Transcriptomics

  • Article
    | Open Access

    RNA sequencing reveals widespread transcriptomic changes across the cerebral cortex in autism spectrum disorder, including primary sensory regions, in addition to association regions, as well as an attenuation of regional identity.

    • Michael J. Gandal
    • , Jillian R. Haney
    •  & Daniel H. Geschwind
  • 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 |

    A time-resolved high-resolution map of human cardiac remodelling after myocardial infarction, integrating single-cell transcriptomic, chromatin accessibility and spatial transcriptomic data, provides a valuable resource for the field.

    • Christoph Kuppe
    • , Ricardo O. Ramirez Flores
    •  & Rafael Kramann
  • Article |

    cis-RNA editing quantitative trait loci, which are associated with immunogenic double-stranded RNAs, underlie genome-wide association study variants in common autoimmune and inflammatory diseases.

    • Qin Li
    • , Michael J. Gloudemans
    •  & Jin Billy Li
  • Article |

    The systematic categorization of human enhancers by their cofactor dependencies provides a conceptual framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes.

    • Christoph Neumayr
    • , Vanja Haberle
    •  & Alexander Stark
  • Article
    | Open Access

    Experiments in yeast show that introns have a role in inducing phenotypic heterogeneity and that intron-mediated regulation of ribosomal proteins confers a fitness advantage by enabling yeast populations to diversify under nutrient-scarce conditions.

    • Martin Lukačišin
    • , Adriana Espinosa-Cantú
    •  & Tobias Bollenbach
  • Article |

    A transcriptomics study demonstrates cell-type-specific responses to differentially aged blood and shows young blood to have restorative and rejuvenating effects that may be invoked through enhanced mitochondrial function.

    • Róbert Pálovics
    • , Andreas Keller
    •  & Tony Wyss-Coray
  • Article |

    A study describes single-cell characterization of the human cerebrovasculature, revealing human-specific transcriptomic signatures and providing insights into transcriptional changes associated with Huntington’s disease.

    • Francisco J. Garcia
    • , Na Sun
    •  & Myriam Heiman
  • Review Article |

    This review describes the state of spatial transcriptomics technologies and analysis tools that are being used to generate biological insights in diverse areas of biology.

    • Anjali Rao
    • , Dalia Barkley
    •  & Itai Yanai
  • Article |

    A comprehensive single-cell transcriptomic atlas of the mouse brain between gastrulation and birth identifies hundreds of cellular states and reveals the spatiotemporal organization of brain development.

    • Gioele La Manno
    • , Kimberly Siletti
    •  & Sten Linnarsson
  • Article |

    Single-nucleus transcriptomes of frontal cortex and choroid plexus samples from patients with COVID-19 reveal pathological cell states that are similar to those associated with human neurodegenerative diseases and chronic brain disorders.

    • Andrew C. Yang
    • , Fabian Kern
    •  & Tony Wyss-Coray
  • Article |

    Single-nucleus RNA-sequencing analyses of brain from humans, macaques, marmosets, mice and ferrets reveal diverse ways that interneuron populations have changed during evolution.

    • Fenna M. Krienen
    • , Melissa Goldman
    •  & Steven A. McCarroll
  • Article |

    Single-cell RNA-sequencing analysis of embryogenesis and X chromosome inactivation in the opossum (Monodelphis domestica) resolves the developmental trajectory of a marsupial, and sheds light on the evolution of embryogenesis in mammals.

    • Shantha K. Mahadevaiah
    • , Mahesh N. Sangrithi
    •  & James M. A. Turner
  • Perspective |

    The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

    • Federico Abascal
    • , Reyes Acosta
    •  & Richard M. Myers
  • Article
    | Open Access

    ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.

    • E. Christopher Partridge
    • , Surya B. Chhetri
    •  & Eric M. Mendenhall
  • Article |

    Bulk RNA sequencing of organs and plasma proteomics at different ages across the mouse lifespan is integrated with data from the Tabula Muris Senis, a transcriptomic atlas of ageing mouse tissues, to describe organ-specific changes in gene expression during ageing.

    • Nicholas Schaum
    • , Benoit Lehallier
    •  & Tony Wyss-Coray
  • Article
    | Open Access

    Single-cell RNA sequencing identifies the pattern of gene expression during lineage progression in endosymbiotic cells of the fast-growing soft coral Xenia, revealing principles that underlie uptake and maintenance of endosymbionts by this coral.

