scholarly journals Flanking HS-62.5 and 3′ HS1, and regions upstream of the LCR, are not required for β-globin transcription

Blood ◽  
2006 ◽  
Vol 108 (4) ◽  
pp. 1395-1401 ◽  
Author(s):  
M. A. Bender ◽  
Rachel Byron ◽  
Tobias Ragoczy ◽  
Agnes Telling ◽  
Michael Bulger ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Globin Gene ◽  
Gene Activation ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Open Domain ◽  
Binding Factor ◽  
Necessary And Sufficient ◽  
Globin Gene Regulation ◽  
Endogenous Locus

Abstract The locus control region (LCR) was thought to be necessary and sufficient for establishing and maintaining an open β-globin locus chromatin domain in the repressive environment of the developing erythrocyte. However, deletion of the LCR from the endogenous locus had no significant effect on chromatin structure and did not silence transcription. Thus, the cis-regulatory elements that confer the open domain remain unidentified. The conserved DNaseI hypersensitivity sites (HSs) HS-62.5 and 3′HS1 that flank the locus, and the region upstream of the LCR have been implicated in globin gene regulation. The flanking HSs bind CCCTC binding factor (CTCF) and are thought to interact with the LCR to form a “chromatin hub” involved in β-globin gene activation. Hispanic thalassemia, a deletion of the LCR and 27 kb upstream, leads to heterochromatinization and silencing of the locus. Thus, the region upstream of the LCR deleted in Hispanic thalassemia (upstream Hispanic region [UHR]) may be required for expression. To determine the importance of the UHR and flanking HSs for β-globin expression, we generated and analyzed mice with targeted deletions of these elements. We demonstrate deletion of these regions alone, and in combination, do not affect transcription, bringing into question current models for the regulation of the β-globin locus.

scholarly journals Role of ZBP-89 in human globin gene regulation and erythroid differentiation

Blood ◽  
2011 ◽  
Vol 118 (13) ◽  
pp. 3684-3693 ◽  
Author(s):  
Andrew J. Woo ◽  
Jonghwan Kim ◽  
Jian Xu ◽  
Hui Huang ◽  
Alan B. Cantor
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Globin Gene ◽  
Erythroid Differentiation ◽  
Regulatory Elements ◽  
Specific Gene ◽  
Specific Gene Expression ◽  
Erythroid Maturation ◽  
Globin Gene Regulation

Abstract The molecular mechanisms underlying erythroid-specific gene regulation remain incompletely understood. Closely spaced binding sites for GATA, NF-E2/maf, and CACCC interacting transcription factors play functionally important roles in globin and other erythroid-specific gene expression. We and others recently identified the CACCC-binding transcription factor ZBP-89 as a novel GATA-1 and NF-E2/mafK interacting partner. Here, we examined the role of ZBP-89 in human globin gene regulation and erythroid maturation using a primary CD34+ cell ex vivo differentiation system. We show that ZBP-89 protein levels rise dramatically during human erythroid differentiation and that ZBP-89 occupies key cis-regulatory elements within the globin and other erythroid gene loci. ZBP-89 binding correlates strongly with RNA Pol II occupancy, active histone marks, and high-level gene expression. ZBP-89 physically associates with the histone acetyltransferases p300 and Gcn5/Trrap, and occupies common sites with Gcn5 within the human globin loci. Lentiviral short hairpin RNAs knockdown of ZBP-89 results in reduced Gcn5 occupancy, decreased acetylated histone 3 levels, lower globin and erythroid-specific gene expression, and impaired erythroid maturation. Addition of the histone deacetylase inhibitor valproic acid partially reverses the reduced globin gene expression. These findings reveal an activating role for ZBP-89 in human globin gene regulation and erythroid differentiation.

Fishing for evolutionary clues to globin gene regulation

Blood ◽  
2003 ◽  
Vol 101 (7) ◽  
pp. 2451-2451
Author(s):  
Ross C. Hardison
Keyword(s):  
Gene Regulation ◽  
Globin Gene ◽  
Globin Gene Regulation

Understanding α-Globin Gene Regulation: Aiming to Improve the Management of Thalassemia

2005 ◽  
Vol 1054 (1) ◽  
pp. 92-102 ◽  
Author(s):  
D.R. HIGGS ◽  
D. GARRICK ◽  
E. ANGUITA ◽  
M. GOBBI ◽  
J. HUGHES ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Globin Gene ◽  
Globin Gene Regulation

Role of the Krüppel-Type Zinc Finger Transcription Factor ZBP-89 In Human Globin Gene Regulation and Erythroid Development

