which appeared to represent either up- or downregulated mRNA species in induced K562 cells were identified. Sixty-four of these fragments had more than 95% homology to known GenBank sequences. Seventeen fragments with characteristics of transcription factors were cloned. These include differentiation-related gene-1 (drg-1), PAX 3/forkhead transcription factor, HZF2 which is a Kruppel-related zinc finger protein, three helix-loop-helix proteins (heir-1, Id3, and GOS8), alpha-NAC transcriptional coactivator, LIM domain protein, and trophoblast hypoxia regulating factor. Differential expression of all 17 fragments over 72 h was confirmed by reverse Northern dot blot analysis, semiquantitative PCR using nested primers, and Northern analysis. Erythroid maturation in induced K562 cells is associated with differential expression of numerous genes. Some encode transcription factors that could effect the initiation of HbF synthesis. Almost half of the differentially expressed clones contained cDNAs of unidentified open reading frames and these are the object of continued study.

NF-Y binding to twin CCAAT boxes: role of Q-rich domains and histone fold helices

NF-Y (CBF) is a CCAAT-binding trimer that activates 25 % of eukaryotic promoters. It contains putative histone fold motifs (HFMs) and distorts DNA. By using electrophoretic mobility shift assays with the twin CCAAT boxes of the human gamma-globin promoter and several combinations of subunit mutants, we dissected some of the structural features of CCAAT-box binding. NF-YA and NF-YC Q-rich domains significantly influence bending angles quantitatively, but not qualitatively, since they do not modify DNA orientation. They are both required for co-operative interactions among NF-Y molecules: for this, a precise alignement of two CCAAT boxes, 32 bp, three turns of the helix, is essential. Unlike the wild-type (wt) protein, steric hindrance does not impede simultaneous binding of the mutant composed of the short homology domains to CCAAT boxes closer than 22 bp: the addition of 11 amino acid residues to NF-YB and 13 to NF-YC flanking the HFM, restores wt behaviour. These stretches are predicted to form H2B-like alphaC and H2A-like alphaN fourth helices. A further support to this hypothesis comes from off-rates analysis of mutant combinations: the half-life of NF-Y, which is dependent on the type of NF-YB used, is extremely shortened, when the putative alphaC is present, nearly as much as in the wt NF-YB. These data (i) provide further evidence that NF-YB-NF-YC belong to the H2B-H2A subclasses, (ii) uncover new features of Q-rich domains, and (iii) define rules for NF-Y synergy that are potentially important for the regulation of many eukaryotic promoters.

Slow and Steady Wins The Race? Progress in the Development of Vectors for Gene Therapy of β-Thalassemia and Sickle Cell Disease

The cloning of the human β-globin genes more than 20 years ago led to predictions that β-thalassemia and sickle cell disease would be among the first monogenic diseases to be successfully treated by gene replacement therapy. However, despite the worldwide enrollment of more than 3,000 patients in approved gene transfer protocols, none have involved therapy for these diseases. This has been due to several technical hurdles that need to be overcome before gene replacement therapy for β-thalassemia and sickle cell disease can become practical. These problems include inefficient transduction of hematopoietic stem cells and an inability to achieve consistent, long-term, high-level expression of transferred β-like globin genes with current gene transfer vectors. In this review we highlight the relationships between understanding the fundamental mechanisms of β-globin gene locus function and basic vector biology and the development of strategies for β-globin gene replacement therapy. Despite slow initial progress in this field, recent advances in a variety of critical areas provide hope that clinical trials may not be far away.

Inhibition of gene expression by the Ggamma 5' flanking region of the Bantu beta(s) chromosome

Beta(s)-chromosome haplotypes are peculiar to specific regions of Africa and Asia and are associated with the occurrence of different fetal hemoglobin (Hb) levels in sickle cell patients. Among these haplotypes, beta(s)-chromosomes found in the Senegal and the Arab-India regions are associated with relatively high levels of HbF expression, whereas those around the Benin, Bantu, and the Cameroon regions show low levels of HbF expression. The roles of 5'HS2 and the 5' flanking (promoter region) region in the expression of globin genes are well documented. Haplotype specific variations are found in these regions and have been postulated to be involved in the regulation of HbF expression. In this study, we have analyzed the effect of sequence variations in regulatory regions of the Bantu 5'HS2 and 5' flanking region of the Ggamma gene on CAT expression. A diminution was observed in K562 cells when the promoter originated from the Bantu beta(s) chromosome. The decreased expression was independent of the origin of the 5'HS2 sequence--combinations of the Bantu promoter were measured with the Benin, Bantu, or Senegal 5'HS2 sequences in K562 cells. However, expression of the same plasmids in murine erythroleukemic (MEL) cells showed no difference in CAT expression among the various sequence combinations studied.

