Linker scanning mutagenesis of the 5'-flanking region of the mouse beta-major-globin gene: sequence requirements for transcription in erythroid and nonerythroid cells

The regulation of human globin promoters by CCAAT box elements and the recruitment of NF-Y

CCAAT boxes are motifs found within the proximal promoter of many genes, including the human globin genes. The highly conserved nature of CCAAT box motifs within the promoter region of both α-like and β-like globin genes emphasises the functional importance of the CCAAT sequence in globin gene regulation. Mutations within the β-globin CCAAT box result in β-thalassaemia, while mutations within the distal γ-globin CCAAT box cause the Hereditary Persistence of Foetal Haemoglobin, a benign condition which results in continued γ-globin expression during adult life. Understanding the transcriptional regulation of the globin genes is of particular interest, as reactivating the foetal γ-globin gene alleviates the symptoms of β-thalassaemia and sickle cell anaemia. NF-Y is considered to be the primary activating transcription factor which binds to globin CCAAT box motifs. Here we review recruitment of NF-Y to globin CCAAT boxes and the role NF-Y plays in regulating globin gene expression. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.

Erythroid Kruppel-like factor (EKLF) is recruited to the gamma-globin gene promoter as a co-activator and is required for gamma-globin gene induction by short-chain fatty acid derivatives

OBJECTIVES

The erythroid Kruppel-like factor (EKLF) is an essential transcription factor for beta-type globin gene switching, and specifically activates transcription of the adult beta-globin gene promoter. We sought to determine if EKLF is also required for activation of the gamma-globin gene by short-chain fatty acid (SCFA) derivatives, which are now entering clinical trials.

METHODS

The functional and physical interaction of EKLF and co-regulatory molecules with the endogenous human globin gene promoters was studied in primary human erythroid progenitors and cell lines, using chromatin immunoprecipitation (ChIP) assays and genetic manipulation of the levels of EKLF and co-regulators.

RESULTS AND CONCLUSIONS

Knockdown of EKLF prevents SCFA-induced expression of the gamma-globin promoter in a stably expressed microLCRbeta(pr)R(luc) (A)gamma(pr)F(luc) cassette, and prevents induction of the endogenous gamma-globin gene in primary human erythroid progenitors. EKLF is actively recruited to endogenous gamma-globin gene promoters after exposure of primary human erythroid progenitors, and murine hematopoietic cell lines, to SCFA derivatives. The core ATPase BRG1 subunit of the human SWI/WNF complex, a ubiquitous multimeric complex that regulates gene expression by remodeling nucleosomal structure, is also required for gamma-globin gene induction by SCFA derivatives. BRG1 is actively recruited to the endogenous gamma-globin promoter of primary human erythroid progenitors by exposure to SCFA derivatives, and this recruitment is dependent upon the presence of EKLF. These findings demonstrate that EKLF, and the co-activator BRG1, previously demonstrated to be required for definitive or adult erythropoietic patterns of globin gene expression, are co-opted by SCFA derivatives to activate the fetal globin genes.

A global role for EKLF in definitive and primitive erythropoiesis

Erythroid Kruppel-like factor (EKLF, KLF1) plays an important role in definitive erythropoiesis and beta-globin gene regulation but failure to rectify lethal fetal anemia upon correction of globin chain imbalance suggested additional critical EKLF target genes. We employed expression profiling of EKLF-null fetal liver and EKLF-null erythroid cell lines containing an inducible EKLF-estrogen receptor (EKLF-ER) fusion construct to search for such targets. An overlapping list of EKLF-regulated genes from the 2 systems included alpha-hemoglobin stabilizing protein (AHSP), cytoskeletal proteins, hemesynthesis enzymes, transcription factors, and blood group antigens. One EKLF target gene, dematin, which encodes an erythrocyte cytoskeletal protein (band 4.9), contains several phylogenetically conserved consensus CACC motifs predicted to bind EKLF. Chromatin immunoprecipitation demonstrated in vivo EKLF occupancy at these sites and promoter reporter assays showed that EKLF activates gene transcription through these DNA elements. Furthermore, investigation of EKLF target genes in the yolk sac led to the discovery of unexpected additional defects in the embryonic red cell membrane and cytoskeleton. In short, EKLF regulates global erythroid gene expression that is critical for the development of primitive and definitive red cells.

