Evolutionary Constraints in the β-Globin Cluster: The Signature of Purifying Selection at the δ-Globin (HBD) Locus and Its Role in Developmental Gene Regulation

Abstract

Human hemoglobins, the oxygen carriers in the blood, are composed by two α-like and two β-like globin monomers. The β-globin gene cluster located at 11p15.5 comprises one pseudogene and five genes whose expression undergoes two critical switches: the embryonic-to-fetal and fetal-to-adult transition. HBD encodes the δ-globin chain of the minor adult hemoglobin (HbA2), which is assumed to be physiologically irrelevant. Paradoxically, reduced diversity levels have been reported for this gene. In this study, we sought a detailed portrait of the genetic variation within the β-globin cluster in a large human population panel from different geographic backgrounds. We resequenced the coding and noncoding regions of the two adult β-globin genes (HBD and HBB) in European and African populations, and analyzed the data from the β-globin cluster (HBE, HBG2, HBG1, HBBP1, HBD, and HBB) in 1,092 individuals representing 14 populations sequenced as part of the 1000 Genomes Project. Additionally, we assessed the diversity levels in nonhuman primates using chimpanzee sequence data provided by the PanMap Project. Comprehensive analyses, based on classic neutrality tests, empirical and haplotype-based studies, revealed that HBD and its neighbor pseudogene HBBP1 have mainly evolved under purifying selection, suggesting that their roles are essential and nonredundant. Moreover, in the light of recent studies on the chromatin conformation of the β-globin cluster, we present evidence sustaining that the strong functional constraints underlying the decreased contemporary diversity at these two regions were not driven by protein function but instead are likely due to a regulatory role in ontogenic switches of gene expression.

Distinctive Patterns of Evolution of the δ-Globin Gene (HBD) in Primates

“…In humans and in chimpanzees, unusually high levels of HBD sequence conservation, when compared to functional paralogs, have been described [ 49 ]. Such pattern of conservation has been difficult to reconcile with the negligible expression of HbA 2 .…”

“…Surprisingly, in some eutherians HBD shows a level of sequence conservation typical of genes under strong evolutionary constraints [ 91 ]. In humans for example, HBD was found to have lower nucleotide diversity than HBB , suggesting that purifying selection has shaped the evolutionary history of HBD [ 49 , 87 ] through an unrecognized role not associated with oxygen transport [ 46 , 74 , 86 ].…”

“…The involvement of HBD in the fetal/adult Hb switch was proposed decades ago [ 5 , 55 ] and since then some studies have provided evidence supporting this hypothesis [ 6 , 49 , 67 ]. In fact, the fetal to adult Hb switch of anthropoid primates is unique.…”

An Experimental Study of the Effect of Rare Polymorphisms of Human Hbb, HBD and F9 Promoter Tata Boxes on the Kinetics of Interaction With the Tata-Binding Protein

“…Мутации в кодирующей и регуляторной областях гена βглобина приводят к наследственным нарушениям синтеза гемоглобина -βталассемиям различной тяжести и серповидноклеточной анемии (Galanello, Origa, 2010). Ранее роль гемоглобина δ считали несущественной, но авторы работы (Moleirinho et al, 2013) в результате комплексного анализа, основанного на эмпирических и гаплотипных ис следованиях, пришли к выводу о его важной роли в ре гуляции кластера этих генов.…”

Characterisation of Duplicated Haemoglobin Genes in Bivalves

“…and is comprised of five loci (NC_000011.10; 5'-epsilon -gammaG -gammaA -delta -beta -3') (Moleirinho et al, 2013). The order in which the genes are found within these clusters, determines the timeline at which they are expressed during development (Hardison et al, 1997) with those closest to the locus control region at the 5'end, expressed in early development and those further away expressed at a later stage (Hanscombe et al, 1991).…”