Comparison of Fetal and Adult Erythroid Chromosomal Architectures Identifies a Novel Fetal Hemoglobin Regulatory Region

Chromatin structure is tightly intertwined with transcription regulation. The extent to which global chromatin architecture is subjected to alterations at different developmental stages within the same cell lineage has not been examined in great depth. Erythropoiesis offers an ideal model system to study the molecular mechanisms of gene regulation within the same cell lineage during development. Here, we comparatively defined via RNA-seq the transcriptomes, and via Hi-C and Capture-C the chromosome architectures of primary human fetal and adult erythroid cells.

Overall, fetal and adult chromosomal conformations displayed a high degree of similarity. This includes the maintenance of A and B compartments representing active and inactive chromatin regions, respectively. Only ~5% of the genome switched compartments from A to B or vice versa, in agreement with the highly similar gene expression profiles. Moreover, topologically associating domains (TADs) were extensively preserved from fetal to adult stages. The developmentally regulated β-globin gene cluster is contained within one topologically associating domain (TAD) but folds into a three sub-TADs structure, the central one of which encompasses the β-globin locus. Notably, although the three sub-TAD structures are flanked by tissue invariant CTCF bound sites, they engage in looped contacts only in erythroid cells, indicating that erythroid specific transcription factors are required for CTCF mediated boundary contacts.

At a finer scale, Capture-C detected distinct folding patterns at the developmentally controlled β-globin locus, including the expected stage-specific interactions between the enhancer (LCR) and the fetal γ-globin and adult β-globin genes. Importantly, we identified new developmental stage-specific chromatin contacts involving a region compassing a pseudogene (HBBP1) that resides between the fetal and adult globin genes. Specifically, HBBP1 engages in fetal stage-specific contacts with DNase hypersensitive sites HS5 and 3'HS1 while contacting the embryonic ε-globin gene at the adult stage. Deletion of a 2.3kb fragment encompassing HBBP1 (but not its transcriptional silencing) leads to strong reactivation of γ-globin gene expression in an adult erythroid cell line. This is accompanied by an architecturally restructured locus, including increased LCR-γ-globin chromatin interactions. Notably, the effects of HBBP1 deletion on chromatin architecture and gene expression closely mimic those of deleting the fetal globin repressor BCL11A, implicating BCL11A in the function of the HBBP1 region.

In sum, our results identify a new segment, distinct from previously described regions linked to hereditary persistence of fetal hemoglobin, which engages in functionally important chromatin contacts. Since the HBBP1 region resides quite distantly from the structural globin genes, it might be a useful target for therapeutic genome editing without risking damage to the globin genes. Finally, our study highlights the power of high resolution chromosome architectural analysis to identify new regulatory regions.