Gene regulation in immune cells articles within Nature

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  • Article |

    Single-cell and spatial gene expression analyses of pancreatic ductal adenocarcinoma uncover a population of interleukin-1β-expressing macrophages that drive inflammatory reprogramming of neighboring tumour cells leading to disease progression and poor prognosis for patients.

    • Nicoletta Caronni
    • , Federica La Terza
    •  & Renato Ostuni

  • Article |

    Multiomic analyses of mouse thymic epithelial cells identify several unconventional subsets that are mimetics of various populations of terminally differentiated parenchymal cells and provide insights into their development, molecular features and function.

    • Tal Givony
    • , Dena Leshkowitz
    •  & Jakub Abramson

  • Article
    | Open Access

    Population differences in immune responses to SARS-CoV-2 can be explained by environmental exposures, but also by local adaptation acting through genetic variants acquired after admixture with archaic hominin forms.

    • Yann Aquino
    • , Aurélie Bisiaux
    •  & Lluis Quintana-Murci

  • Article
    | Open Access

    CD62L+ precursors of exhausted T cells retain long-term proliferative potential, multipotency and repopulation capacity, and the transcription factor MYB is essential for the development and function of this population of cells.

    • Carlson Tsui
    • , Lorenz Kretschmer
    •  & Axel Kallies

  • Article |

    A subset of group 3 innate lymphoid cells (ILC3s) expresses the transcription factor ZBTB46—which was previously thought to be restricted to conventional dendritic cells—and these ILC3s have a role in regulating intestinal health.

    • Wenqing Zhou
    • , Lei Zhou
    •  & Gregory F. Sonnenberg

  • Article |

    NOD2 deficiency drives fibrosis and stricturing complications in Crohn’s disease through dysregulated homeostasis of activated fibroblasts and macrophages, which is ameliorated by gp130 blockade in human cell and zebrafish models.

    • Shikha Nayar
    • , Joshua K. Morrison
    •  & Judy H. Cho

  • Article |

    Experiments using a conditional triple-knockout mouse strain show that histone H1 regulates the activity of chromatin domains by controlling chromatin compaction, genome architecture and  histone methylation.

    • Michael A. Willcockson
    • , Sean E. Healton
    •  & Arthur I. Skoultchi

  • Article |

    During the activation of mouse macrophages by lipopolysaccharides, histone deacetylase 3 controls inflammatory responses by both repressing and activating gene transcription depending on its differential association with transcription factors.

    • Hoang C. B. Nguyen
    • , Marine Adlanmerini
    •  & Mitchell A. Lazar

  • Article |

    The histone variant H3.3 is phosphorylated at Ser31 in induced genes, and this selective mark stimulates the histone methyltransferase SETD2 and ejects the ZMYND11 repressor, thus revealing a role for histone phosphorylation in amplifying de novo transcription.

    • Anja Armache
    • , Shuang Yang
    •  & Steven Z. Josefowicz

  • Article |

    Shared synteny guides loss-of-function analysis of human enhancer homologues in mice, identifying a distal enhancer at the autoimmune and allergic disease risk locus at chromosome 11q13.5 whose function in regulatory T cells provides a mechanistic basis for its role in disease.

    • Rabab Nasrallah
    • , Charlotte J. Imianowski
    •  & Rahul Roychoudhuri

  • Article |

    A CRISPR-based screening platform was used to identify previously uncharacterized genes that regulate the regulatory T cell-specific master transcription factor Foxp3, indicating that this screening method may be broadly applicable for the discovery of other genes involved in autoimmunity and immune responses to cancer.

    • Jessica T. Cortez
    • , Elena Montauti
    •  & Deyu Fang

  • Article |

    Visceral adipose tissue contains populations of regulatory T cells that exhibit sexual dimorphism, determined by the surrounding niche, and differ between male and female mice in terms of cell number, phenotype, transcriptional landscape and chromatin accessibility.

    • Ajithkumar Vasanthakumar
    • , David Chisanga
    •  & Axel Kallies

  • Letter |

    Transfer of NR4A-deficient T cells expressing chimeric antigen receptors is shown to reduce tumour burden and increase survival by shifting T cell transcriptional programs away from exhaustion and towards increased effector function.

    • Joyce Chen
    • , Isaac F. López-Moyado
    •  & Anjana Rao

  • Article |

    The ability of the DEAD-box RNA helicase DDX5 to interact with master transcription factor RORγt is dependent on binding of the long noncoding RNA Rmrp; the DDX5–RORγt complex coordinates transcription of selective TH17 genes and is required for the pathogenicity of TH17 cells.

    • Wendy Huang
    • , Benjamin Thomas
    •  & Dan R. Littman

  • Letter |

    Immunoglobulin genes are expressed from either the maternal or paternal chromosome; it is now shown that in early haematopoietic stem cells, an individual cell can choose either of the two alleles, but as they develop they become committed to only one.

    • Marganit Farago
    • , Chaggai Rosenbluh
    •  & Yehudit Bergman

  • Letter |

    The pleiotropic transcription factor IRF4 is shown to regulate CD4+ T-cell differentiation and TH17 function through cooperative binding interactions with BATF and JUN family proteins via AP1–IRF4 composite elements (AICEs).

    • Peng Li
    • , Rosanne Spolski
    •  & Warren J. Leonard

  • Letter |

    Double-stranded RNA-dependent protein kinase (PKR) is shown to be a key regulator of the inflammasome; PKR is central for caspase-1 activation and the release of interleukin (IL)-1β, IL-18 and high-mobility group box 1 (HMGB1) in response to a diverse range of stimuli.

    • Ben Lu
    • , Takahisa Nakamura
    •  & Kevin J. Tracey

  • Letter |

    The histone modification H3K9me3, the histone methyltransferase SUV39H1 and the H3K9me3-binding protein HP1α participate in maintaining the silent state of the two canonical T helper 1 cell signature genes (which encode interferon-γ and T-bet), ensuring T helper 2 lineage stability in vitro and in vivo; targeting this pathway has the potential to reduce asthma-related pathology.

    • Rhys S. Allan
    • , Elina Zueva
    •  & Sebastian Amigorena

  • Article |

    After introducing the T-cell receptor and other essential signalling genes, a non-immune cell is capable of displaying the early events of T-cell activation when placed in contact with antigen-presenting cells, and the initial signalling in this reconstituted system is shown to require the spatial reorganization of molecules at the cell interface.

    • John R. James
    •  & Ronald D. Vale

  • Outlook |

    Some people get horribly sick from the flu, and even die. Others just rest for a few days. What's behind this fateful variation?

    • Christine Junge

  • Letter |

    Activation of inflammatory gene expression by toll-like receptor (TLR) signalling pathways involves the removal of gene repression complexes such as NCoR. Here, coronin 2A, a component of the NCoR complex, is shown to mediate TLR-induced NCoR turnover and de-repression of inflammatory genes by a mechanism involving interaction with oligomeric nuclear actin.

    • Wendy Huang
    • , Serena Ghisletti
    •  & Christopher K. Glass

  • Letter |

    CD4+ T cells that selectively produce interleukin (IL)-17 (TH17 cells) are essential for host defence and autoimmunity. It has been thought that IL-6 and transforming growth factor (TGF)-β1 are the factors responsible for initiating the specification of TH17 cells. Here, however, it is shown that TH17 differentiation can occur in the absence of TGF-β signalling. IL-6, IL-23 and IL-1β effectively induced IL-17 production in naive precursors. These data reveal an alternative mode for TH17 differentiation and the importance of IL-23.

    • Kamran Ghoreschi
    • , Arian Laurence
    •  & John J. O’Shea

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