DNA methylation analysis of murine hematopoietic side population cells during aging.
Stem cells have been found in most tissues/organs. These somatic stem cells produce replacements for lost and damaged cells, and it is not completely understood how this regenerative capacity becomes diminished during aging. To study the possible involvement of epigenetic changes in somatic stem cell aging, we used murine hematopoiesis as a model system. Hematopoietic stem cells (HSCs) were enriched for via Hoechst exclusion activity (SP-HSC) from young, medium-aged and old mice and subjected to comprehensive, global methylome (MeDIP-seq) analysis. With age, we observed a global loss of DNA methylation of approximately 5%, but an increase in methylation at some CpG islands. Just over 100 significant (FDR<0.2) aging-specific differentially methylated regions (aDMRs) were identified, which are surprisingly few considering the profound age-based changes that occur in HSC biology. Interestingly, the polycomb repressive complex -2 (PCRC2) target genes Kiss1r, Nav2 and Hsf4 were hypermethylated with age. The promoter for the Sdpr gene was determined to be progressively hypomethylated with age. This occurred concurrently with an increase in gene expression with age. To explore this relationship further, we cultured isolated SP-HSC in the presence of 5-aza-deoxycytdine and demonstrated a negative correlation between Sdpr promoter methylation and gene expression. We report that DNA methylation patterns are well preserved during hematopoietic stem cell aging, confirm that PCRC2 targets are increasingly methylated with age, and suggest that SDPR expression changes with age in HSCs may be regulated via age-based alterations in DNA methylation.
Medical Genomics; UCL Cancer Institute; University College London; London, UK; UCL Institute of Healthy Ageing; University College London; London, UK.
Oluwatosin
O
Taiwo
Medical Genomics; UCL Cancer Institute; University College London; London, UK.
Gareth A
GA
Wilson
UCL Genetics Institute; University College London; London, UK.
Warren
W
Emmett
Medical Genomics; UCL Cancer Institute; University College London; London, UK.
Tiffany
T
Morris
Cancer Research UK; London Research Institute; Lincoln's Inn Fields; London, UK.
Dominique
D
Bonnet
UCL Institute of Healthy Ageing; University College London; London, UK.
Eugene
E
Schuster
Scientific Support Services; Flow Facility; University College London; London, UK.
Tomas
T
Adejumo
Medical Genomics; UCL Cancer Institute; University College London; London, UK; These senior authors contributed equally to this work.
Stephan
S
Beck
UCL Institute of Healthy Ageing; University College London; London, UK; These senior authors contributed equally to this work.
Daniel J
DJ
Pearce
D000375:Aging / Q000235:genetics* / Q000378:metabolism; D000818:Animals; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation / Q000502:physiology*; D005260:Female; D006410:Hematopoiesis; D006412:Hematopoietic Stem Cells / Q000378:metabolism*; D006801:Humans; D051379:Mice; D008810:Mice, Inbred C57BL; D028044:Phosphate-Binding Proteins; D063151:Polycomb Repressive Complex 2 / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D058985:Side-Population Cells / Q000378:metabolism*
C112303:CAVIN2 protein, human; D002352:Carrier Proteins; D028044:Phosphate-Binding Proteins; D063151:Polycomb Repressive Complex 2
DNA methylation; Hsf4; Kiss1r; Nano-MeDIP-seq; Nav2; Sdpr polycomb repressive complex -2 (PCRC2); aging; epigenetics; hematopoietic stem cells; methylome; methylomics