Genetic dissection of a mammalian replicator in the human beta-globin locus

The timing and localization of DNA replication initiation in mammalian cells are heritable traits, but it is not known whether initiation requires specific DNA sequences. A site-specific recombination strategy was used to show that DNA sequences previously identified as replication initiation sites could initiate replication when transferred to new chromosomal locations. An 8-kilobase DNA sequence encompassing the origin of DNA replication in the human beta-globin locus initiated replication in the simian genome. Specific deletions within the globin origin did not initiate replication in these chromosomal sites. These data suggest that initiation of DNA replication in mammalian cells requires specific sequence information and extend the replicon hypothesis to higher eukaryotes.

NF-Y organizes the gamma-globin CCAAT boxes region

The CCAAT-binding activator NF-Y is formed by three evolutionary conserved subunits, two of which contain putative histone-like domains. We investigated NF-Y binding to all CCAAT boxes of globin promoters in direct binding, competition, and supershift electrophoretic mobility shift assay; we found that the alpha, zeta, and proximal gamma CCAAT boxes of human and the prosimian Galago bind avidly, and distal gamma CCAAT boxes have intermediate affinity, whereas the epsilon and beta sequences bind NF-Y very poorly. We developed an efficient in vitro transcription system from erythroid K562 cells and established that both the distal and the proximal CCAAT boxes are important for optimal gamma-globin promoter activity. Surprisingly, NF-Y binding to a mutated distal CCAAT box (a C to T at position -114) is remarkably increased upon occupancy of the high affinity proximal element, located 27 base pairs away. Shortening the distance between the two CCAAT boxes progressively prevents simultaneous CCAAT binding, indicating that NF-Y interacts in a mutually exclusive way with CCAAT boxes closer than 24 base pairs apart. A combination of circular permutation and phasing analysis proved that (i) NF-Y-induced angles of the two gamma-globin CCAAT boxes have similar amplitudes; (ii) occupancy of the two CCAAT boxes leads to compensatory distortions; (iii) the two NF-Y bends are spatially oriented with combined twisting angles of about 100 degrees. Interestingly, such distortions are reminiscent of core histone-DNA interactions. We conclude that NF-Y binding imposes a high level of functionally important coordinate organization to the gamma-globin promoter.

Fetal hemoglobin in sickle cell anemia: examination of phylogenetically conserved sequences within the locus control region but outside the cores of hypersensitive sites 2 and 3

Regulatory elements linked to the beta-globin gene cluster modulates gamma-globin gene expression. The location of all of these elements and their mechanisms of action are still incompletely defined. Phylogenetically conserved DNA within the beta-globin gene cluster locus control region (LCR), but outside the core sequences of its hypersensitive sites (HS), were identified and we searched for any differences between HS 3 and HS 2, and HS 2 and HS 1, among patients with sickle cell anemia with different levels of Hb F who were homozygous for the common haplotypes. DNA was amplified with and without GC clamps, digested with restriction endonucleases, and examined by denaturing gradient gel electrophoresis (DGGE). We found limited fragment size diversity. However, the type of differences found and their distribution among haplotypes did not suggest that they represented distinctive changes that might explain the differential expression of the gamma-globin genes in sickle cell anemia.

