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

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posted on 12.04.2016, 00:00 authored by Jozef Madzo, Hui Liu, Alexis Rodriguez, Aparna Vasanthakumar, Sriram Sundaravel, Donne Bennett D Caces, Timothy J Looney, Li Zhang, Janet B Lepore, Trisha Macrae, Robert Duszynski, Alan H Shih, Chun-Xiao Song, Miao Yu, Yiting Yu, Robert Grossman, Brigitte Raumann, Amit Verma, Chuan He, Ross L Levine, Don Lavelle, Bruce T Lahn, Amittha Wickrema, Lucy A Godley
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 lineage. 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.


We gratefully acknowledge all of the members of the Wickrema and Godley laboratories for helpful discussions as well as constructive comments on this work from Emery Bresnick, Ursula Storb, and Vincent Marchesi. This work was supported in part by NIH grants CA129831 (to L.A.G.) and CA129831-03S1 (to C.H., B.T.L., and L.A.G.), HL116336 (to A.W. and A. Verma), F32-DK092030 (to A. Vasanthakumar), and the Giving Tree Foundation (to A.W.).


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