Epigenetic and genetic mechanisms in red cell biology

Abstract

Purpose of review: Erythropoiesis, in which hematopoietic stem cells (HSCs) generate lineage-committed progenitors that mature into erythrocytes, is regulated by numerous chromatin modifying and remodeling proteins. We will focus on how epigenetic and genetic mechanisms mesh to establish the erythroid transcriptome and how studying erythropoiesis can yield genomic principles.

Recent findings: Trans-acting factor binding to small DNA motifs (cis-elements) underlies regulatory complex assembly at specific chromatin sites, and therefore unique transcriptomes. As cis-elements are often very small, thousands or millions of copies of a given element reside in a genome. Chromatin restricts factor access in a context-dependent manner, and cis-element-binding factors recruit chromatin regulators that mediate functional outputs. Technologies to map chromatin attributes of loci in vivo, to edit genomes and to sequence whole genomes have been transformative in discovering critical cis-elements linked to human disease.

Summary: Cis-elements mediate chromatin-targeting specificity, and chromatin regulators dictate cis-element accessibility/function, illustrating an amalgamation of genetic and epigenetic mechanisms. Cis-elements often function ectopically when studied outside of their endogenous loci, and complex strategies to identify nonredundant cis-elements require further development. Facile genome-editing technologies provide a new approach to address this problem. Extending genetic analyses beyond exons and promoters will yield a rich pipeline of cis-element alterations with importance for red cell biology and disease.

FIGURE 1

Gata2 +9.5 cis-element. The Gata2 intronic +9.5 GATA switch site, which contains an E-box–GATA motif composite element, functions nonredundantly to confer hematopoietic stem cell (HSC) generation in the aorta gonad mesonephros (AGM) region, the fetal liver hematopoietic stem/progenitor cell (HSPC) compartment and vascular integrity. Heterozygous mutation of the +9.5 element leads to monocytopenia and mycobacteria infection (MonoMAC) syndrome, with a phenotype indistinguishable from MonoMAC patients with GATA2 zinc finger mutations. Adapted with permission from [33^▪].

FIGURE 2

Cis-element variation in normal and disease states. Mutational generation of a GATA motif interferes with α-globin transcription leading to α-thalassemia [133]. Natural variation in a GATA-1-binding region of the BCL11A locus as a determinant of γ-globin expression [132^▪▪]. Mutational disruption of a GATA-1 motif reduces expression of ALAS2, which encodes a critical heme biosynthetic enzyme [134^▪].

FIGURE 3

Erythroid cistrome discovery strategy. Prospective cis-elements are prioritized based on multiple parameters and subjected to functional analysis by cis-element editing. GATA-1-occupied cis-elements functional at their endogenous loci are predicted to be important determinants of erythroid cell genesis and/or function.