Analysis of Enhancer Function of the HS-40 Core Sequence of the Human Alpha-Globin Cluster

HS-40 is the major regulatory element of the human α-globin locus, located 40 kb upstream of the ζ-globin gene. To test for potential interactions between HS-40 and the β- or the γ-globin gene promoters in stable transfection assays, the HS-40 core sequence was cloned upstream of either the β promoter or the γ promoter driving the neomycin phosphotransferase gene and enhancer activity was measured using a colony assay. In K562 or in MEL cells, enhancer activity of HS-40 was higher than that of the individual core sequences of the DNase I hypersensitive sites (HS) of the β-globin locus control region (LCR), and ∼60% of the enhancer activity of a 2.5 kb μLCR, which contains the core elements of DNase I hypersensitive sites 1–4. In contrast to the synergistic interaction between the DNase I hypersensitive sites of β locus LCR, combination of HS-40 with these DNase I hypersensitive sites failed to display cooperativity in K562 cells and inhibited enhancer function in MEL cells. Inhibition of enhancer function was also observed when two copies of the HS-40 were arranged tandemly. We conclude that the core element of HS-40 (i) is a powerful enhancer of γ- and β-globin gene expression, (ii) in contrast to other classical enhancers, acts best as a single copy, (iii) does not cooperate with the regulatory elements of the β-globin locus control region

CpG Hypomethylation in a Large Domain Encompassing the Embryonic β-Like Globin Genes in Primitive Erythrocytes▿ †

There is little evidence addressing the role of CpG methylation in transcriptional control of genes that do not contain CpG islands. This is reflected in the ongoing debate about whether CpG methylation merely suppresses retroelements or if it also plays a role in developmental and tissue-specific gene regulation. The genes of the β-globin locus are an important model of mammalian developmental gene regulation and do not contain CpG islands. We have analyzed the methylation status of regions in the murine β-like globin locus in uncultured primitive and definitive erythroblasts and other cultured primary and transformed cell types. A large (∼20-kb) domain is hypomethylated only in primitive erythroid cells; it extends from the region just past the locus control region to before β-major and encompasses the embryonic genes Ey, βh1, and βh0. Even retrotransposons in this region are hypomethylated in primitive erythroid cells. The existence of this large developmentally regulated domain of hypomethylation supports a mechanistic role for DNA methylation in developmental regulation of globin genes

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Developmentally regulated extended domains of DNA hypomethylation encompass highly transcribed genes of the human β-globin locus

Objective<p></p> DNA methylation has long been implicated in developmental β-globin gene regulation. However, the mechanism underlying this regulation is unclear, especially because these genes do not contain CpG islands. This has led us to propose and test the hypothesis that, just as for histone modifications, developmentally specific changes in human β-like globin gene expression are associated with long-range changes in DNA methylation.<p></p> Materials and Methods<p></p> Bisulfite sequencing was used to determine the methylation state of individual CpG dinucleotides across the β-globin locus in uncultured primary human erythroblasts from fetal liver and bone marrow, and in primitive-like erythroid cells derived from human embryonic stem cells.<p></p> Results<p></p> β-globin locus CpGs are generally highly methylated, but domains of DNA hypomethylation spanning thousands of base pairs are established around the most highly expressed genes during each developmental stage. These large domains of DNA hypomethylation are found within domains of histone modifications associated with gene expression. We also find hypomethylation of a small proportion of γ-globin promoters in adult erythroid cells, suggesting a mechanism by which adult erythroid cells produce fetal hemoglobin.<p></p> Conclusion<p></p> This is one of the first reports to show that changes in DNA methylation patterns across large domains around non-CpG island genes correspond with changes in developmentally regulated histone modifications and gene expression. These data support a new model in which extended domains of DNA hypomethylation and active histone marks are coordinately established to achieve developmentally specific gene expression of non-CpG island genes