Restoration of the CCAAT Box or Insertion of the CACCC Motif Activate δ-Globin Gene Expression

Hemoglobin A2 (HbA2 ), which contains δ-globin as its non–α-globin, represents a minor fraction of the Hb found in normal adults. It has been shown recently that HbA2 is as potent as HbF in inhibiting intracellular deoxy-HbS polymerization, and its expression is therefore relevant to sickle cell disease treatment strategies. To elucidate the mechanisms responsible for the low-level expression of the δ-globin gene in adult erythroid cells, we first compared promoter sequences and found that the δ-globin gene differs from the β-globin gene in the absence of an erythroid Krüppel-like factor (EKLF ) binding site, the alteration of the CCAAT box to CCAAC, and the presence of a GATA-1 binding site. Second, serial deletions of the human δ-globin promoter sequence fused to a luciferase (LUC) reporter gene were transfected into K562 cells. We identified both positive and negative regulatory regions in the 5′ flanking sequence. Furthermore, a plasmid containing a single base pair (bp) mutation in the CCAAC box of the δ promoter, restoring the CCAAT box, caused a 5.6-fold and 2.4-fold (P < .05) increase of LUC activity in transfected K562 cells and MEL cells, respectively, in comparison to the wild-type δ promoter. A set of substitutions that create an EKLF binding site centered at −85 bp increased the expression by 26.8-fold and 6.5-fold (P < .05) in K562 and MEL cells, respectively. These results clearly demonstrate that the restoration of either an EKLF binding site or the CCAAT box can increase δ-globin gene expression, with potential future clinical benefit.

Restoration of the CCAAT Box or Insertion of the CACCC Motif Activate δ-Globin Gene Expression

Hemoglobin A2 (HbA2 ), which contains δ-globin as its non–α-globin, represents a minor fraction of the Hb found in normal adults. It has been shown recently that HbA2 is as potent as HbF in inhibiting intracellular deoxy-HbS polymerization, and its expression is therefore relevant to sickle cell disease treatment strategies. To elucidate the mechanisms responsible for the low-level expression of the δ-globin gene in adult erythroid cells, we first compared promoter sequences and found that the δ-globin gene differs from the β-globin gene in the absence of an erythroid Krüppel-like factor (EKLF ) binding site, the alteration of the CCAAT box to CCAAC, and the presence of a GATA-1 binding site. Second, serial deletions of the human δ-globin promoter sequence fused to a luciferase (LUC) reporter gene were transfected into K562 cells. We identified both positive and negative regulatory regions in the 5′ flanking sequence. Furthermore, a plasmid containing a single base pair (bp) mutation in the CCAAC box of the δ promoter, restoring the CCAAT box, caused a 5.6-fold and 2.4-fold (P < .05) increase of LUC activity in transfected K562 cells and MEL cells, respectively, in comparison to the wild-type δ promoter. A set of substitutions that create an EKLF binding site centered at −85 bp increased the expression by 26.8-fold and 6.5-fold (P < .05) in K562 and MEL cells, respectively. These results clearly demonstrate that the restoration of either an EKLF binding site or the CCAAT box can increase δ-globin gene expression, with potential future clinical benefit.

Molecular cloning and characterization of the promoter for the Chinese hamster DNA topoisomerase II alpha gene

To investigate the mechanisms governing the expression of DNA topoisomerase II alpha, the Chinese hamster topoisomerase II alpha gene has been cloned and the promoter region analyzed. There are several transcriptional start sites clustered in a region of 30 base pairs, with the major one being 102 nucleotides upstream from the ATG translation initiation site. Sequencing data reveal one GC box and a total of five inverted CCAAT elements (ICEs) within a region of 530 base pairs upstream from the major transcription start site. Sequence comparison between the human and Chinese hamster topoisomerase II alpha gene promoter regions shows a high degree of homology centered at the ICEs and GC box. In vitro DNase I footprinting results indicate protection by binding proteins at and around each ICE on both DNA strands. However, no obvious protection was observed for the GC box. Competition gel mobility shift assays with oligonucleotides containing either the wild-type or mutated ICE sequences suggest that identical or similar proteins specifically bind at each ICE, although with different affinities for individual ICE sequences. Chloramphenicol acetyltransferase assays employing nested 5'-deletions of the 5'-flanking sequence of the gene demonstrate that the sequence between -186 and +102, which contains three proximal ICEs, is sufficient for near wild-type level of promoter activity. When these three ICEs were gradually replaced with sequences which do not interact with the binding proteins, reducing promoter activity of the resulted constructs was observed. In conjunction with results from footprinting and gel mobility shift studies, the transient gene expression finding suggests that the ICEs are functionally important for the transcriptional regulation of the topoisomerase II alpha gene.

