TY - JOUR
T1 - Comprehensive methylome map of lineage commitment from haematopoietic progenitors
AU - Ji, Hong
AU - Ehrlich, Lauren I.R.
AU - Seita, Jun
AU - Murakami, Peter
AU - Doi, Akiko
AU - Lindau, Paul
AU - Lee, Hwajin
AU - Aryee, Martin J.
AU - Irizarry, Rafael A.
AU - Kim, Kitai
AU - Rossi, Derrick J.
AU - Inlay, Matthew A.
AU - Serwold, Thomas
AU - Karsunky, Holger
AU - Ho, Lena
AU - Daley, George Q.
AU - Weissman, Irving L.
AU - Feinberg, Andrew P.
N1 - Funding Information:
Acknowledgements We thank L. Jerabek for laboratory management, C. Richter and N. Teja for antibody production, A. Mosley, J. Dollaga and D. Escoto for animal care, E. Zuo and the Stanford PAN facility for microarray processing, and E. Briem and A. N. Allen for CHARM array processing. This investigation was supported by National Institutes of Health grants R37CA053458 and P50HG003233 (to A.P.F), R01AI047457 and R01AI047458 (to I.L.W.), and a grant from the Thomas and Stacey Siebel Foundation (to I.L.W). L.I.R.E. was supported by Special Fellow Career Development award from the Leukemia and Lymphoma Society; J.S. was supported by a fellowship from the California Institute for Regenerative Medicine (T1-00001); D.J.R. was supported by National Institutes of Health grant R00AGO29760; M.A.I. was supported by National Institutes of Health grant CA09151 and a fellowship from the California Institute for Regenerative Medicine (T1-00001); T.S. was supported by a fellowship from the National Institutes of Health (F32AI058521).
PY - 2010/9
Y1 - 2010/9
N2 - 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.
AB - 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.
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U2 - 10.1038/nature09367
DO - 10.1038/nature09367
M3 - Article
C2 - 20720541
AN - SCOPUS:77956902023
SN - 0028-0836
VL - 467
SP - 338
EP - 342
JO - Nature
JF - Nature
IS - 7313
ER -