title: Comprehensive methylome map of lineage commitment from haematopoietic progenitors.
abstract: Epigenetic modifications must underlie lineage-specific differentiation as terminally differentiated cells express tissue-specific genes, but their DNA sequence is unchanged. Haematopoiesis provides a well-defined model to study epigenetic modifications during cell-fate decisions, as multipotent progenitors (MPPs) differentiate into progressively restricted myeloid or lymphoid progenitors. Although DNA methylation is critical for myeloid versus lymphoid differentiation, as demonstrated by the myeloerythroid bias in Dnmt1 hypomorphs, a comprehensive DNA methylation map of haematopoietic progenitors, or of any multipotent/oligopotent lineage, does not exist. Here we examined 4.6 million CpG sites throughout the genome for MPPs, common lymphoid progenitors (CLPs), common myeloid progenitors (CMPs), granulocyte/macrophage progenitors (GMPs), and thymocyte progenitors (DN1, DN2, DN3). Marked epigenetic plasticity accompanied both lymphoid and myeloid restriction. Myeloid commitment involved less global DNA methylation than lymphoid commitment, supported functionally by myeloid skewing of progenitors following treatment with a DNA methyltransferase inhibitor. Differential DNA methylation correlated with gene expression more strongly at CpG island shores than CpG islands. Many examples of genes and pathways not previously known to be involved in choice between lymphoid/myeloid differentiation have been identified, such as Arl4c and Jdp2. Several transcription factors, including Meis1, were methylated and silenced during differentiation, indicating a role in maintaining an undifferentiated state. Additionally, epigenetic modification of modifiers of the epigenome seems to be important in haematopoietic differentiation. Our results directly demonstrate that modulation of DNA methylation occurs during lineage-specific differentiation and defines a comprehensive map of the methylation and transcriptional changes that accompany myeloid versus lymphoid fate decisions.
authors: Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, 570 Rangos, 725 N. Wolfe St., Baltimore, Maryland 21205, USA.
authors: Hong
authors: H
authors: Ji
authors: Lauren I R
authors: LI
authors: Ehrlich
authors: Jun
authors: J
authors: Seita
authors: Peter
authors: P
authors: Murakami
authors: Akiko
authors: A
authors: Doi
authors: Paul
authors: P
authors: Lindau
authors: Hwajin
authors: H
authors: Lee
authors: Martin J
authors: MJ
authors: Aryee
authors: Rafael A
authors: RA
authors: Irizarry
authors: Kitai
authors: K
authors: Kim
authors: Derrick J
authors: DJ
authors: Rossi
authors: Matthew A
authors: MA
authors: Inlay
authors: Thomas
authors: T
authors: Serwold
authors: Holger
authors: H
authors: Karsunky
authors: Lena
authors: L
authors: Ho
authors: George Q
authors: GQ
authors: Daley
authors: Irving L
authors: IL
authors: Weissman
authors: Andrew P
authors: AP
authors: Feinberg
mesh_terms: D000818:Animals; D002460:Cell Line; D019070:Cell Lineage / Q000235:genetics; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D006410:Hematopoiesis / Q000235:genetics; D006412:Hematopoietic Stem Cells / Q000166:cytology* / Q000378:metabolism*; D008214:Lymphocytes / Q000166:cytology / Q000378:metabolism; D055442:Metabolome; D055432:Metabolomics; D051379:Mice; D022423:Myeloid Cells / Q000166:cytology / Q000378:metabolism; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism