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@ARTICLE{Jaber:180371,
      author       = {M. Jaber and A. Radwan and N. Loyfer and M. Abdeen and S.
                      Sebban and A. Khatib and H. Yassen and T. Kolb$^*$ and M.
                      Zapatka$^*$ and K. Makedonski and A. Ernst$^*$ and T. Kaplan
                      and Y. Buganim},
      title        = {{C}omparative parallel multi-omics analysis during the
                      induction of pluripotent and trophectoderm states.},
      journal      = {Nature Communications},
      volume       = {13},
      number       = {1},
      issn         = {2041-1723},
      address      = {[London]},
      publisher    = {Nature Publishing Group UK},
      reportid     = {DKFZ-2022-01285},
      pages        = {3475},
      year         = {2022},
      abstract     = {Following fertilization, it is only at the 32-64-cell stage
                      when a clear segregation between cells of the inner cell
                      mass and trophectoderm is observed, suggesting a 'T'-shaped
                      model of specification. Here, we examine whether the
                      acquisition of these two states in vitro, by nuclear
                      reprogramming, share similar dynamics/trajectories. Using a
                      comparative parallel multi-omics analysis (i.e., bulk
                      RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, RRBS and CNVs) on
                      cells undergoing reprogramming to pluripotency and TSC state
                      we show that each reprogramming system exhibits specific
                      trajectories from the onset of the process, suggesting
                      'V'-shaped model. We describe in detail the various
                      trajectories toward the two states and illuminate
                      reprogramming stage-specific markers, blockers, facilitators
                      and TSC subpopulations. Finally, we show that while the
                      acquisition of the TSC state involves the silencing of
                      embryonic programs by DNA methylation, during the
                      acquisition of pluripotency these regions are initially
                      defined but retain inactive by the elimination of H3K27ac.},
      cin          = {B420 / HD01 / B060},
      ddc          = {500},
      cid          = {I:(DE-He78)B420-20160331 / I:(DE-He78)HD01-20160331 /
                      I:(DE-He78)B060-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:35715410},
      doi          = {10.1038/s41467-022-31131-8},
      url          = {https://inrepo02.dkfz.de/record/180371},
}