Tissue-specific histone modification and transcription factor binding in α globin gene expression

Abstract

To address the mechanism by which the human globin genes are activated during erythropoiesis, we have used a tiled microarray to analyze the pattern of transcription factor binding and associated histone modifications across the telomeric region of human chromosome 16 in primary erythroid and nonerythroid cells. This 220-kb region includes the ␣ globin genes and 9 widely expressed genes flanking the ␣ globin locus. This unbiased, comprehensive analysis of transcription factor binding and histone modifications (acetylation and methylation) described here not only identified all known cis-acting regulatory elements in the human ␣ globin cluster but also demonstrated that there are no additional erythroid-specific regulatory elements in the 220-kb region tested. In addition, the pattern of histone modification distinguished promoter elements from potential enhancer elements across this region. Finally, comparison of the human and mouse orthologous regions in a unique mouse model, with both regions coexpressed in the same animal, showed significant differences that may explain how these 2 clusters are regulated differently in vivo. IntroductionGlobin gene expression plays a central role in normal erythropoiesis, and abnormalities of globin synthesis underlie the clinically important thalassaemia syndromes. A long-term goal in the treatment of thalassaemia has been to identify ways in which to manipulate gene expression to redress the imbalance in ␣ and ␤ globin chain synthesis. Progress in this area would be enhanced by understanding in detail how these genes are normally regulated. To address this, it is important to identify all the key cis-acting sequences controlling ␣ and ␤ globin expression, the transcription factors that bind them, and the accompanying modifications of chromatin at different stages of differentiation.To identify and characterize the cis-acting elements controlling ␣ globin expression we have previously used a variety of approaches, including comparative genomics, 1,2 a wide range of chromatin analyses, 3,4 transgenic experiments, 5,6 and the analysis of expression in interspecific hybrids. [7][8][9] Upstream of the 4 ␣-like globin promoters (, ␣D, ␣2, and ␣1) lie 4 multispecies conserved sequences (MCSs) associated with erythroid-specific DNase1 hypersensitive sites (HS), referred to, in human, as HS-48, HS-40, HS-33, and HS-10 ( Figure 1A). The globin genes, the upstream MCSs, and several widely expressed flanking genes all lie within a region of conserved synteny spanning 130 kb of the telomeric region of human chromosome 16 (16p13.3) ( Figure 1A). Functional analyses suggest that HS-40 is the most important of the MCSs. 9 Recently, to develop a relevant experimental system for studying human ␣ globin expression and to evaluate the roles of individual elements, we established a humanized mouse model in which the 117-kb region containing the human ␣-like globin genes and all of their known regulatory elements (the ␣ globin regulatory domain) completely replaces the corresponding, orthologou...

Codanin-1 mutations in congenital dyserythropoietic anemia type 1 affect HP1α localization in erythroblasts

“…ChIP-chip analysis was performed as previously described by De Gobbi et al 17 Sequences were aligned onto the hg17 assembly using the UCSC Genome Browser (www.genome.ucsc.edu). 18 MOLECULAR PATHOGENESIS OF CDA TYPE 1 6929 BLOOD, 23 JUNE 2011 ⅐ VOLUME 117, NUMBER 25…”

Controlling -globin: a review of -globin expression and its impact on -thalassemia

“…24 In primary human erythroblasts, GATA-1, SCL and the entire pentameric erythroid complex were found bound to all four HS sites. 13 In addition to this, both subunits of the NF-E2 transcription factor were also enriched at HS-40 and to a lesser extent at HS-48. 13 Maximal binding of all transcription factors were detected in basophilic and polychromatophilic erythroblasts, coinciding with maximal levels of histone H3 and H4 acetylation.…”

“…13 In addition to this, both subunits of the NF-E2 transcription factor were also enriched at HS-40 and to a lesser extent at HS-48. 13 Maximal binding of all transcription factors were detected in basophilic and polychromatophilic erythroblasts, coinciding with maximal levels of histone H3 and H4 acetylation. 13 At the onset of transcription, the promoter then becomes bound by SP/X-Kruppellike transcription factors (Sp/X-KLF).…”

“…1 The study confirmed that the four known DnaseI HS sites bind erythroid-specific transcription factors and found no additional erythroid-specific regulatory elements in this region. Of these four sites (HS-10, HS-33, HS-40 and HS-48), 13,14 HS-40 forms the major regulatory element [15][16][17] and is the only element capable of directing high level expression of the α-globin gene. 18 Deletion of HS-40 from the human α-globin cluster leads to severe reductions in α-globin expression to <5% of normal.…”

“…22 Analysis of the mouse α-globin locus revealed the presence of an additional HS-12 element capable of binding the pentameric erythroid complex essential for activating α-globin transcription while the human homologous region lacks these critical binding sites. 13 In addition, the mouse α-globin promoter also binds GATA1, a crucial erythroid regulator, while the human promoter which lacks the consensus binding site, does not ( Figure 1B). 23 This is the final step in the activation of α-globin transcription which begins with a range of chromatin modifications.…”