Nuclear proteins that interact with the beta maj globin promoter start to accumulate in MEL cells within 12 hours of induction and RNA copies of the promoter successfully compete their binding in vitro

The induction of differentiation in mouse erythroleukemia (MEL) cells by dimethylsulfoxide (DMSO) is characterized by increased transcription of globin genes. We have determined that DMSO treated cells increase the levels of nuclear factors capable of overall interactions with the beta maj globin promoter during the initial 24 h post induction, as measured by gel mobility analysis. Two unprocessed beta maj globin mRNA precursors, which are present in MEL cell nuclei early in differentiation, were previously shown to contain the 5' promoter flanking region, and thereby provided the nucleus with a pool of regulatory sequences in multiple RNA copies. We have studied the effect of RNA copies of the promoter region on binding interactions between DNA sequences of the beta maj globin promoter and nuclear factors that interact with these sequences. The promoter region RNA transcripts competed effectively for DNA binding proteins in vitro, while the antisense RNA from the same region did not. The most pronounced competition was observed with proteins from 12 h after DMSO induction, when the concentration of the DNA binding proteins was still increasing. Since the 'upstream' transcripts predominate at 12 h after DMSO induction, these results indicate that the promoter region transcripts may influence the equilibrium of binding between the beta maj globin promoter and the nuclear factors that bind to this region during DMSO induction.

Erythropoietin-induced transcription at the murine beta maj-globin promoter. A central role for GATA-1

Using J2E cells and the murine beta maj-globin promoter as a model, we have performed the first direct analyses of erythropoietin (EPO)-activated transcription from defined templates. The -346 to +26 beta maj promoter was shown to comprise a target for maximal activation. This included a positive role for a -346 to -107-base pair (bp) domain in J2E cells, but not in F-MEL cells. Mutagenesis of a -215-bp AGATAA element within this domain showed that this effect did not require GATA-1 binding. In contrast, a critical role for GATA-1 at a -60-bp (G)GATAG element was defined by mutagenesis (GGg-TAG and TGATAG), complementation with a synthetic TGATAA element, and the demonstrated specific binding of GATA-1. Proximal CCAAT (-75) and CACCC (-90) elements also were shown to contribute to transcriptional activation in J2E cells, yet exerted quantitatively distinct effects in the F-MEL system. Based on these results, minimal [TGATAA]4-TATA and TGATAA-CACCC-TATA promoters were constructed and assayed in each system. Remarkably, the [TGATAA]4-TATA promoter, but not the TGATAA-CACCC-TATA promoter, was induced efficiently by EPO in J2E cells, whereas the TGATAA-CACCC-TATA promoter was highly induced by Me2SO in F-MEL cells. These findings suggest that mechanisms of EPO-induced transcription in J2E cells involve GATA-1 and differ from chemically activated mechanisms studied previously in F-MEL cells. Globin induction in J2E cells was not associated with effects of EPO on levels or nuclear translocation of GATA-1. However, hemoglobinization was induced by okadaic acid, 8-Br-cAMP, and forskolin, a finding consistent with induction mechanisms that may involve modulated serine/threonine phosphorylation.

Role of erythroid Kruppel-like factor in human gamma- to beta-globin gene switching

Erythroid Kruppel-like factor (EKLF) is an erythroid-specific transcription factor that contains zinc finger domains similar to the Kruppel protein of Drosophila melanogaster. Previous studies demonstrated that EKLF binds to the CACCC box in the human beta-globin gene promoter and activates transcription. CACCC box mutations that cause severe beta-thalassemias in humans inhibit EKLF binding. Results described in this paper suggest that EKLF functions predominately in adult erythroid tissue. The EKLF gene is expressed at a 3-fold higher level in adult erythroid tissue than in fetal erythroid tissue, and the EKLF protein binds to the human beta-globin promoter 8-fold more efficiently than to the human gamma-globin promoter. Co-transfection experiments in the human fetal-like erythroleukemia cell line K562 demonstrate that over-expression of EKLF activates a beta-globin reporter construct 1000-fold; a linked gamma-globin reporter is activated only 3-fold. Mutation of the beta-globin CACCC box severely inhibits activation. These results demonstrate that EKLF is a developmental stage-enriched protein that preferentially activates human beta-globin gene expression. The data strongly suggest that EKLF is an important factor involved in human gamma- to beta-globin gene switching.

