Spatial organization of the chicken beta-globin gene domain in erythroid cells of embryonic and adult lineages

Abstract

BackgroundThe β-globin gene domains of vertebrate animals constitute popular models for studying the regulation of eukaryotic gene transcription. It has previously been shown that in the mouse the developmental switching of globin gene expression correlates with the reconfiguration of an active chromatin hub (ACH), a complex of promoters of transcribed genes with distant regulatory elements. Although it is likely that observations made in the mouse β-globin gene domain are also relevant for this locus in other species, the validity of this supposition still lacks direct experimental evidence. Here, we have studied the spatial organization of the chicken β-globin gene domain. This domain is of particular interest because it represents the perfect example of the so-called ‘strong’ tissue-specific gene domain flanked by insulators, which delimit the area of preferential sensitivity to DNase I in erythroid cells.ResultsUsing chromosome conformation capture (3C), we have compared the spatial configuration of the β-globin gene domain in chicken red blood cells (RBCs) expressing embryonic (3-day-old RBCs) and adult (9-day-old RBCs) β-globin genes. In contrast to observations made in the mouse model, we found that in the chicken, the early embryonic β-globin gene, Ε, did not interact with the locus control region in RBCs of embryonic lineage (3-day RBCs), where this gene is actively transcribed. In contrast to the mouse model, a strong interaction of the promoter of another embryonic β-globin gene, ρ, with the promoter of the adult β-globin gene, βA, was observed in RBCs from both 3-day and 9-day chicken embryos. Finally, we have demonstrated that insulators flanking the chicken β-globin gene domain from the upstream and from the downstream interact with each other, which places the area characterized by lineage-specific sensitivity to DNase I in a separate chromatin loop.ConclusionsTaken together, our results strongly support the ACH model but show that within a domain of tissue-specific genes, the active status of a promoter does not necessarily correlate with the recruitment of this promoter to the ACH.

3D genomics imposes evolution of the domain model of eukaryotic genome organization

“…In the both abovementioned cases, the alternate spatial configurations of the genomic domains were attributed to different cell populations. However, various genomic domains, including that of chicken alpha and beta-globin genes, can adopt various spatial configurations in the same cellular populations (Philonenko et al 2009;Ulianov et al 2012). Evidently, this allows alternate activation of different genes by the same enhancer element.…”

Compartmentalization of the cell nucleus and spatial organization of the genome

“…Substantial progress in understanding the spa tial organization of the genome was made with the development of chromosome conformation capture (3C) technology [22], which is based on in situ ligation of closely spaced DNA fragments [23], and 3C based genome wide methods, such as high throughput 3C (HiC) [24,25]. Apart from reporting numerous exam ples of spatial interactions between distant regulatory elements, such as promoters, enhancers, and insula tors [26][27][28][29][30], HiC made it possible to advance a glob ular model for genome organization [17]. The model suggests that the genome is divided into topologically isolated globular domains, which are termed the topo logically associated domains (TADs) or just topologi …”

Joint locus of a/b-globin genes in Danio rerio is segregated into structural subdomains active at different stages of development

“…In nonerythroid cells, the domain of b globin genes is rather DNase I resistant and replicates in late S phase [2,9,10]. The domain of b globin genes is flanked by a cluster of olfactory receptor genes [11] and is sepa rated from them by insulators, which organize the domain in a separate chromatin loop [12]. The domain of b globin genes is regulated by the locus control region (LCR) that ensures erythroid specific expression and determines chromatin status and repli cation timing [9,13,14].…”