@unpublished{21920,
  abstract     = {Vertebrates display remarkable diversity of sensorimotor behaviors, each adapted to distinct ecological and survival demands. This diversity raises fundamental questions about the evolutionary origin of motor control: do conserved spinal circuits underlie these behaviors, and how have they diverged across species. Recent studies detail spinal cell-type architecture in mammals but comparable, high-resolution atlases of the non-mammalian spinal cord are lacking. Here, we compare spinal cord cell types between fish, frogs, mice and humans, spanning ∼450 million years of evolution. Across species, we define highly conserved programs of cell type specification that segregate spinal neurons into nearly identical cardinal classes during development. This contrasts with adult stages, when spinal cell-type composition selectively diverges for excitatory neuron subpopulations. Using spatial transcriptomics, we localize this species divergence to the superficial, dorsal spinal cord, where variant neuropeptide expression defines mammalian-specific cell types. The most dorsal spinal cord thus emerges as a recently evolved hub for sensory integration in mammals, a neospinal cord analogous to the neocortex.</jats:p>},
  author       = {Ignatyev, Yuri and Papadopoulos, Stavros and Soretić, Mateja and Yeung, Jake and Lin, Tzi-Yang and Tanaka, Elly M and Peshkin, Leonid and Levine, Ariel J and Gabitto, Mariano I and Sweeney, Lora Beatrice Jaeger},
  booktitle    = {bioRxiv},
  title        = {{Innovations in spinal cord cell type heterogeneity across vertebrate evolution}},
  doi          = {10.1101/2025.10.09.680955},
  year         = {2025},
}

@article{12106,
  abstract     = {Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.},
  author       = {Yeung, Jake and Florescu, Maria and Zeller, Peter and De Barbanson, Buys Anton and Wellenstein, Max D. and Van Oudenaarden, Alexander},
  issn         = {1546-1696},
  journal      = {Nature Biotechnology},
  pages        = {813–823},
  publisher    = {Springer Nature},
  title        = {{scChIX-seq infers dynamic relationships between histone modifications in single cells}},
  doi          = {10.1038/s41587-022-01560-3},
  volume       = {41},
  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},
}