High levels of human gamma-globin gene expression in adult mice carrying a transgene of deletion-type hereditary persistence of fetal hemoglobin

Persistent expression of the gamma-globin genes in adults with deletion types of hereditary persistence of fetal hemoglobin (HPFH) is thought to be mediated by enhancer-like effects of DNA sequences at the 3' breakpoints of the deletions. A transgenic mouse model of deletion-type HPFH was generated by using a DNA fragment containing both human gamma-globin genes and HPFH-2 breakpoint DNA sequences linked to the core sequences of the locus control region (LCR) of the human beta-globin gene cluster. Analysis of gamma-globin expression in six HPFH transgenic lines demonstrated persistence of gamma-globin mRNA and peptides in erythrocytes of adult HPFH transgenic mice. Analysis of the hemoglobin phenotype of adult HPFH transgenic animals by isoelectric focusing showed the presence of hybrid mouse alpha2-human gamma2 tetramers as well as human gamma4 homotetramers (hemoglobin Bart's). In contrast, correct developmental regulation of the gamma-globin genes with essentially absent gamma-globin gene expression in adult erythroid cells was observed in two control non-HPFH transgenic lines, consistent with autonomous silencing of normal human gamma-globin expression in adult transgenic mice. Interestingly, marked preferential overexpression of the LCR-distal (A)gamma-globin gene but not of the LCR-proximal (G)gamma-globin gene was observed at all developmental stages in erythroid cells of HPFH-2 transgenic mice. These findings were also associated with the formation of a DNase I-hypersensitive site in the HPFH-2 breakpoint DNA of transgenic murine erythroid cells, as occurs in normal human erythroid cells in vivo. These results indicate that breakpoint DNA sequences in deletion-type HPFH-2 can modify the developmentally regulated expression of the gamma-globin genes.

Fetal globin expression in New World monkeys

Reverse phase chromatography of the globin chains of adult, newborn, and fetal erythrocytes from three species of New World monkeys (Cebus apella, Aotus azarae, and Callithrix jacchus) representing three of the seven platyrrhine clades showed that gamma-globin expression was fetal in these animals. The globins were identified by a combination of chemical sequencing and mass spectrometric analysis. Since gamma-globin expression is fetal in the other major simian branch, the catarrhines, but embryonic in prosimian primates and nonprimate placental mammals, the evolution of fetal recruitment can now be assigned to the period between the simian-prosimian divergence (55 million years ago) and the platyrrhine-catarrhine divergence (35 million years ago). The gamma-globin gene underwent tandem duplication during the same evolutionary epoch, in accord with a model that suggests that the downstream duplicated gamma-gene (gamma2) was free to acquire the mutations necessary for fetal recruitment. Mass spectrometric analysis of tryptic digests of the gamma-globins verified the amino acid sequences deduced from genomic sequencing. Detailed analysis of high performance liquid chromatography and matrix-assisted laser desorption/ionization mass spectrometry data showed that gamma2-globin in Cebus was expressed to a far greater extent than gamma1-globin, supporting inferences drawn from a study of the promoter sequences. A "pre-gamma"-globin was observed in C. apella and shown to be primarily the glutathionyl adduct. The other species, A. azarae and C. jacchus, also express only one gamma-globin polypeptide. This work provides biochemical evidence of an evolutionary trend in the platyrrhines to alter the duplicated gamma-globin gene locus so that only one gamma-globin polypeptide is expressed.

The major histocompatibility complex class II Ea promoter requires TFIID binding to an initiator sequence

The major histocompatibility complex (MHC) class II Ea promoter is dependent on the presence of conserved upstream X and Y boxes and of initiator (Inr) sequences. In vitro transcription analysis of the Inr region with linker-scanning mutants pinpoints a functionally essential element that shows homology to the terminal deoxynucleotidyltransferase (TdT) Inr; contrary to the TdT Inr and other Inrs identified so far, the key sequence, between positions +5 and +12, is located within a transcribed area. Swapping the TdT sequence into the corresponding Ea position leads to a fivefold increase in transcription rate, without altering start site selection. Inr-binding proteins LBP-1/CP2 and TIP--a TdT Inr-binding protein unrelated to YY1--recognize the Ea Inr; they interact with overlapping yet distinct sequences around the Cap site, but their binding does not coincide with Ea Inr activity. A good correlation is, rather, found with binding of immunopurified holo-TFIID to this element. TFIID interacts both with Ea TATA-like and Inr sequences, but only the latter is functionally relevant. Unlike TBP, TFIID binds in the absence of TFIIA, indicating a stabilizing role for TBP-associated factors in Ea promoter recognition. Sequence comparison with other mouse and human MHC class II promoters suggests a common mechanism of start site(s) selection for the MHC class II gene family.