title: Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis.
abstract: 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.
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Jozef
authors.initials: J
authors.lastname: Madzo
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Hui
authors.initials: H
authors.lastname: Liu
authors.affiliation: Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Alexis
authors.initials: A
authors.lastname: Rodriguez
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Aparna
authors.initials: A
authors.lastname: Vasanthakumar
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Sriram
authors.initials: S
authors.lastname: Sundaravel
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Donne Bennett D
authors.initials: DBD
authors.lastname: Caces
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.|Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Looney
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.|Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Janet B
authors.initials: JB
authors.lastname: Lepore
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Trisha
authors.initials: T
authors.lastname: Macrae
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Duszynski
authors.affiliation: Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
authors.forename: Alan H
authors.initials: AH
authors.lastname: Shih
authors.affiliation: Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.|Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Chun-Xiao
authors.initials: CX
authors.lastname: Song
authors.affiliation: Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.|Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Miao
authors.initials: M
authors.lastname: Yu
authors.affiliation: Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Yiting
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Grossman
authors.affiliation: Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Raumann
authors.affiliation: Albert Einstein College of Medicine, Bronx, NY 10461, USA.
authors.forename: Amit
authors.initials: A
authors.lastname: Verma
authors.affiliation: Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.|Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.affiliation: Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
authors.forename: Ross L
authors.initials: RL
authors.lastname: Levine
authors.affiliation: Department of Medicine, University of Illinois, Chicago, Chicago, IL 60612, USA.|Jesse Brown VA Medical Center, Chicago, IL 60612, USA.
authors.forename: Don
authors.initials: D
authors.lastname: Lavelle
authors.affiliation: Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA.|Howard Hughes Medical Institute, Chevy Chase, MD 20815-6789, USA.
authors.forename: Bruce T
authors.initials: BT
authors.lastname: Lahn
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Amittha
authors.initials: A
authors.lastname: Wickrema
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA.
authors.forename: Lucy A
authors.initials: LA
authors.lastname: Godley
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D018952:Antigens, CD34 / Q000235:genetics / Q000378:metabolism; D002478:Cells, Cultured; D003596:Cytosine / Q000031:analogs & derivatives / Q000032:analysis; D019175:DNA Methylation; D049308:Dioxygenases / Q000235:genetics / Q000378:metabolism; D041905:Erythroid Cells / Q000166:cytology / Q000187:drug effects / Q000378:metabolism*; D004920:Erythropoiesis / Q000235:genetics*; D006657:Histones / Q000378:metabolism; D006801:Humans; D009154:Mutation; D012045:Regulatory Sequences, Nucleic Acid; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D018952:Antigens, CD34; D006657:Histones; D014157:Transcription Factors; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D049308:Dioxygenases