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The comprehensive DNA methylation landscape of hematopoietic stem cell development

Li, Xianlong, Liu, Di, Zhang, Linlin, Wang, Haizhen, Li, Yunqiao, Li, Zongcheng, He, Aibin, Liu, Bing, Zhou, Jie, Tang, Fuchou, Lan, Yu·2021·Cell Discovery
DOI 10.1038/s41421-021-00298-7PMC PMC8452669
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Fig. 1 Dynamic DNA methylation landscape during HSC development. a Dynamic changes of DNA methylation level (mean) and RUVg normalized gene expression during HSC development. b The number of differential DNA methylation region (tiles 1k, cover base 5 bp, P value less than 0.01, the absolute value of differential methylation levels bigger than 25) was calculated between each two consecutive stages. c Histograms of the numbers of tiles with gain and lost DNA methylation between each two consecutive stages in the annotated genomic regions. d Heatmap of differential DNA methylation region between each two consecutive stages and Gene ontology (GO) analysis of DMRs by using GREAT and top five GO term are displayed. e Heatmap and hierarchical clustering of genes (row scale) from the highlighted GO term in d and three dynamic gene expression patterns and the corresponding methylation level displayed on the right side and highlighted with shadow. f Motif analysis of each gene-set (annotated from DMRs between each two consecutive stage) and normalized enrichment score bigger than 3.5 is showed. g Representative TF regulatory network was calculated based on iCisTarget. h Dynamic mCH level and mitochondrial genes expression level during HSC development. i GO analysis of mCH DMRs from HEC to T1 pre-HSC and top nine GO terms are shown.
Fig. 1 Dynamic DNA methylation landscape during HSC development. a Dynamic changes of DNA methylation level (mean) and RUVg normalized gene expression during HSC development. b The number of differential DNA methylation region (tiles 1k, cover base 5 bp, P value less than 0.01, the absolute value of differential methylation levels bigger than 25) was calculated between each two consecutive stages. c Histograms of the numbers of tiles with gain and lost DNA methylation between each two consecutive stages in the annotated genomic regions. d Heatmap of differential DNA methylation region between each two consecutive stages and Gene ontology (GO) analysis of DMRs by using GREAT and top five GO term are displayed. e Heatmap and hierarchical clustering of genes (row scale) from the highlighted GO term in d and three dynamic gene expression patterns and the corresponding methylation level displayed on the right side and highlighted with shadow. f Motif analysis of each gene-set (annotated from DMRs between each two consecutive stage) and normalized enrichment score bigger than 3.5 is showed. g Representative TF regulatory network was calculated based on iCisTarget. h Dynamic mCH level and mitochondrial genes expression level during HSC development. i GO analysis of mCH DMRs from HEC to T1 pre-HSC and top nine GO terms are shown.CC BY · PubMed Central

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Research works printed but not linked: 10

  1. Dzierzak, E. & Bigas, A. Blood development: hematopoietic stem cell dependence and independence. Cell Stem Cell 22, 639–651 (2018). · DOI
  2. Hou, S. et al. Embryonic endothelial evolution towards first hematopoietic stem cells revealed by single-cell transcriptomic and functional analyses. Cell Res. 30, 376–392 (2020). · DOI
  3. Zhu, Q. et al. Developmental trajectory of prehematopoietic stem cell formation from endothelium. Blood 136, 845–856 (2020). · DOI
  4. Zhou, F. et al. Tracing haematopoietic stem cell formation at single-cell resolution. Nature 533, 487–492 (2016). · DOI
  5. Zhou, J. et al. Combined single-cell profiling of lncRNAs and functional screening reveals that H19 is pivotal for embryonic hematopoietic stem cell development. Cell Sem Cell 24, 285–298 (2019). e285. · DOI
  6. Webber, B. R. et al. DNA methylation of Runx1 regulatory regions correlates with transition from primitive to definitive hematopoietic potential in vitro and in vivo. Blood 122, 2978–2986 (2013). · DOI
  7. Elbarbary, R. A., Lucas, B. A. & Maquat, L. E. Retrotransposons as regulators of gene expression. Science 351, aac7247 (2016). · DOI
  8. Lorincz, M. C., Dickerson, D. R., Schmitt, M. & Groudine, M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat. Struct. Mol. Biol. 11, 1068–1075 (2004). · DOI
  9. Chen, X. et al. Key role for CTCF in establishing chromatin structure in human embryos. Nature 576, 306–310 (2019). · DOI
  10. He, Y. et al. Spatiotemporal DNA methylome dynamics of the developing mouse fetus. Nature 583, 752–759 (2020). · DOI

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Metadata

Authors
Li, X., Liu, D., Zhang, L., Wang, H., Li, Y., Li, Z., He, A., Liu, B., Zhou, J., Tang, F., & Lan, Y.
Venue
Cell Discovery
Publisher
Springer Science and Business Media LLC
Published
2021-09-21
Volume
7
Issue
1
ISSN
2056-5968
DOI
10.1038/s41421-021-00298-7
PMC
PMC8452669
Cited by
11
References
0
Language
en
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CoChat. (2026). Citation check: The comprehensive DNA methylation landscape of hematopoietic stem cell development. https://app.cochat.ai/papers/10.1038/s41421-021-00298-7
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Li, X., Liu, D., Zhang, L., Wang, H., Li, Y., Li, Z., He, A., Liu, B., Zhou, J., Tang, F., & Lan, Y. (2021). The comprehensive DNA methylation landscape of hematopoietic stem cell development. Cell Discovery. https://doi.org/10.1038/s41421-021-00298-7