CCACC-binding or simian-virus-40-protein-1-binding proteins cooperate with human GATA-1 to direct erythroid-specific transcription and to mediate 5' hypersensitive site 2 sensitivity of a TATA-less promoter

Previous studies have shown that a -112 to +78 DNA fragment from the erythroid promoter of the human porphobilinogen deaminase (PBGD) gene has erythroid-specific activity. This PBGD-(-112 to +78) promoter contains a CCACC binding site (position -100), a GATA binding site (position -70) and an initiator element around the cap site. Using a cotransfection assay, we find that the human factor GATA-1 trans-activates the PBGD-(-112 to +78) promoter in non-erythroid cells. We show that, if trans-activation is abolished by mutations that destroy either the -100 CCACC binding or the -70 GATA binding sites, replacement of the -100 CCACC binding site by a simian-virus-40-protein-1 (Sp1) binding site maintains both the erythroid-specific activity of this promoter and the human GATA-1 trans-activation. Thus, human GATA-1 acts on the PBGD promoter in association with Sp1 or CCACC binding proteins. This PBGD-(-112 to +78) promoter is activated 20-fold by a cis-linked 5' hypersensitive site 2 (5'HS-2) of the human beta-globin locus control region. This activation depends on the -70 GATA and -100 CCACC or Sp1 binding sites. When a longer -714 to +78 fragment of the PBGD promoter is used, the -70 GATA mutant still displays erythroid-specific activity and is cis-activated by the 5'HS-2 enhancer, while the -100 CCACC mutant is completely inactive in the absence or in the presence of the 5'HS-2 enhancer. Thus, the -100 CCACC binding site is indispensable for the correct activity and sensitivity of the human PBGD promoter to the 5'HS-2 enhancer, whereas the -70 GATA binding site can functionally be replaced by upstream cis-acting elements.

Expression of the human ADH2 gene: an unusual Sp1-binding site in the promoter of a gene expressed at high levels in liver

The sequence 5'-GTGGGTGTGGC (G3T) is important for the efficient initiation of transcription from the human ADH2 promoter. We show here that the purified transcription factor Sp1 binds with high affinity to the G3T site of ADH2 (encoding beta beta-alcohol dehydrogenase), even though the G3T sequence does not contain the canonical Sp1-binding site, GGGCGG. Proteins from mouse liver nuclei and purified Sp1 both footprint the same sequence of the ADH2 promoter with similar patterns. UV crosslinking demonstrates that the major G3T-binding protein in the liver extract is similar in size to Sp1. Mouse liver nuclear extract resembles purified Sp1 in its relative binding affinity to a series of oligodeoxyribonucleotides containing either the Sp1-binding site or variants of the G3T sequence. These data indicate that the G3T sequence can interact with Sp1 and that Sp1 may be important in the expression of ADH2. The G3T sequence from the closely related ADH3 gene (encoding gamma gamma-alcohol dehydrogenase) differs from that of ADH2 in the first two nucleotides; it binds both the liver protein and purified Sp1 with lower affinity. This might explain why ADH3 is expressed at lower levels than ADH2 in the liver.

The beta globin gene cluster of the prosimian primate Galago crassicaudatus: nucleotide sequence determination of the 41-kb cluster and comparative sequence analyses

The nucleotide sequence of the beta globin gene cluster of the prosimian Galago crassicaudatus has been determined. A total sequence spanning 41,101 bp contains and links together previously published sequences of the five galago beta-like globin genes (5'-epsilon-gamma-psi eta-delta-beta-3'). A computer-aided search for middle interspersed repetitive sequences identified 10 LINE (L1) elements, including a 5' truncated repeat that is orthologous to the full-length L1 element found in the human epsilon-gamma intergenic region. SINE elements that were identified included one Alu type I repeat, four Alu type II repeats, and two methionine tRNA-derived Monomer (type III) elements. Alu type II and Monomer sequences are unique to the galago genome. Structural analyses of the cluster sequence reveals that it is relatively A+T rich (about 62%) and regions with high G+C content are associated primarily with globin coding regions. Comparative analyses with the beta globin cluster sequences of human, rabbit, and mouse reveal extensive sequence homologies in their genic regions, but only human, galago, and rabbit sequences share extensive intergenic sequence homologies. Divergence analyses of aligned intergenic and flanking sequences from orthologous human, galago, and rabbit sequences show a gradation in the rate of nucleotide sequence evolution along the cluster where sequences 5' of the epsilon globin gene region show the least sequence divergence and sequences just 5' of the beta globin gene region show the greatest sequence divergence.

