Hematopoietic transcriptional mechanisms: from locus-specific to genome-wide vantage points

Abstract

Hematopoiesis is an exquisitely regulated process in which stem cells in the developing embryo and the adult generate progenitor cells that give rise to all blood lineages. Master regulatory transcription factors control hematopoiesis by integrating signals from the microenvironment and dynamically establishing and maintaining genetic networks. One of the most rudimentary aspects of cell type-specific transcription factor function, how they occupy a highly restricted cohort of cis-elements in chromatin, remains poorly understood. Transformative technologic advances involving the coupling of next-generation DNA sequencing technology with the chromatin immunoprecipitation assay (ChIP-seq) have enabled genome-wide mapping of factor occupancy patterns. However, formidable problems remain; notably, ChIP-seq analysis yields hundreds to thousands of chromatin sites occupied by a given transcription factor, and only a fraction of the sites appear to be endowed with critical, non-redundant function. It has become en vogue to map transcription factor occupancy patterns genome-wide, while using powerful statistical tools to establish correlations to inform biology and mechanisms. With the advent of revolutionary genome editing technologies, one can now reach beyond correlations to conduct definitive hypothesis testing. This review focuses on key discoveries that have emerged during the path from single loci to genome-wide analyses, specifically in the context of hematopoietic transcriptional mechanisms.

Figure 1

Distinct functional properties of Gata2 GATA switch sites. (A) ChIP-seq profiles of GATA-2 chromatin occupancy at GATA2 locus in model erythroid cell systems: human K562 and mouse MEL cells. GATA-2 occupies established GATA factor binding regions termed GATA switch sites, which contain evolutionarily conserved GATA motifs and multiple attributes of transcriptional enhancers. (B) Schematic showing the GATA switch sites (−3.9, −2.8, −1.8 and +9.5 kb upstream of the 1S promoter transcription start site), and phenotypes resulting from deletion of the respective sites. The red X mark denotes the cis-element deletion from the mouse genome.