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@ARTICLE{Schnung:182554,
      author       = {M. Schönung$^*$ and M. Hartmann$^*$ and S. Krämer$^*$ and
                      S. Stäble$^*$ and M. Hakobyan$^*$ and E. Kleinert$^*$ and
                      T. Aurich$^*$ and D. Cobanoglu$^*$ and F. H. Heidel and S.
                      Fröhling$^*$ and M. D. Milsom$^*$ and M. Schlesner and P.
                      Lutsik$^*$ and D. Lipka$^*$},
      title        = {{D}ynamic {DNA} methylation reveals novel cis-regulatory
                      elements in mouse hematopoiesis.},
      journal      = {Experimental hematology},
      volume       = {117},
      issn         = {0301-472X},
      address      = {Amsterdam [u.a.]},
      publisher    = {Elsevier Science},
      reportid     = {DKFZ-2022-02735},
      pages        = {24-42.e7},
      year         = {2023},
      note         = {#EA:B340#LA:B340# / 2023 Jan;117:24-42.e7},
      abstract     = {Differentiation of hematopoietic stem and progenitor cells
                      (HSPCs) to terminally differentiated immune cells is
                      accompanied by large-scale remodeling of the DNA methylation
                      landscape. While significant insights into the molecular
                      mechanisms of hematopoietic tissue regeneration were derived
                      from mouse models, profiling of DNA methylation has been
                      hampered by high cost or low resolution using the methods
                      available. This problem has been overcome by the recent
                      development of the Infinium Mouse Methylation BeadChip
                      (MMBC) array, facilitating methylation profiling of the
                      mouse genome at single CpG resolution at affordable cost. We
                      extended the RnBeads package to provide a computational
                      framework for the analysis of MMBC data. This framework was
                      applied to a newly generated reference map of mouse
                      hematopoiesis encompassing nine different cell types. The
                      analysis of dynamically regulated CpG sites showed
                      progressive and unidirectional DNA methylation changes from
                      HSPCs to differentiated hematopoietic cells and allowed the
                      identification of lineage- and cell type-specific DNA
                      methylation programs. Comparison to previously published
                      catalogues of cis-regulatory elements (CREs) revealed 12,856
                      novel putative CREs which were dynamically regulated by DNA
                      methylation (mdCREs). These mdCREs were predominantly
                      associated with patterns of cell type-specific DNA
                      hypomethylation and could be identified as epigenetic
                      control regions regulating the expression of key
                      hematopoietic genes during differentiation. In summary, we
                      established an analysis pipeline for MMBC datasets and
                      provide a DNA methylation atlas of mouse hematopoiesis. This
                      resource allowed us to identify novel putative CREs involved
                      in hematopoiesis and will serve as a platform to study
                      epigenetic regulation of normal and malignant
                      hematopoiesis.},
      keywords     = {285k methylation array (Other) / DNA methylation (Other) /
                      cis regulatory elements (Other) / epigenetics (Other) /
                      hematopoiesis (Other) / hematopoietic stem cells (Other) /
                      mouse methylation bead chip (Other)},
      cin          = {B340 / A012 / B370},
      ddc          = {610},
      cid          = {I:(DE-He78)B340-20160331 / I:(DE-He78)A012-20160331 /
                      I:(DE-He78)B370-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:36368558},
      doi          = {10.1016/j.exphem.2022.11.001},
      url          = {https://inrepo02.dkfz.de/record/182554},
}