Cloning of the rat insulin-like growth factor binding protein-1 gene and analysis of its 5' promoter region

To understand specific mechanisms involved in the regulation of insulin-like growth factor binding protein-1 (IGFBP-1), an important modulator of IGF bioactivity, we cloned the rat IGFBP-1 gene and sequenced a 1.5 kb Sph1-Sph1 fragment containing 1110 bases upstream from the translation start site. Computer analysis reveals the presence of ATA, CACCC, and CCAAT elements, and putative homeodomain, AP-1, insulin and glucocorticoid response elements in the 5' promoter. Primer extension and ribonuclease protection studies reveal a single cap site in RNA from rat hepatoma cells and both control and diabetic rat liver.

Regulatory elements mediating transcription of the human Ha-ras gene

In order to identify transcriptional regulatory elements controlling the expression of the human Ha-ras gene and to quantitatively assess the role of each element, we made mutations of the transcriptional regulatory region, including 5' and internal deletions, linker scanning and replacement mutations, and combinations of these mutations all fused to the bacterial chloramphenicol acetyltransferase gene. The promoter activity of each of these mutants was determined by measuring the transient expression of chloramphenicol acetyltransferase activity after transfection into human epithelial HeLa cells. We found that the most important regulatory region consists of two closely linked but functionally independent elements, the non-consensus GC-II element, CGGGCGGGC, centered at position -153 from the major transcription start site cluster and a new element, CCGGAA, centered at position -161 directly upstream from GC-II. In addition, there are two functional regulatory elements which make minor contributions to the full promoter activity; a double CCAAT NF-I binding site at position -88 and an unidentified upstream element between positions -199 and -252. Aside from GC-II, the GC boxes, of which there are a total of six between positions -185 and +85, make little or no contribution to Ha-ras promoter activity when individual mutations are tested in growing HeLa cells. The three potential AP2 sites and a weak single NF-I binding site make no contribution. The basal promoter region extending to position -75 from the major start site cluster has no independent activity in this TATA-less gene.

Enhancer dependent expression of the chicken beta-hatching globin gene during erythroid differentiation

The activity of the chicken beta H globin gene promoter has been analysed in functional assays in both chicken and murine erythroleukaemia cells. Sequences between -251 and -146 bp, in the presence or absence of the chicken beta globin locus enhancer, strongly repress transcription in erythroid cells before and after the induction of terminal differentiation. A 50 bp sequence (-98 to -146 bp), which contains adjacent cGATA-1 and NF1 protein binding sites in vitro, and which is bound by non-histone protein in vivo, is essential for full promoter activity. Mutagenesis studies indicate that both protein binding sites are required. During terminal differentiation, both the absence of repressor and the presence of the erythroid enhancer are required for maximal promoter activity, suggesting that the beta A, beta epsilon and beta H globin gene promoters compete for the enhancer during development.

Dynamics of demethylation and activation of the alpha-actin gene in myoblasts

Transient transfection into L8 myoblasts has been used to study the rat alpha-actin gene promoter. Demodification of specific sites occurs in two stages, with a hemimethylated intermediate formed within a few hours after entry of the alpha-actin gene construct into the cell. The removal of the methyl moiety from the complementary strand takes place after a delay of at least 48 hr, and both events are actively carried out in the absence of DNA replication. By assaying gene activity during the course of the transfection, it was possible to demonstrate that demethylation of both strands at the critical CpG loci is essential to activate transcription. Genetic analysis revealed the existence of cis-acting elements required for demethylation. The recognition of these sites early in the differentiation process probably leads to the demodification events required to make the gene accessible to its transcription factors.

The mouse keratin 19-encoding gene: sequence, structure and chromosomal assignment

Keratin 19 (K19) is synthesized mainly in embryonic and adult simple epithelia, but has also been found in stratified epithelia as well. K19 is the smallest known keratin and is remarkable in that, contrary to all other keratins, it does not have a designated partner for the formation of filaments, implying that regulation of its expression is different from other keratin-encoding genes. As a first step in elucidating the mechanisms by which the K19 gene is regulated in relatively undifferentiated embryonic and in terminally differentiated adult tissues, a series of overlapping clones containing the complete mouse K19 gene was isolated from a mouse genomic library and characterized. The nucleotide (nt) sequence extends over 5119 nt and includes six exons. A region of 303 nt upstream from the transcription start point (tsp) was also sequenced. Comparison with the human and bovine K19 genes revealed the existence of homologies in both the coding and noncoding regions. The putative promoter region of the mouse K19 gene is highly homologous to the corresponding sequences of the human and bovine K19 genes. It contains an ATA box, a CAAT box and two potential Sp1-binding sites. Significant homologies were also found between the sequences of the introns of the mouse, human and bovine genes: this was particularly evident in introns 2, 3, 4 and 5. Intron 1, which showed the greatest degree of divergence, was found to contain many repetitive elements. Finally, it is shown that the mouse K19 gene cosegregates with the type-I keratin-encoding gene locus (Krt-1) on chromosome 11.

