@article{14689,
  author       = {Ing-Simmons, Elizabeth and Machnik, Nick N and Vaquerizas, Juan M.},
  issn         = {1546-1718},
  journal      = {Nature Genetics},
  number       = {12},
  pages        = {2053--2055},
  publisher    = {Springer Nature},
  title        = {{Reply to: Revisiting the use of structural similarity index in Hi-C}},
  doi          = {10.1038/s41588-023-01595-5},
  volume       = {55},
  year         = {2023},
}

@article{12158,
  abstract     = {Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.},
  author       = {Zeller, Peter and Yeung, Jake and Viñas Gaza, Helena and de Barbanson, Buys Anton and Bhardwaj, Vivek and Florescu, Maria and van der Linden, Reinier and van Oudenaarden, Alexander},
  issn         = {1546-1718},
  journal      = {Nature Genetics},
  keywords     = {Genetics},
  pages        = {333--345},
  publisher    = {Springer Nature},
  title        = {{Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis}},
  doi          = {10.1038/s41588-022-01260-3},
  volume       = {55},
  year         = {2023},
}

@article{12193,
  abstract     = {DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.},
  author       = {Walker, James and Gao, Hongbo and Zhang, Jingyi and Aldridge, Billy and Vickers, Martin and Higgins, James D. and Feng, Xiaoqi},
  issn         = {1546-1718},
  journal      = {Nature Genetics},
  keywords     = {Genetics},
  number       = {1},
  pages        = {130--137},
  publisher    = {Nature Research},
  title        = {{Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis}},
  doi          = {10.1038/s41588-017-0008-5},
  volume       = {50},
  year         = {2017},
}

@misc{9504,
  author       = {Zilberman, Daniel},
  booktitle    = {Nature Genetics},
  issn         = {1546-1718},
  number       = {4},
  pages        = {442--443},
  publisher    = {Nature Publishing Group},
  title        = {{The human promoter methylome}},
  doi          = {10.1038/ng0407-442},
  volume       = {39},
  year         = {2007},
}

@article{9505,
  abstract     = {Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes.},
  author       = {Zilberman, Daniel and Gehring, Mary and Tran, Robert K. and Ballinger, Tracy and Henikoff, Steven},
  issn         = {1546-1718},
  journal      = {Nature Genetics},
  number       = {1},
  pages        = {61--69},
  publisher    = {Nature Publishing Group},
  title        = {{Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription}},
  doi          = {10.1038/ng1929},
  volume       = {39},
  year         = {2006},
}