Nuclear morphology is shaped by loop-extrusion programs

  • Friedl, P. & Weigelin, B. Interstitial leukocyte migration and immune function. Nat. Immunol. 9, 960–969 (2008).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Rowat, A. C. et al. Nuclear envelope composition determines the ability of neutrophil-type cells to passage through micron-scale constrictions. J. Biol. Chem. 288, 8610–8618 (2013).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kalukula, Y., Stephens, A. D., Lammerding, J. & Gabriele, S. Mechanics and functional consequences of nuclear deformations. Nat. Rev. Mol. Cell Biol. 23, 583–602 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Georgopoulos, K. In search of the mechanism that shapes the neutrophil’s nucleus. Genes Dev. 31, 85–87 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nasmyth, K. & Haering, C. H. Cohesin: its roles and mechanisms. Annu. Rev. Genet. 43, 525–558 (2009).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Cavaillon, J. The historical milestones in the understanding of leucocyte biology initiated by Elie Metchnikoff. J. Leuc. Biol. 90, 413–424 (2011).

    Article 
    CAS 

    Google Scholar
     

  • Metchnikoff, E. Über eine Sprosspilzkrankheit der Daphnien. Beitrag zur Lehre über den Kampf der Phagozyten gegen Krankheitserreger. Arch. Pathol. Anat. Physiol. Klin. Med. 96, 177–195 (1884).

    Article 

    Google Scholar
     

  • Schultze, M. Ein heizbarer Objecttisch und seine Verwendung bei Untersuchungen des Blutes. Arch. Mikrosc. Anat. 1, 1–42 (1865).

    Article 

    Google Scholar
     

  • Hoffmann, K. et al. Mutations in the gene encoding the lamin B receptor produce an altered nuclear morphology in granulocytes (Pelger–Huët anomaly). Nat. Genet. 31, 410–414 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Shultz, L. D. et al. Mutations at the mouse ichthyosis locus are within the lamin B receptor gene: a single gene model for human Pelger–Huët anomaly. Hum. Mol. Gen. 12, 61–69 (2003).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bolzer, A. et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 3, e157 (2005).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hoencamp, C. et al. 3D genomics across the tree of life reveals condensing II as a determinant of architecture type. Science 372, 984–989 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Keenan, C. R. et al. Chromosomes distribute randomly to, but not within, human nuclear lobes. iScience 24, 102161 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Waugh, B. et al. Three-dimensional deconvolution processing for STEM cryotomography. Proc. Natl Acad. Sci. USA 117, 27374–27380 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sedat, J. W. et al. A proposed unified interphase nucleus chromosome structure: preliminary preponderance of evidence. Proc. Natl Acad. Sci. USA 119, e2119107119 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dixon, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hafner, A. et al. Loop stacking organizes genome folding from TADs to chromosomes. Mol. Cell 83, 1377–1392 (2021).

    Article 

    Google Scholar
     

  • Yatskevich, S., Rhodes, J. & Nasmyth, K. Organization of chromosomal DNA by SMC complexes. Annu. Rev. Genet. 53, 445–482 (2019).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Schwartzer, W. et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature 551, 51–56 (2017).

    Article 

    Google Scholar
     

  • Rao, S. S. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Haarhuis, J. H. et al. The cohesin release factor WAPL restricts chromatin loop extension. Cell 169, 693–707 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sykes, D. B. & Kamps, M. P. Estrogen-dependent E2A/Pbx1 myeloid cell lines exhibit conditional differentiation that can be arrested by other leukemic oncoproteins. Blood 98, 2308–2318 (2001).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Zhu, Y. et al. Comprehensive characterization of neutrophil genome topology. Genes Dev. 31, 141–153 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grieshaber-Bouyer, R. et al. The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments. Nat. Commun. 12, 2856 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhu, Y., Denholtz, M., Lu, H. & Murre, C. Calcium signaling instructs NIPBL recruitment at active enhancers and promoters via distinct mechanisms to reconstruct genome compartmentalization. Genes Dev. 35, 65–81 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nabet, B. et al. The dTAG system for immediate and target-specific protein degradation. Nat. Chem. Biol. 14, 431–441 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Khoyratty, T. E. et al. Distinct transcription factor networks control neutrophil-driven inflammation. Nat. Immunol. 22, 1093–1106 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, Y. et al. Super-enhancer reprogramming drives a B cell-epithelial transition and high-risk leukemia. Genes Dev. 30, 1971–1990 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophages and B cell identities. Mol. Cell 38, 576–589 (2010).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martinon, F., Burns, K. & Tschopp, J. The inflammasome: a molecular platform triggering activation of inflammatory caspases and processing of proIL-β. Mol. Cell 10, 417–426 (2002).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Thomas, P. G. et al. The intracellular sensor NLRP3 mediates key innate and healing responses to influenza A virus via the regulation of caspase-1. Immunity 30, 566–575 (2009).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, M. T. et al. Negative regulation of RIG-I mediated innate antiviral signaling by SEC14L1. J. Virol. 87, 10037-46 (2013).