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2067-2067
Author(s):  
Andrew J. Woo ◽  
Jonghwan Kim ◽  
Jian Xu ◽  
Hui Huang ◽  
Alan Cantor
Keyword(s):  
Globin Gene ◽  
Regulatory Elements ◽  
Beta Globin ◽  
Beta Globin Gene ◽  
Histone 3 ◽  
Cd34 Cells ◽  
Alpha Globin ◽  
Globin Gene Regulation ◽  
Erythroid Development

Abstract Abstract 2067 The molecular mechanisms underlying developmental globin gene regulation remain incompletely understood. Prior studies have identified key cis-regulatory elements within the beta globin locus that contain core regions of closely spaced functional binding sites for GATA, NF-E2p45/maf and GT/GC box binding transcription factors. We recently identified the GT/GC-box binding transcription factor ZBP-89 as a novel GATA-1 interacting partner, and showed that it is involved in erythroid development in mice (Woo et al. 2008. Mol. Cell Bio. 28:2675-2689). Brand et al. independently isolated ZBP-89 in NF-E2p45/mafk complexes from induced mouse erythroid leukemia (MEL) cells (Brand et al. 2004. Nat. Struct. Mol Biol. 11:73-80). In the current study, we show that ZBP-89 protein levels increase during in vitro erythroid differentiation of human bone marrow derived CD34+ cells. This correlates with the onset of alpha and beta globin gene transcription. ChIP-chip studies using ENCODE v2.0 arrays demonstrate that ZBP-89 occupies key cis-regulatory elements within both the beta globin (locus control regions HS3, HS2; delta and beta proximal promoters; and an intergenic region between gamma1 and delta globin) and alpha globin (HS-48, HS-40, HS-10 and alpha globin proximal promoters) loci in primary human erythroid precursors. Comparative analysis across the entire ENCODE array reveals a strong positive correlation between ZBP-89 occupancy, RNA polymerase II occupancy, and the activating histone marks acetylated histone 3 (AcH3) and trimethylated histone 3 lysine 4 (H3K4me3); and a negative correlation with the repressive mark trimethylated histone 3 lysine 27 (H3K27me3). Motif analysis under the ZBP-89 occupancy peaks indicates a preference for GGGG(G/A)NGGGG in vivo binding sites. Lentiviral shRNA mediated knock down of ZBP-89 in the in vitro differentiated CD34+ cells results in 30–50% reduction of alpha-, gamma-, and beta-globin gene expression, as well as modestly decreased expression of a number of additional erythroid-specific genes. Co-immunoprecipitation experiments demonstrate physical association between ZBP-89 and the GCN5/Trapp histone acetyltransferase complex. Based on these findings, we propose that ZBP-89 participates with GATA-1 and NF-E2 in the final epigenetic changes required for high-level expression of globin and other erythroid genes in terminally differentiating human erythroid cells. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Understanding α-globin gene regulation and implications for the treatment of β-thalassemia

2015 ◽  
Vol 1368 (1) ◽  
pp. 16-24 ◽  
Author(s):  
Sachith Mettananda ◽  
Richard J. Gibbons ◽  
Douglas R. Higgs
Keyword(s):  
Gene Regulation ◽  
Globin Gene ◽  
Globin Gene Regulation

scholarly journals CTCF mediates insulator function at the CFTR locus

2007 ◽  
Vol 408 (2) ◽  
pp. 267-275 ◽  
Author(s):  
Neil P. Blackledge ◽  
Emma J. Carter ◽  
Joanne R. Evans ◽  
Victoria Lawson ◽  
Rebecca K. Rowntree ◽  
...  
Keyword(s):  
Regulatory Elements ◽  
Cftr Gene ◽  
Chromatin Domain ◽  
Transmembrane Conductance Regulator ◽  
Binding Factor ◽  
Hypersensitive Sites ◽  
Insulator Elements ◽  
Translational Start

Regulatory elements that lie outside the basal promoter of a gene may be revealed by local changes in chromatin structure and histone modifications. The promoter of the CFTR (cystic fibrosis transmembrane conductance regulator) gene is not responsible for its complex pattern of expression. To identify important regulatory elements for CFTR we have previously mapped DHS (DNase I-hypersensitive sites) across 400 kb spanning the locus. Of particular interest were two DHS that flank the CFTR gene, upstream at −20.9 kb with respect to the translational start site, and downstream at +15.6 kb. In the present study we show that these two DHS possess enhancer-blocking activity and bind proteins that are characteristic of known insulator elements. The DHS core at −20.9 kb binds CTCF (CCCTC-binding factor) both in vitro and in vivo; however, the +15.6 kb core appears to bind other factors. Histone-modification analysis across the CFTR locus highlights structural differences between the −20.9 kb and +15.6 kb DHS, further suggesting that these two insulator elements may operate by distinct mechanisms. We propose that these two DHS mark the boundaries of the CFTR gene functional unit and establish a chromatin domain within which the complex profile of CFTR expression is maintained.

Hemoglobins from bacteria to man: evolution of different patterns of gene expression.

