Histone hyperacetylation within the β-globin locus is context-dependent and precedes high-level gene expression

Abstract

Active gene promoters are associated with covalent histone modifications, such as hyperacetylation, which can modulate chromatin structure and stabilize binding of transcription factors that recognize these modifications. At the ␤-globin locus and several other loci, however, histone hyperacetylation extends beyond the promoter, over tens of kilobases; we term such patterns of histone modifications "hyperacetylated domains." Little is known of either the mechanism by which these domains form or their function. Here, we show that domain formation within the murine ␤-globin locus occurs before either high-level gene expression or erythroid commitment. Analysis of ␤-globin alleles harboring deletions of promoters or the locus control region demonstrates that these sequences are not required for domain formation, suggesting the existence of additional regulatory sequences within the locus. Deletion of embryonic globin gene promoters, however, resulted in the formation of a hyperacetylated domain over these genes in definitive erythroid cells, where they are otherwise inactive. Finally, sequences within ␤-globin domains exhibit hyperacetylation in a context-dependent manner, and domains are maintained when transcriptional elongation is inhibited. These data narrow the range of possible mechanisms by which hyperacetylated domains form. (Blood. 2009;114: 3479-3488) IntroductionA crucial feature of gene activation is the interaction between transcription factors and chromatin. All eukaryotic genomic DNA, with limited exceptions, is packaged with core histones to form chromatin. The fundamental subunit of chromatin is the nucleosome, consisting of approximately 147 bp of DNA wrapped in approximately 1.75 turns about an octamer of core histones; a variable length of linker DNA extends between nucleosomes and can in turn be partially sequestered by interactions with core histone amino-terminal "tail" regions and/or linker histones, such as histone H1. The resulting structure, when observed on low-salt spreads by electron microscopy, has been termed "beads on a string" based on its appearance. 1,2 At physiologically relevant salt concentrations, however, this structure spontaneously condenses, first to a helical array of nucleosomes termed the 30-nm fiber, then through additional levels of higher-order structure, which are not well understood. 3 Nevertheless, this packaging renders the eukaryotic DNA relatively inaccessible to transcription factors. [4][5][6] The transcriptional machinery possesses mechanisms for modulating chromatin structure. One of these is covalent modification of core histones, including acetylation, methylation, phosphorylation, ubiquitylation, SUMOylation, and ADP ribosylation, in short, the gamut of modifications known to occur on cellular proteins. Different modifications can lead to different functional consequences. Histone acetylation is associated with transcriptional activation; indeed, core histones proximal to active gene promoters are universally hyperacetylated. 7,8 Histone methylation can...

Transcription Factors KLF1 and KLF2 Positively Regulate Embryonic and Fetal β-Globin Genes through Direct Promoter Binding

“…In K562, a human cell line that expresses the fetal ␥-but not the adult ␤-globin gene, H3Ac, H3K4me2, and H3K4me3 are enriched specifically at the ␥-globin gene (52). H3K4me3 is enriched only in the actively transcribed fetal and adult ␤-globin genes in human and mouse tissue culture cell models, respectively (52,53). Our results in native embryonic erythroid cells differ in that H3K4me3 is somewhat enriched at the mouse adult ␤ maj -globin gene at E10.5 prior to its activation.…”

Crosstalk between histone modifications maintains the developmental pattern of gene expression on a tissue-specific locus

“…It has been shown in vitro that WDR5 interacts with MLL1 via its histone H3-binding pocket and that the WDR5-MLL1 interaction is preferentially competed by mono-or dimethylated H3K4. 86 We speculate that a similar mechanism might occur at the LCR, where the H3K4me2 mark, present at this location, 27 could lead to the displacement of MLL2 from its interacting partner WDR5, thereby initiating spreading of the MLL2 subunit. It remains to be established whether WDR5 remains at the LCR upon erythroid differentiation or travels with MLL2 across the β-globin locus.…”

“…MLL2 contains a CxxC domain, which mediates binding to non-methylated CpG-rich DNA, 89,90 however the region between the LCR and β maj promoter is quite heavily DNA methylated in adult cells. 46 While it has been proposed that MLL2 could bind to methylated H3K4 through its PHD domains, 91 H3K4me2, 27 and H3K4me3, 21 marks are not continuous across the β-globin locus in adult cells. Therefore, it is unlikely that MLL2 uses these domains for self-propagation.…”

“…There are also "medium-sized" 10 kb domains comprised of H3K4me2 and H3/H4ac that encompass the active β-globin genes. 27 In addition, there is a well-characterized distal enhancer, called HS2, 28 the H3K4me1 enhancer signature of which is established early on in multipotent hematopoietic progenitors.…”

An embryonic stage–specific enhancer within the murine β-globin locus mediates domain-wide histone hyperacetylation

“…9,10 Previously, we determined that the formation of this embryonic-specific hyperacetylated domain occurs independently of the LCR and the gene promoters, suggesting that the cis-acting DNA sequence determinants of domain formation reside elsewhere. 11 In this study we report the discovery of a novel, evolutionarily conserved enhancer element located within the embryonic ␤-globin The online version of this article includes a data supplement.…”