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

Blood. 2014 Apr 24;123(17):e79-89. doi: 10.1182/blood-2013-02-482893. Epub 2014 Mar 26.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Differentiation
  • Cell Separation
  • CpG Islands
  • Cytosine / metabolism
  • DNA Methylation*
  • Enhancer Elements, Genetic*
  • Epigenesis, Genetic
  • Flow Cytometry
  • Gene Expression Profiling
  • Gene Expression Regulation
  • Genomics
  • Granulocytes / cytology*
  • Humans
  • Neutrophils / metabolism
  • Oligonucleotide Array Sequence Analysis
  • RNA / metabolism
  • Stem Cells / cytology
  • Transcription Factors / metabolism
  • Transcriptome*

Substances

  • Transcription Factors
  • RNA
  • Cytosine