    • Minjie Hu
    • , Xiaobin Zheng
    •  & Yixian Zheng
  • Article
    | Open Access

    A novel variant annotation metric that quantifies the level of expression of genetic variants across tissues is validated in the Genome Aggregation Database (gnomAD) and is shown to improve rare variant interpretation.

    • Beryl B. Cummings
    • , Konrad J. Karczewski
    •  & Daniel G. MacArthur
  • Article |

    Single-cell RNA sequencing is used to generate a dataset covering all major human organs in both adult and fetal stages, enabling comparison with similar datasets for mouse tissues.

    • Xiaoping Han
    • , Ziming Zhou
    •  & Guoji Guo
  • Letter |

    Species of the eukaryotic phylum Rhodelphidia are non-photosynthetic, flagellate predators with gene-rich genomes, in contrast to their closely related sister lineage—the red algae—which are immotile, typically photoautotrophic and have relatively small intron-poor genomes and reduced metabolism.

    • Ryan M. R. Gawryluk
    • , Denis V. Tikhonenkov
    •  & Patrick J. Keeling
  • Article |

    Comprehensive single-cell transcriptomes in the proto-vertebrate Ciona intestinalis identified provisional gene networks for 41 different neural subtypes, providing insights into the swimming circuit of tadpoles and the evolution of the vertebrate telencephalon.

    • Chen Cao
    • , Laurence A. Lemaire
    •  & Kai Chen
  • Article |

    A transcriptome dataset from seven organs and seven mammalian species throughout development is used to analyse the expression of long noncoding RNAs in tissues within and between species, and at different stages of organ development.

    • Ioannis Sarropoulos
    • , Ray Marin
    •  & Henrik Kaessmann
  • Article |

    Data from single-cell combinatorial-indexing RNA-sequencing analysis of 2 million cells from mouse embryos between embryonic days 9.5 and 13.5 are compiled in a cell atlas of mouse organogenesis, which provides a global view of developmental processes occurring during this critical period.

    • Junyue Cao
    • , Malte Spielmann
    •  & Jay Shendure
  • Article |

    A set of 34 excised introns in Saccharomyces cerevisiae, characterized by having a short distance between the lariat branch point and the 3′ splice site, have a biological function within the TOR growth-signalling network.

    • Jeffrey T. Morgan
    • , Gerald R. Fink
    •  & David P. Bartel
  • Letter |

    Allele-specific single-cell RNA sequencing provides insights into transcription kinetics, with data indicating that core promoter sequences affect burst size, whereas enhancers mainly affect burst frequency.

    • Anton J. M. Larsson
    • , Per Johnsson
    •  & Rickard Sandberg
  • Letter |

    Ikzf2, which encodes the transcription factor Helios, is identified as a crucial regulator of gene expression in maturing cochlear outer hair cells, and overexpression of Ikzf2 in inner hair cells induces prestin expression and electromotility.

    • Lauren Chessum
    • , Maggie S. Matern
    •  & Ronna Hertzano
  • Article |

    Single-cell transcriptomics of more than 20,000 cells from two functionally distinct areas of the mouse neocortex identifies 133 transcriptomic types, and provides a foundation for understanding the diversity of cortical cell types.

    • Bosiljka Tasic
    • , Zizhen Yao
    •  & Hongkui Zeng
  • Article |

    Profiling of 53,193 individual epithelial cells from the mouse small intestine identifies previously unknown cell subtypes and corresponding gene markers, providing insight into gut homeostasis and response to pathogens.

    • Adam L. Haber
    • , Moshe Biton
    •  & Aviv Regev
  • Article
    | Open Access

    Samples of different body regions from hundreds of human donors are used to study how genetic variation influences gene expression levels in 44 disease-relevant tissues.

    • François Aguet
    • , Andrew A. Brown
    •  & Jingchun Zhu
  • Letter |

    Using the GTEx data and others, a comprehensive analysis of adenosine-to-inosine RNA editing in mammals is presented; targets of the various ADAR enzymes are identified, as are several potential regulators of editing, such as AIMP2.

    • Meng How Tan
    • , Qin Li
    •  & Jin Billy Li