In vivo DNA-protein interactions at hypersensitive site 3.5 of the human β-globin locus control region

2001 ◽  
Vol 79 (6) ◽  
pp. 747-754 ◽  
Author(s):  
Dong-dong Xu ◽  
De-pei Liu ◽  
Xin-jun Ji ◽  
Xiang Lv ◽  
Chih-chuan Liang

Using ligation-mediated polymerase chain reaction and in vivo footprinting methods to study the status of DNA–protein interactions at hypersensitive site 3.5 (HS3.5) of the locus control region in K562 and HEL cells, we found that there was protein occupancy in vivo at HS3.5 in both cell lines and the status of DNA–protein interaction was different between K562 and HEL. These data provide direct evidence that specific nuclear factor – DNA complexes form in vivo at functionally important sequence motifs of the HS3.5 in erythroid cells. This indicates that HS3.5 may play an important role in the regulation of the β-globin gene cluster. K562 is a human erythroleukemia cell line in which the embryonic ε-globin gene is predominantly expressed, while the HEL cell line expresses predominantly the fetal β-globin genes. Thus, HS3.5 might also be involved in the regulation of developmental stage-specific expression of β-globin genes. Our results are also consistent with the model that each hypersensitive site acts as a functional unit and HS3.5 may facilitate the formation of the HS3 functional unit.Key words: β-globin gene, hypersensitive site, phylogenetic footprint, differential phylogenetic footprint, in vivo footprinting, developmental regulation.

1996 ◽  
Vol 16 (11) ◽  
pp. 6055-6064 ◽  
Author(s):  
Q H Gong ◽  
J C McDowell ◽  
A Dean

Much of our understanding of the process by which enhancers activate transcription has been gained from transient-transfection studies in which the DNA is not assembled with histones and other chromatin proteins as it is in the cell nucleus. To study the activation of a mammalian gene in a natural chromatin context in vivo, we constructed a minichromosome containing the human epsilon-globin gene and portions of the beta-globin locus control region (LCR). The minichromosomes replicate and are maintained at stable copy number in human erythroid cells. Expression of the minichromosomal epsilon-globin gene requires the presence of beta-globin LCR elements in cis, as is the case for the chromosomal gene. We determined the chromatin structure of the epsilon-globin gene in both the active and inactive states. The transcriptionally inactive locus is covered by an array of positioned nucleosomes extending over 1,400 bp. In minichromosomes with a (mu)LCR or DNase I-hypersensitive site 2 (HS2) which actively transcribe the epsilon-globin gene, the nucleosome at the promoter is altered or disrupted while positioning of nucleosomes in the rest of the locus is retained. All or virtually all minichromosomes are simultaneously hypersensitive to DNase I both at the promoter and at HS2. Transcriptional activation and promoter remodeling, as well as formation of the HS2 structure itself, depended on the presence of the NF-E2 binding motif in HS2. The nucleosome at the promoter which is altered upon activation is positioned over the transcriptional elements of the epsilon-globin gene, i.e., the TATA, CCAAT, and CACCC elements, and the GATA-1 site at -165. The simple availability of erythroid transcription factors that recognize these motifs is insufficient to allow expression. As in the chromosomal globin locus, regulation also occurs at the level of chromatin structure. These observations are consistent with the idea that one role of the beta-globin LCR is to maintain promoters free of nucleosomes. The restricted structural change observed upon transcriptional activation may indicate that the LCR need only make a specific contact with the proximal gene promoter to activate transcription.


1992 ◽  
Vol 12 (5) ◽  
pp. 2057-2066 ◽  
Author(s):  
B J Morley ◽  
C A Abbott ◽  
J A Sharpe ◽  
J Lida ◽  
P S Chan-Thomas ◽  
...  

The beta-globin gene complex is regulated by an upstream locus control region (LCR) which is responsible for high-level, position-independent, erythroid-cell-specific expression of the genes in the cluster. Its role in the developmental regulation of beta-like globin gene transcription remains to be established. We have examined the effect of a single LCR element, hypersensitive site 2 (HS2), on the developmental regulation of the human fetal gamma and adult beta genes in transgenic mice. In mice bearing HS2A gamma beta and HS2G gamma A gamma-117 delta beta human globin gene constructs, switching from gamma- to beta-gene expression begins at about day 13.5 of gestation and is largely completed shortly after birth. The larger construct also demonstrates a switch in G gamma- to A gamma-gene expression during the gamma-to-beta switch similar to that observed during normal human development. We conclude that HS2 alone is sufficient for developmental regulation of the human beta-globin genes.


1992 ◽  
Vol 12 (5) ◽  
pp. 2057-2066
Author(s):  
B J Morley ◽  
C A Abbott ◽  
J A Sharpe ◽  
J Lida ◽  
P S Chan-Thomas ◽  
...  

