Hydroxymethylation at Gene Regulatory Regions Directs Stem/Early Progenitor Cell Commitment during Erythropoiesis

Abstract

SUMMARY Hematopoietic stem cell differentiation involves the silencing of self-renewal genes and induction of a specific transcriptional program. Identification of multiple covalent cytosine modifications raises the question of how these derivatized bases influence stem cell commitment. Using a replicative primary human hematopoietic stem/progenitor cell differentiation system, we demonstrate dynamic changes of 5-hydroxymethylcytosine (5-hmC) during stem cell commitment and differentiation to the erythroid line-age. Genomic loci that maintain or gain 5-hmC density throughout erythroid differentiation contain binding sites for erythroid transcription factors and several factors not previously recognized as erythroid-specific factors. The functional importance of 5-hmC was demonstrated by impaired erythroid differentiation, with augmentation of myeloid potential, and disrupted 5-hmC patterning in leukemia patient-derived CD34+ stem/early progenitor cells with TET methylcytosine dioxygenase 2 (TET2) mutations. Thus, chemical conjugation and affinity purification of 5-hmC-enriched sequences followed by sequencing serve as resources for deciphering functional implications for gene expression during stem cell commitment and differentiation along a particular lineage.

CMML: Clinical and molecular aspects

“…This differentiation bias seems to be an evolutionary neutral 'by-product' of the competitive advantage provided in HSCs by TET2 loss of function [40]. This model has yet to be formally demonstrated, but is in keeping with the role of TET enzymes in embryonic stem cells [46]. Non-cell autonomous mechanisms involving dialogue between clonal differentiated cells and clonal HSCs, or between leukemic cells and the micro-environment may also contribute to the disease.…”

Mathematical modeling reveals differential effects of erythropoietin on proliferation and lineage commitment of human hematopoietic progenitors in early erythroid culture

“…Understanding the fundamental mechanisms controlling lineage commitment, proliferation and survival during erythropoiesis is becoming an achievable goal thanks to the advent of novel high throughput technologies to explore the transcriptome, 39-42 proteome 43 and epigenome. 44,45 In order to maximize the specificity of the information afforded by these techniques, it is essential to start with well-defined populations.…”

Fumarate and Succinate Regulate Expression of Hypoxia-inducible Genes via TET Enzymes

“…Genomic DNA was hydrolyzed enzymatically to nucleosides and run on a Zorbax XDB-C18 2.1 ϫ 50-mm column (1.8-mm particle size) attached to an Agilent 1200 Series liquid chromatography machine coupled to an Agilent 6410 Triple Quad Mass Spectrometer (13,28,29).…”