Friedl, P. & Weigelin, B. Interstitial leukocyte migration and immune function. Nat. Immunol. 9, 960–969 (2008).
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).
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).
Georgopoulos, K. In search of the mechanism that shapes the neutrophil’s nucleus. Genes Dev. 31, 85–87 (2017).
Nasmyth, K. & Haering, C. H. Cohesin: its roles and mechanisms. Annu. Rev. Genet. 43, 525–558 (2009).
Cavaillon, J. The historical milestones in the understanding of leucocyte biology initiated by Elie Metchnikoff. J. Leuc. Biol. 90, 413–424 (2011).
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).
Schultze, M. Ein heizbarer Objecttisch und seine Verwendung bei Untersuchungen des Blutes. Arch. Mikrosc. Anat. 1, 1–42 (1865).
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).
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).
Bolzer, A. et al. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. PLoS Biol. 3, e157 (2005).
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).
Keenan, C. R. et al. Chromosomes distribute randomly to, but not within, human nuclear lobes. iScience 24, 102161 (2021).
Waugh, B. et al. Three-dimensional deconvolution processing for STEM cryotomography. Proc. Natl Acad. Sci. USA 117, 27374–27380 (2020).
Sedat, J. W. et al. A proposed unified interphase nucleus chromosome structure: preliminary preponderance of evidence. Proc. Natl Acad. Sci. USA 119, e2119107119 (2022).
Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).
Dixon, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).
Hafner, A. et al. Loop stacking organizes genome folding from TADs to chromosomes. Mol. Cell 83, 1377–1392 (2021).
Yatskevich, S., Rhodes, J. & Nasmyth, K. Organization of chromosomal DNA by SMC complexes. Annu. Rev. Genet. 53, 445–482 (2019).
Schwartzer, W. et al. Two independent modes of chromatin organization revealed by cohesin removal. Nature 551, 51–56 (2017).
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).
Haarhuis, J. H. et al. The cohesin release factor WAPL restricts chromatin loop extension. Cell 169, 693–707 (2017).
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).
Zhu, Y. et al. Comprehensive characterization of neutrophil genome topology. Genes Dev. 31, 141–153 (2017).
Grieshaber-Bouyer, R. et al. The neutrotime transcriptional signature defines a single continuum of neutrophils across biological compartments. Nat. Commun. 12, 2856 (2021).
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).
Nabet, B. et al. The dTAG system for immediate and target-specific protein degradation. Nat. Chem. Biol. 14, 431–441 (2018).
Khoyratty, T. E. et al. Distinct transcription factor networks control neutrophil-driven inflammation. Nat. Immunol. 22, 1093–1106 (2021).
Hu, Y. et al. Super-enhancer reprogramming drives a B cell-epithelial transition and high-risk leukemia. Genes Dev. 30, 1971–1990 (2016).
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).
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).
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).
Li, M. T. et al. Negative regulation of RIG-I mediated innate antiviral signaling by SEC14L1. J. Virol. 87, 10037-46 (2013).
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).
Chao, W. C. H. et al. Structural studies reveal the functional modularity of the Scc2-Scc4 cohesin loader. Cell Rep. 12, 719–725 (2015).
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).
Hendel, A. et al. Chemically modified guide RNAs enhance CRISPR–Cas genome editing in human primary cells. Nat. Biotechnol. 33, 985–989 (2015).
Xie, X. et al. Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection. Nat. Immunol. 21, 1119–1133 (2020).
Rao, S. S. et al. Cohesin loss eliminates all loop domains. Cell 171, 305–320 (2017).
Calderon, L. et al. Cohesin-dependence of neuronal gene expression relates to chromatin loop length. eLife 11, e76539 (2022).
Cuartero, S. et al. Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation. Nat. Immunol. 9, 932–941 (2018).
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).
Mohana, G. et al. Chromosome-level organization of the regulatory genome in the Drosophila nervous system. Cell 186, 3826–3844 (2023).
Bashkirova, E. & Lomvardas, S. Olfactory receptor genes make the case for inter-chromosomal interactions. Curr. Opin. Genet. Dev. 55, 106–113 (2019).
Hu, Y. et al. Lineage specific 3D genome organization is assembled at multiple scales by Ikaros. Cell 186, 5260–5289 (2023).
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).
Robinson, M. D. et al. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 26, 139–40 (2010).
Raudvere, U. et al. gProfiler: a web server for functional enrichment analysis and conversion of gene lists. Nucleic Acids Res. 47, W191–W198 (2019).
Yu, G., Wang, L. & He, Q. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 31, 2382–2383 (2015).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Zhang, et al. Fast alignment and preprocessing of chromatin profiles with Chromap. Nat. Commun. 12, 6566 (2021).
Yang, et al.HiCRep: assessing the reproducibility of HiC data using a stratum-adjusted correlation coefficient. Genome Res. 11, 1939–1949 (2017).
Kuleshov, M. V. et al. Enrichr: a comprehensive gene set enrichment analysis web served 2016 update. Nucleic Acids Res. 44, W90–W97 (2016).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).
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).
Lange, M. et al. CellRank for directed single-cell fate mapping. Nat. Methods 19, 159–170 (2022).
Gulati, G. S. et al. Single-cell transcriptional diversity is a hallmark of developmental potential. Science 367, 405–411 (2020).
Source link