The beta-globin gene complex is regulated by an upstream locus control region (LCR) which is responsible for high-level, position-independent, erythroid-cell-specific expression of the genes in the cluster. Its role in the developmental regulation of beta-like globin gene transcription remains to be established. We have examined the effect of a single LCR element, hypersensitive site 2 (HS2), on the developmental regulation of the human fetal gamma and adult beta genes in transgenic mice. In mice bearing HS2A gamma beta and HS2G gamma A gamma-117 delta beta human globin gene constructs, switching from gamma- to beta-gene expression begins at about day 13.5 of gestation and is largely completed shortly after birth. The larger construct also demonstrates a switch in G gamma- to A gamma-gene expression during the gamma-to-beta switch similar to that observed during normal human development. We conclude that HS2 alone is sufficient for developmental regulation of the human beta-globin genes.


1989 ◽  
Vol 9 (8) ◽  
pp. 3524-3532
Author(s):  
V Dhar ◽  
A I Skoultchi ◽  
C L Schildkraut

To investigate whether a switch in the transcriptional activity of a gene is associated with a change in the timing of replication during the S phase, we examined the replication timing of the beta-globin genes in two different types of somatic cell hybrids. In mouse hepatoma (Hepa 1a) x mouse erythroleukemia (MEL) hybrid cells, the beta-globin gene from the MEL parent is transcriptionally inactivated and is later replicating than in the parental MEL cell line. In human fibroblast (GM3552) x MEL hybrid cells, the human beta-globin gene is transcriptionally activated, and all of the sequences within the human beta-globin domain (200 kilobases) we have examined appear to be earlier replicating than those in the parental fibroblast cell line. The chromatin configuration of the activated human beta-globin domain in the hybrids is relatively more sensitive to nucleases than that in the fibroblasts. Furthermore, major nuclease-hypersensitive sites that were absent in the chromatin flanking the distal 5' region of the human beta-globin gene cluster in the parental fibroblast cell line are present in the transcriptionally activated domain in the hybrid cell line. These results suggest that timing of replication of globin genes has been altered in these hybrid cells and thus is not fixed during the process of differentiation.


Blood ◽  
1993 ◽  
Vol 81 (10) ◽  
pp. 2781-2790
Author(s):  
DE Fleenor ◽  
RE Kaufman

The members of the human beta globin gene family are flanked by strong DNase I hypersensitive sites. The collection of sites 5' to the epsilon globin gene is able to confer high levels of expression of linked globin genes, but a function has not been assigned to the site 3' to the beta globin gene (3'HS1). Our analysis of this DNase I super hypersensitive site shows that the region is composed of multiple DNase I sites. By examination of the DNA sequence, we have determined that the region is very A/T-rich and contains topoisomerase II recognition sequences, as well as several consensus binding motifs for GATA-1 and AP-1/NF-E2. Gel mobility shift assays indicate that the region can interact in vitro with GATA-1 and AP-1/NF-E2, and functional studies show that the region serves as a scaffold attachment region in both erythroid and nonerythroid cell lines. Whereas many of the physical features of 3'HS1 are shared by 5'HS2 (a component of the 5' locus control region), transient expression studies show that 3' HS1 does not share the erythroid-specific enhancer activity exhibited by 5'HS2.


2001 ◽  
Vol 21 (4) ◽  
pp. 1155-1163 ◽  
Author(s):  
Chang-Yun Gui ◽  
Ann Dean

ABSTRACT On stably replicating episomes, transcriptional activation of the ɛ-globin promoter by the β-globin locus control region HS2 enhancer is correlated with an increase in nuclease sensitivity which is limited to the TATA-proximal nucleosome (N1). To elucidate what underlies this increase in nuclease sensitivity and the link between chromatin modification and gene expression, we examined the nucleoprotein composition and histone acetylation status of transcriptionally active and inactive promoters. Micrococcal nuclease digestion of active promoters in nuclei released few nucleosome-like nucleoprotein complexes containing N1 sequences in comparison to results with inactive promoters. We also observed that N1 DNA fragments from active promoters are of a subnucleosomal length. Nevertheless, chromatin immunoprecipitation experiments indicate that histones H3 and H4 are present on N1 sequences from active promoters, with H3 being dramatically hyperacetylated compared with that from inactive promoters and vector sequences. Strikingly, H3 in the adjacent upstream nucleosome (N2) does not appear to be differentially acetylated in active and inactive promoters, indicating that the nucleosome modification of the promoter that accompanies transactivation by HS2 is highly directed and specific. However, global acetylation of histones in vivo by trichostatin A did not activate transcription in the absence of HS2, suggesting that HS2 contributes additional activities necessary for transactivation. N1 sequences from active promoters also contain reduced levels of linker histone H1. The detection of a protected subnucleosomal sized N1 DNA fragment and the recovery of N1 DNA sequences in immunoprecipitations using anti-acetylated H3 and H4 antibodies argue that N1 is present, but in an altered conformation, in the active promoters.


