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Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation

Michelle Rönnerblad, Robin Andersson, Tor Olofsson, Iyadh Douagi, Mohsen Karimi, Sören Lehmann, Ilka Hoof, Michiel de Hoon, Masayoshi Itoh, Sayaka Nagao-Sato, Hideya Kawaji, Timo Lassmann, Piero Carninci, Yoshihide Hayashizaki, Alistair R. R. Forrest, Albin Sandelin, Karl Ekwall, Erik Arner and Andreas Lennartsson

Key points

  • In granulopoiesis, changes in DNA methylation preferably occur at points of lineage restriction in low CpG areas.

  • DNA methylation is dynamic in enhancer elements and appears to regulate the expression of key transcription factors and neutrophil genes.

Abstract

In development, epigenetic mechanisms such as DNA methylation have been suggested to provide a cellular memory to maintain multipotency but also stabilize cell fate decisions and direct lineage restriction. In this study, we set out to characterize changes in DNA methylation and gene expression during granulopoiesis using 4 distinct cell populations ranging from the oligopotent common myeloid progenitor stage to terminally differentiated neutrophils. We observed that differentially methylated sites (DMSs) generally show decreased methylation during granulopoiesis. Methylation appears to change at specific differentiation stages and overlap with changes in transcription and activity of key hematopoietic transcription factors. DMSs were preferentially located in areas distal to CpG islands and shores. Also, DMSs were overrepresented in enhancer elements and enriched in enhancers that become active during differentiation. Overall, this study depicts in detail the epigenetic and transcriptional changes that occur during granulopoiesis and supports the role of DNA methylation as a regulatory mechanism in blood cell differentiation.

  • Submitted February 4, 2013.
  • Accepted October 15, 2013.