Gene expression profiling articles within Nature

Featured

  • Article
    | Open Access

    Using single-cell and spatial transcriptomics, human embryonic limb development across space and time and the diversification and cross-species conservation of cells are demonstrated.

    • Bao Zhang
    • , Peng He
    •  & Sarah A. Teichmann

  • Article |

    Integration of multiomics data with functional analysis of pancreatic tissues from individuals with early-stage type 2 diabetes indicates that the genetic risk converges on RFX6, which regulates chromatin architecture at multiple risk loci.

    • John T. Walker
    • , Diane C. Saunders
    •  & Marcela Brissova

  • Perspective |

    Technical developments and large collaborative research networks in neurogenomics promise rapid progress in neuroscience, but translation of results from model systems to human brains is limited by sample availability, technical challenges and ethical issues.

    • Genevieve Konopka
    •  & Aparna Bhaduri

  • Article
    | Open Access

    An in vivo single-cell CRISPR screening method identifies transcriptional phenotypes of 22q11.2 deletion syndrome associated with a broad dysregulation of a class of disease susceptibility genes that are important for RNA processing and synaptic function.

    • Antonio J. Santinha
    • , Esther Klingler
    •  & Randall J. Platt

  • Article
    | Open Access

    Evolutionary analyses of single-nucleus transcriptome data for testes from 11 species are reported, illuminating the molecular evolution of spermatogenesis and associated forces, and providing a resource for investigating the testis across mammals.

    • Florent Murat
    • , Noe Mbengue
    •  & Henrik Kaessmann

  • Article
    | Open Access

    Single-cell transcriptomic profiling and functional assays are used to identify subpopulations of eosinophils that are present in the mouse gastrointestinal tract and provide insight into the role of these cells in inflammatory bowel diseases in humans.

    • Alessandra Gurtner
    • , Costanza Borrelli
    •  & Isabelle C. Arnold

  • Article
    | Open Access

    Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy, can address a range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.

    • Wanze Chen
    • , Orane Guillaume-Gentil
    •  & Bart Deplancke

  • Article |

    To understand the contribution of variants to transcript expression regulation, long-read transcriptome data are generated from the GTEx resource, and a new software package to perform allele-specific analysis is developed.

    • Dafni A. Glinos
    • , Garrett Garborcauskas
    •  & Beryl B. Cummings

  • Article
    | Open Access

    Analyses of circulating cell-free RNA (cfRNA) in blood samples from pregnant mothers identify changes in gene expression that could be used in liquid biopsy tests to identify and monitor individuals who are at risk of preeclampsia.

    • Mira N. Moufarrej
    • , Sevahn K. Vorperian
    •  & Stephen R. Quake

  • Article |

    Single-cell RNA sequencing is used to characterize and compare the functional diversity of cells from liver biopsies of human scarred and normal liver, and identifies markers for scar-associated macrophages and endothelial cells.

    • P. Ramachandran
    • , R. Dobie
    •  & N. C. Henderson

  • Article |

    The transcriptomes of seven major organs across developmental stages from several mammalian species are used for comparative analyses of gene expression and evolution across organ development.

    • Margarida Cardoso-Moreira
    • , Jean Halbert
    •  & Henrik Kaessmann

  • Letter
    | Open Access

    The authors show that rare genetic variants contribute to large gene expression changes across diverse human tissues and provide an integrative method for interpretation of rare variants in individual genomes.

    • Xin Li
    • , Yungil Kim
    •  & Stephen B. Montgomery

  • Letter |

    This study demonstrates a role for the Integrator complex in the stimulus-dependent induction of eRNAs and their 3′ processing; together with previously known roles of Integrator in transcription elongation and RNA processing, these results indicate that Integrator has broad functions in the regulation of eukaryotic gene expression.

    • Fan Lai
    • , Alessandro Gardini
    •  & Ramin Shiekhattar

  • Article
    | Open Access

    A large-scale transcriptome analysis in Drosophila melanogaster, across tissues, cell types and conditions, provides insights into global patterns and diversity of transcription initiation, splicing, polyadenylation and non-coding RNA expression.

    • James B. Brown
    • , Nathan Boley
    •  & Susan E. Celniker

  • Article |

    Evolutionary study of long noncoding RNA (lncRNA) repertoires and expression patterns in 11 tetrapod species identifies approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have ancient origins; many lncRNAs, particularly ancient ones, are actively regulated and may function mainly in embryonic development.

    • Anamaria Necsulea
    • , Magali Soumillon
    •  & Henrik Kaessmann

  • Letter |

    Single-cell RNA sequencing is used to investigate the transcriptional response of 18 mouse bone-marrow-derived dendritic cells after lipopolysaccharide stimulation; many highly expressed genes, such as key immune genes and cytokines, show bimodal variation in both transcript abundance and splicing patterns. This variation reflects differences in both cell state and usage of an interferon-driven pathway involving Stat2 and Irf7.

    • Alex K. Shalek
    • , Rahul Satija
    •  & Aviv Regev

  • Letter |

    Genetic analysis of breakthrough infections in people vaccinated against HIV-1 show that vaccine efficacy increased by up to 80% against viruses carrying two mutations in Env V2, but also raises the possibility of population-level adaptation to the vaccine.

    • Morgane Rolland
    • , Paul T. Edlefsen
    •  & Jerome H. Kim

  • Outlook |

    Despite its rarity, multiple myeloma is an ideal testing ground for cancer biology, says William Matsui.

    • William Matsui

  • Article |

    A meta-analysis of genome-wide association studies in more than 66,000 individuals identifies 68 new genomic loci that reliably associate with platelet count and volume, and reveals new gene functions.

    • Christian Gieger
    • , Aparna Radhakrishnan
    •  & Nicole Soranzo

  • Letter |

    The blood–brain barrier (BBB) is made up of vascular endothelial cells and was thought to have formed postnatally from astrocytes. Two independent studies demonstrate that this barrier forms during embryogenesis, with pericyte/endothelial cell interactions being critical to regulate the BBB during development. A better understanding of the relationship among pericytes, neuroendothelial cells and astrocytes in BBB function will contribute to our understanding of BBB breakdown during central nervous system injury and disease.

    • Annika Armulik
    • , Guillem Genové
    •  & Christer Betsholtz

  • News |

    How human proteins are made from DNA can be followed in real time.

    • Brendan Borrell

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