2001 ◽  
Vol 280 (3) ◽  
pp. L390-L399 ◽  
Author(s):  
Jane K. Mellott ◽  
Harry S. Nick ◽  
Michael F. Waters ◽  
Timothy R. Billiar ◽  
David A. Geller ◽  
...  

Transcription of the human inducible nitric oxide synthase ( iNOS) gene is regulated by inflammatory cytokines in a tissue-specific manner. To determine whether differences in cytokine-induced mRNA levels between pulmonary epithelial cells (A549) and hepatic biliary epithelial cells (AKN-1) result from different protein or DNA regulatory mechanisms, we identified cytokine-induced changes in DNase I-hypersensitive (HS) sites in 13 kb of the iNOS 5′-flanking region. Data showed both constitutive and inducible HS sites in an overlapping yet cell type-specific pattern. Using in vivo footprinting and ligation-mediated PCR to detect potential DNA or protein interactions, we examined one promoter region near −5 kb containing both constitutive and cytokine-induced HS sites. In both cell types, three in vivo footprints were present in both control and cytokine-treated cells, and each mapped within a constitutive HS site. The remaining footprint appeared only in response to cytokine treatment and mapped to an inducible HS site. These studies, performed on chromatin in situ, identify a portion of the molecular mechanisms regulating transcription of the human iNOS gene in both lung- and liver-derived epithelial cells.


1999 ◽  
Vol 19 (11) ◽  
pp. 7600-7609 ◽  
Author(s):  
Jennifer C. McDowell ◽  
Ann Dean

ABSTRACT We investigated the requirements for enhancer-promoter communication by using the human β-globin locus control region (LCR) DNase I-hypersensitive site 2 (HS2) enhancer and the ɛ-globin gene in chromatinized minichromosomes in erythroid cells. Activation of globin genes during development is accompanied by localized alterations of chromatin structure, and CACCC binding factors and GATA-1, which interact with both globin promoters and the LCR, are believed to be critical for globin gene transcription activation. We found that an HS2 element mutated in its GATA motif failed to remodel the ɛ-globin promoter or activate transcription yet HS2 nuclease accessibility did not change. Accessibility and transcription were reduced at promoters with mutated GATA-1 or CACCC sites. Strikingly, these mutations also resulted in reduced accessibility at HS2. In the absence of a globin gene, HS2 is similarly resistant to nuclease digestion. In contrast to observations in Saccharomyces cerevisiae, HS2-dependent promoter remodeling was diminished when we mutated the TATA box, crippling transcription. This mutation also reduced HS2 accessibility. The results indicate that the ɛ-globin promoter and HS2 interact both structurally and functionally and that both upstream activators and the basal transcription apparatus contribute to the interaction. Further, at least in this instance, transcription activation and promoter remodeling by a distant enhancer are not separable.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1590-1590
Author(s):  
Donald Lavelle ◽  
Kestis Vaitkus ◽  
Mahipal Singh ◽  
Maria Hankewych ◽  
Joseph DeSimone