1998 ◽  
Vol 201 (8) ◽  
pp. 1099-1117 ◽  
Author(s):  
R Hardison
Keyword(s):  
Dna Sequences ◽  
Cpg Island ◽  
Globin Gene ◽  
Gene Clusters ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Regulatory Sequences ◽  
Beta Globin ◽  
Ancestral Gene ◽  
Beta Globin Gene

The discovery of hemoglobins in virtually all kingdoms of organisms has shown (1) that the ancestral gene for hemoglobin is ancient, and (2) that hemoglobins can serve additional functions besides transport of oxygen between tissues, ranging from intracellular oxygen transport to catalysis of redox reactions. These different functions of the hemoglobins illustrate the acquisition of new roles by a pre-existing structural gene, which requires changes not only in the coding regions but also in the regulatory elements of the genes. The evolution of different regulated functions within an ancient gene family allows an examination of the types of biosequence data that are informative for various types of issues. Alignment of amino acid sequences is informative for the phylogenetic relationships among the hemoglobins in bacteria, fungi, protists, plants and animals. Although many of these diverse hemoglobins are induced by low oxygen concentrations, to date none of the molecular mechanisms for their hypoxic induction shows common regulatory proteins; hence, a search for matches in non-coding DNA sequences would not be expected to be fruitful. Indeed, alignments of non-coding DNA sequences do not reveal significant matches even between mammalian alpha- and beta-globin gene clusters, which diverged approximately 450 million years ago and are still expressed in a coordinated and balanced manner. They are in very different genomic contexts that show pronounced differences in regulatory mechanisms. The alpha-globin gene is in constitutively active chromatin and is encompassed by a CpG island, which is a dominant determinant of its regulation, whereas the beta-globin gene is in A+T-rich genomic DNA. Non-coding sequence matches are not seen between avian and mammalian beta-globin gene clusters, which diverged approximately 250 million years ago, despite the fact that regulation of both gene clusters requires tissue-specific activation of a chromatin domain regulated by a locus control region. The cis-regulatory sequences needed for domain opening and enhancement do show common binding sites for transcription factors. In contrast, alignments of non-coding sequences from species representing multiple eutherian mammalian orders, some of which diverged as long as 135 million years ago, are reliable predictors of novel cis-regulatory elements, both proximal and distal to the genes. Examples include a potential target for the hematopoietic transcription factor TAL1.

Altered Expression of Transcription and Chromatin Remodeling Factors in Deletional HPFH.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2705-2705
Author(s):  
Fernando F. Costa ◽  
Tiago G. de Andrade ◽  
Anderson F. Cunha ◽  
André Fattori ◽  
Sara T.O. Saad
Keyword(s):  
Gene Regulation ◽  
Chromatin Remodeling ◽  
Globin Gene ◽  
Fetal Hemoglobin ◽  
Subtractive Hybridization ◽  
Cdna Libraries ◽  
Altered Expression ◽  
Hereditary Disorders ◽  
Altered Gene ◽  
Globin Gene Regulation

Abstract Hereditary Persistence of Fetal Hemoglobin is a rare, heterogeneous and benign group of hereditary disorders with an abnormal switch from fetal to adult hemoglobin, resulting in high levels of Hb F in the adult stage. A total of six deletions related to HPFH have been described, associated with increased levels of both gamma chains. Three main hypotheses have been proposed to explain the relationship between these deletions and the non-suppression of gamma genes: the removal of competitive regions that interact with the LCR; the juxtaposition of enhancer elements; and the removal of silencers. Despite evidence to support these hypotheses, however, they are not conclusive. Recently, Xiang and cols (Abstract #1215, 2004 ASH Meeting; Blood, Volume 104, issue 11, November 16, 2004) developed a YAC construct with the whole beta-globin locus containing a deletion of approximately 83.5 Kb responsible for the HPFH-2. Unexpectedly, the gamma gene was completely silenced in the adult transgenic mice. These data suggest that other mechanisms could be involved in the increased levels of HbF in these conditions. The authors speculate that other regions upstream from the cluster may harbor this activity. We, herein, investigate the possible involvement of transcription factors, using the subtractive hybridization method to identify differentially expressed transcripts in reticulocytes from a normal subject and a HPFH-2 subject. We have identified 56 and 106 unique genes in the normal and HPFH-2 cDNA libraries, respectively. Some of these are transcription (zinc fingers and homeobox proteins) and chromatin remodeling (NAP and SWI like proteins) factors that could participate in globin gene regulation. These genes are located in cis or in trans to the deletion and their altered gene expression has been confirmed by Quantitative Real-time PCR in other two HPFH subjects. The data may present new clues about globin gene regulation, the increased expression of gamma gene in deletional HPFH and the dynamic organization of genes and chromosomes in cells.

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