Genomic structure of the human cytosolic aldehyde dehydrogenase gene

We have isolated and characterized several overlapping clones from two human genomic libraries constructed in cosmid and bacteriophage vectors. They span about 80 kbp and include the entire human cytosolic aldehyde dehydrogenase (ALDH1) gene. Restriction endonuclease mapping, Southern blotting with cDNA and specific oligonucleotide probes, and DNA sequencing were performed to analyze the cloned genomic DNA. The ALDH1 gene is about 53 kbp long and is divided into 13 exons which encode 501 amino acid residues. Primer extension results defined the transcription initiation site to 53 bp upstream from the A of the initiation codon ATG. The promoter region of the gene contains an ATA box and a CCAAT box, which are located 32 and 74 bp upstream, respectively, from the transcription initiation site. The possible functional domains of the protein encoded by exons are discussed. A similar intron-exon organization between the genes of cytosolic ALDH1 and its mitochondrial ALDH2 isozyme in which both enzymes are encoded by 13 exons and 9 of the 12 introns interrupt the coding sequence at homologous positions was observed. This is consistent with the model that the two isozyme genes evolved after the duplication of a common ancestor gene.

Interaction of a developmentally regulated DNA-binding factor with sites flanking two different fruit-ripening genes from tomato

To investigate mechanisms that control fruit development, we have begun experiments to identify proteins that control gene expression during tomato fruit ripening. We focused on the regulation of two different genes, E4 and E8, whose transcription is coordinately activated at the onset of fruit ripening. We report here that a DNA-binding protein specifically reacts with similar sequences flanking the E4 and E8 genes. The E4 binding site is at position -34 to -18 and, therefore, overlaps the region (TATA box) that in many eukaryotic genes serves to determine the efficiency and initiation site of transcription. In contrast, the E8 binding site is distal, located at -936 to -920 relative to the start of E8 gene transcription. Gel electrophoresis mobility retardation experiments indicate that the DNA binding activity that interacts with these two sites increases at the onset of fruit ripening. Taken together, these results suggest that this DNA-binding protein may function to coordinate E4 and E8 gene expression during fruit ripening.

Evolution and transcription of old world monkey globin genes

Although apparently inactive in the whole animal, the delta globin genes from three species of Old World monkey (rhesus, baboon and green monkey) are all functional in an in vitro transcription assay. Their activities in vitro are similar to that of the functional human delta gene. A fourth monkey gene, from the colobus monkey, is transcribed approximately fivefold less efficiently than the others. This reduced in vitro activity results from a 20 base-pair deletion, which removes the normal site of mRNA initiation. When the deletion is repaired by site-directed mutagenesis, transcriptional activity increases to the level observed for the other delta genes. We also report the complete nucleotide sequences of the colobus beta, colobus delta, and rhesus delta genes. Sequence comparisons show that the delta and beta genes in the same species have not exchanged genetic information since the divergence of the human and monkey lineages. Phylogenetic analysis of these sequences affirms that the Old World monkey delta genes are evolving more rapidly than their functional counterparts. Moreover, the rate of replacement substitutions has risen to equal that of non-coding DNA, as expected for genes no longer under selective constraint.

In vitro characterization of tissue-specific nuclear proteins preferentially bound to the mouse beta-globin gene during MEL cell terminal differentiation

Using DNA restriction fragments of the mouse beta-globin gene and other promoter-containing DNA fragments (LTR-MMTV and pBR322) as controls, we have characterized by protein blotting, in extracts of mouse erythroleukemia (MEL) cells, specific nuclear DNA binding proteins with a preferential affinity for the beta-globin DNA. Some proteins (110 and 75 kDa) appear in differentiated MEL cells while others (100, 95, and 35 kDa) are present in immature MEL and normal erythroblast cells and bind selectively to the far-upstream region of the gene. These proteins could modulate either positively or negatively the expression of the beta-globin gene and maybe, of other genes, during the terminal differentiation of erythroid cells.

