Nuclear morphology is shaped by

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 

You May Also Like

More From Author

+ There are no comments

Add yours