Abstract The human Gγ-globin and Aγ-globin genes differ by the presence of a single amino acid, either glycine or alanine, at position 136. The ratio of Gγ/Aγ-globin expression is approximately 7/3 at birth and changes to 2/3 in the adult. The mechanism responsible for this developmental switch is unknown. In the baboon, the duplicated γ-globin genes differ by the presence of a single amino acid at position 75. The Iγ-globin gene contains isoleucine at position 75, while the Vγ-globin gene contains valine at this position. The ratio of expression of the Iγ and Vγ-globin chains also differs in the fetal and adult stages. The Iγ/Vγ ratio is 3/2 in the fetus and 2/3 in the adult. Thus the pattern of expression of the baboon Iγ-globin gene is analogous to the human Gγ-globin gene, and that of the Vγ-globin gene is analogous to the human Aγ-globin gene. During stress erythropoiesis, moderately increased HbF levels are observed (5–10% HbF) and the Iγ/Vγ-globin chains are expressed in the characteristic adult ratio. Decitabine treatment reactivates HbF expression to high levels (50–70% HbF) and Iγ/Vγ ratios of approximately 1:1 have been observed following decitabine treatment. Thus decitabine treatment alters the Iγ/Vγ ratio but does not cause a complete reversion to the fetal pattern of expression. HbF is also reactivated to high levels in cultured baboon BFUe. In this investigation the pattern of expression of the Iγ- and Vγ-globin genes in cultured baboon CD34+ bone marrow (BM) cells was analyzed to determine whether reactivation of HbF in culture was associated with a change in the pattern of expression of the Iγ-and Vγ-globin genes. CD34+ cells were enriched from baboon BM using the 12.8 monoclonal antibody in combination with immunomagnetic microbead columns (Miltenyi) and cultured in Iscove’s media supplemented with 30% fetal bovine serum, stem cell factor (SCF; 200ng/ml), erythropoietin (EPO; 2U/ml), and dexamethasone (Dex; 1μM). The pattern of globin chain expression in d12 cultures, cord blood (CB) of a 58d fetus, and peripheral blood (PB) of adult baboons following phlebotomy and decitabine treatment was compared by HPLC analysis of hemolysates. The baboon 58d CB contained >90% HbF and the ratio of Iγ/Vγ was 1.85. In the adult (phlebotomized) PB the level of HbF was 8.1% and the Iγ/Vγ ratio was 0.75 thus confirming that the ratio of the baboon Iγ and Vγ-globin chains differs in the fetal and adult stages of development in a manner similar to that of the human Gγ and Aγ-globin chains. Following decitabine treatment (PA 7002) an HbF level of 55% was attained with an Iγ/Vγ ratio of 1.1. Hemolysates prepared from d12 cultures of CD34+ baboon (PA 7002) BM cells grown in the presence of SCF, EPO, and Dex contained 57.6% HbF, nearly the same level observed following decitabine treatment in vivo. The Iγ/Vγ ratio was 1.94, markedly different from that observed in this same baboon following decitabine in vivo and, moreover, nearly identical to the fetal ratio. Thus HbF reactivation in cultured adult baboon CD34+ BM cells was associated with a change in the ratio of expression of the two baboon γ-globin genes to that characteristic of the fetal stage. Recapitulation of the fetal pattern of γ-globin chain expression in cultured baboon CD34+ progenitors demonstrates yet another advantage of the baboon model for investigations of hemoglobin switching.


Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 3830-3830
Author(s):  
Alexander Felice ◽  
Joseph Borg ◽  
Wilma Cassar ◽  
Ruth Galdies ◽  
Monica Pizzuto ◽  
...  

Abstract Although the precise biochemical mechanisms of globin gene switching remain elusive, considerable insight is gained by in vivo expression profiling through quantification of the hemoglobin / globin phenotype of informative heterozygosities and homozygosities / compound heterozygosities in the context of specific regulatory DNA sequence diversity such as the XMN-I or the [(AT)xTy] sequence polymorphisms. The quantification of normal and abnormal globins of Hb F Malta-I (or a2b2, 117(G19)His>Arg) heterozygotes which are in tight linkage disequilibrium with Hb Valletta (or a2b2 287(f3)Thr>Pro) i.e. Gyo, GyFMalta-I, AyI, bV and bA together with extensive haplotyping of homozygotes and heterozygotes including the XMN-I dimorphism in the Gy promoter and the (AT)xTy polymorphism (BP1 binding site) 5′ to the b globin genes had suggested that the XMN-I dimorphism was largely inactive in the normal newborn. In contrast the Hb F levels and the proportion of Gy globin in anemic adult beta-thalassemia homozygotes and compound heterozygotes differed significantly, depending on the XMN-I genotype (TT, TC or CC) Here, we document the occurrence of seven newborn who were heterozygous at three globin loci permitting quantification by reverse phase liquid chromatography of the six globin products; Gyo, GyFMalta-I, AyI, AyT, bV and bA in the context of genotypic variation at the XMN-I and (AT)xTy sequences. The data were compared with those of newborn HbF-Malta-I-Hb-Valletta heterozygotes and anemic adult beta thalassemia homozygotes / compound heterozygotes. The globin quantification together with haplotype data were analysed using the general linear model (two-way ANOVA) by SPSS version 12. The data excluded significant effect of the XMN-I dimorphism alone on relative y/b globin gene expression in the newborn. On the other hand, the (AT)xTy polymorphism with BP1 binding sites of 21 [(AT)7T7], 23 [(AT)9T5], or 25 [(AT)11T3], nucleotides in trans over-ride XMN-I. In contrast, it is the XMN-I dimorphism that over-rides the (AT)xTy diversity in the anemic adult beta thalassemia homozygotes or compound heterozygotes. The GyFMalta-I/Gyo ratio of the newborn heterozygotes with Hb F Malta-I and the AyT/AyI ratio of the newborn heterozygotes with HbF-Malta-I and HbF-Sardinia suggested that the developmental regulation of the XMN-I site may be subject to cis/trans interplay with the (AT)xTy sequences.


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