Structure of the gene encoding the beta-subunit of chicken prolyl 4-hydroxylase

Prolyl 4-hydroxylase (EC 1.14.11.2) converts peptidyl proline to peptidyl hydroxyproline in procollagen polypeptides during collagen biosynthesis. The active enzyme is a tetramer which is composed of two pairs of non-identical subunits in a molecular form of alpha 2 beta 2. In addition to the tetrameric prolyl 4-hydroxylase (alpha 2 beta 2), the free beta-subunit is also found inside cells. Recently it was shown that the beta-subunit of prolyl 4-hydroxylase is identical to the protein disulfide isomerase and cellular thyroid hormone-binding protein. We previously isolated and characterized cDNAs of the beta-subunit of chicken prolyl 4-hydroxylase. The cDNA of beta-subunit was used to screen a chicken genomic DNA library constructed with the lambda EMBL-3 vector. Two clones, lambda gCPH beta-22 and beta-50, were isolated and characterized by restriction enzyme analysis, heteroduplex analysis, and nucleotide sequencing. The results showed that the 2.5-kb mRNA of the beta-subunit is divided into eleven exons and that the gene is 9.0 kb long. The gene contains consensus sequence for TATA at -24 bp and four CAAT at -57, -157, -194 and -223 bp in the 5' end flanking sequence of the transcription start point. In addition, there are three GC boxes upstream from the TATA box and four GC boxes in the first intron. This is similar to the structure of the alpha 1(I) collagen coding gene (COL1A1). These elements may interact with nuclear factors and play important roles in expression regulation of the beta-subunit gene as has been described in COL1A1.

Human CCAAT-binding proteins have heterologous subunits

We have characterized three distinct proteins present in HeLa cell extracts that specifically recognize different subsets of transcriptional elements containing the pentanucleotide sequence CCAAT. One of these CCAAT-binding proteins, CP1, binds with high affinity to CCAAT elements present in the human alpha-globin promoter and the adenovirus major late promoter (MLP). A second protein, CP2, binds with high affinity to a CCAAT element present in the rat gamma-fibrinogen promoter. Finally, the third CCAAT-binding protein is nuclear factor I (NF-I), a cellular DNA-binding protein that binds to the adenovirus origin of replication and is required for the initiation of adenoviral replication. CP1, CP2, and NF-I are distinct activities in that each binds to its own recognition site with an affinity that is at least three orders of magnitude higher than that with which it binds to the recognition sites of the other two proteins. Surprisingly, CP1, CP2, and NF-I each appear to recognize their binding site with highest affinity as a multisubunit complex composed of heterologous subunits. In the case of CP1, two different types of subunits form a stable complex in the absence of a DNA-binding site. Moreover, both subunits are present in the CP1-DNA complex. We thus propose the existence of a family of related multisubunit CCAAT-binding proteins that are composed of heterologous subunits.

Lineage-specific expression of a human beta-globin gene in murine bone marrow transplant recipients reconstituted with retrovirus-transduced stem cells

Recombinant retroviral genomes encoding a chromosomal human beta-globin gene have been used to transduce murine haematopoietic stem cells in vitro. After permanent engraftment of lethally irradiated recipients with the transduced cells, the human beta-globin gene is expressed at significant levels only within the erythroid lineage. These results indicate that it is possible to obtain stable expression of exogenous chromosomal DNA sequences introduced into mature haematopoietic cells in vivo via stem cell infection, and that human disorders of haemoglobin production may be more feasible candidates for somatic cell gene therapy than previously suspected.

A multiplicity of CCAAT box-binding proteins

NF-Y is a sequence-specific DNA-binding protein that recognizes the Y box, a promoter element common to all major histocompatibility complex class II genes. Since the 14-base Y element harbors a CCAAT box in reverse, we were prompted to ask whether NF-Y is actually a CCAAT box-binding protein and whether it is related to the previously described CCAAT-binding factors CBP and CTF/NF-I. Data from gel retardation, methylation interference, saturation mutagenesis, and cross-competition experiments establish definitively that NF-Y is an entirely distinct CCAAT box-binding entity. Moreover, these experiments have uncovered a fourth CCAAT-binding protein, NF-Y(star) that interacts with the thymidine kinase promoter. Clearly, then, there exists a multiplicity of factors that recognize CCAAT sequences; it now becomes imperative to understand the functional significance of this multiplicity.