    Article 
    PubMed 

    Google Scholar
     

  • Braunholz, D. et al. Isolated NIPBL-missense mutations that cause Cornelia de Lange syndrome alter MAU2 interaction. Eur. J. Hum. Genet. 20, 271–276 (2012).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Chao, W. C. H. et al. Structural studies reveal the functional modularity of the Scc2-Scc4 cohesin loader. Cell Rep. 12, 719–725 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Seki, A. & Rutz, S. Optimized RNP transfection for highly efficient CRISPR/Cas9-mediated gene knockout in primary T cells. J. Exp. Med. 215, 985–997 (2018).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hendel, A. et al. Chemically modified guide RNAs enhance CRISPR–Cas genome editing in human primary cells. Nat. Biotechnol. 33, 985–989 (2015).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Xie, X. et al. Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection. Nat. Immunol. 21, 1119–1133 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rao, S. S. et al. Cohesin loss eliminates all loop domains. Cell 171, 305–320 (2017).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Calderon, L. et al. Cohesin-dependence of neuronal gene expression relates to chromatin loop length. eLife 11, e76539 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Cuartero, S. et al. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat. Immunol. 9, 932–941 (2018).

    Article 

    Google Scholar
     

  • Kalukula, Y., Stephens, A. D., Lammerding, J. & Gabriele, S. Mechanisms and functional consequences of nuclear deformations. Nat. Rev. Mol. Cell Biol. 23, 583–602 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mohana, G. et al. Chromosome-level organization of the regulatory genome in the Drosophila nervous system. Cell 186, 3826–3844 (2023).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Bashkirova, E. & Lomvardas, S. Olfactory receptor genes make the case for inter-chromosomal interactions. Curr. Opin. Genet. Dev. 55, 106–113 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, Y. et al. Lineage specific 3D genome organization is assembled at multiple scales by Ikaros. Cell 186, 5260–5289 (2023).

    Article 

    Google Scholar
     

  • Andrews, S. FastQC: a quality control tool for high throughput sequence data. Babraham Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010).

  • Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Robinson, M. D. et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26, 139–40 (2010).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Raudvere, U. et al. gProfiler: a web server for functional enrichment analysis and conversion of gene lists. Nucleic Acids Res. 47, W191–W198 (2019).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yu, G., Wang, L. & He, Q. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015).

    Article 
    CAS 
    PubMed 

    Google Scholar
     

  • Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhang, et al. Fast alignment and preprocessing of chromatin profiles with Chromap. Nat. Commun. 12, 6566 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang, et al.HiCRep: assessing the reproducibility of HiC data using a stratum-adjusted correlation coefficient. Genome Res. 11, 1939–1949 (2017).

    Article 

    Google Scholar
     

  • Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web served 2016 update. Nucleic Acids Res. 44, W90–W97 (2016).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Blondel, V. D., Guillaume, J.-L., Lambiotte, R. & Lefebvre, E. Fast unfolding of communities in large networks. J. Stat. Mech. Theory Exp. 2008, P10008 (2008).

    Article 

    Google Scholar
     

  • Lange, M. et al. CellRank for directed single-cell fate mapping. Nat. Methods 19, 159–170 (2022).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gulati, G. S. et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 367, 405–411 (2020).

    Article 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     


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