An octamer oligonucleotide upstream of a TATA motif is sufficient for lymphoid-specific promoter activity

The octamer sequence ATGCAAAT or its inverse complement ATTTGCAT is well-conserved in all immunoglobulin gene promoters and has been implicated in promoter function by deletion analysis. Although immunoglobulin promoters are tissue-specific, the octamer is also a functional element in non-tissue-specific upstream regions--like those controlling U1 and U2 small nuclear RNA and histone H2B genes--where it is associated with additional canonical elements. Specific interactions occur between the octamer motif and both lymphoid-specific and ubiquitous proteins. By using a synthetic octamer oligonucleotide inserted upstream of the beta-globin TATA box we show here that the octamer element by itself is sufficient for directing lymphocyte-specific RNA synthesis when within 70 base pairs of the start site of transcription. We also demonstrate that mutations in any position of the conserved motif interfere with this function.

Characterization of trans-acting factor(s) regulating beta-globin gene expression by in vivo competition

A beta-globin/TK fusion gene was microinjected into non-erythroid cells (Ltk- cells) and erythroid cells (murine erythroleukemia (MEL) cells), and the interactions of the regulatory cellular factors with the beta-globin sequences were investigated by the in vivo competition experiment. The fusion gene was expressed efficiently in Ltk- cells. This expression was inhibited by a co-injection with a three-fold molar excess of the 5'-flanking sequence of the beta-globin gene or with a nine-fold molar excess of the mammary tumor virus LTR, but not with the alpha-globin gene. The fusion gene was expressed very poorly in the uninduced MEL cells and highly in the induced MEL cells. The co-injection of the beta-globin gene did not affect expression in the MEL cells in either uninduced or induced conditions.

Nucleotide sequence of the delta-beta-globin intergenic segment in the macaque: structure and evolutionary rates in higher primates

A 5600-base-pair (bp) fragment including the beta-globin gene and about 4000 bp of its 5' flanking sequence was cloned from the DNA of Macaca cynomolgus (an Old World monkey), and the 5' flanking region was sequenced. Comparison with human, chimpanzee, mouse, rabbit, and Xenopus orthologous sequences reveals a tandemly repeated sequence called RS4 at the same position (about 500 bp 5' from the transcription start of the adult beta-globin gene) in all six species. We suggest that a tandemly repeated sequence has been maintained by functional constraints since the divergence between amphibians and reptiles. Excluding tandemly repeated sequences as well as about 400 nucleotides upstream from the cap site, the average base substitution frequencies among human, chimpanzee, and macaque intergenic sequences were calculated. They appear to be strongly correlated with the delta T50 values measured between the corresponding nuclear DNAs. They are also similar to base substitution frequencies calculated by Chang and Slightom (1984) at the pseudo-eta-globin locus. Thus, exclusion of sequences involved in specific modes of variation might allow the use of intergenic sequences for the accurate calculation of genetic distances. Using a time scale based on the dating of the Atlantic split, we estimate the base substitution rate of primate noncoding DNA to be 1.0 X 10(-9) substitution/site/year.

A cellular DNA-binding protein that activates eukaryotic transcription and DNA replication

Transcription factor CTF, which is responsible for selective recognition of eukaryotic promoters that contain the sequence CCAAT, was purified to apparent homogeneity by sequence-specific DNA affinity chromatography. Binding sites for CTF in the human Ha-ras and alpha-globin promoters were highly homologous to sequences recognized by nuclear factor I (NF-I), a cellular DNA-binding protein that is required for the initiation of adenovirus DNA replication in vitro. To determine the relationship between CTF and NF-I, we compared the biochemical properties of these two proteins. CTF and NF-I were found to be indistinguishable in polypeptide composition, DNA-binding properties, immunological cross-reactivity, and in vitro stimulation of DNA replication and transcription initiation. We conclude that CTF/NF-I can serve both as a transcription selectivity factor for RNA polymerase II and as an initiation factor for adenovirus DNA replication.

Regulated expression of cloned human fetal A gamma-globin genes introduced into murine erythroleukemia cells

We have analysed the expression of cloned human fetal gamma-globin genes introduced into murine erythroleukemia cells by a protoplast fusion procedure. Both the wild-type a gamma-globin gene and a mutant derivative related to a phenotype of hereditary persistence of fetal hemoglobin were studied. In both cases the level of gamma-globin mRNA increased by a factor of approximately sevenfold when erythroid cell differentiation was induced by treatment with hexamethylenebisacetamide. Thus, the regulation of the expression of the cloned fetal A gamma-globin gene in murine erythroleukemia cells resembled that of cloned adult beta-globin genes.