Gene expression articles within Nature

Featured

  • 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 |

    Detailed mechanistic insight into fetal globin gene induction during hypoxia-associated stress erythropoiesis provides new therapeutic approaches to treat β-haemoglobinopathies, such as sickle cell disease and β-thalassaemia.

    • Ruopeng Feng
    • , Thiyagaraj Mayuranathan
    •  & Mitchell J. Weiss

  • Article
    | Open Access

    A multi-omic atlas of brain organoid development facilitates the inference of an underlying gene regulatory network using the newly developed Pando framework and shows—in conjunction with perturbation experiments—that GLI3 controls forebrain fate establishment through interaction with HES4/5 regulomes.

    • Jonas Simon Fleck
    • , Sophie Martina Johanna Jansen
    •  & Barbara Treutlein

  • 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

  • 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 |

    Mapping enhancer regulation across human cell types and tissues illuminates genome function and provides a resource to connect risk variants for common diseases to their molecular and cellular functions.

    • Joseph Nasser
    • , Drew T. Bergman
    •  & Jesse M. Engreitz

  • Article |

    An ultra-high-throughput multiplex protein–DNA binding assay is used to assess binding of 270 human transcription factors to 95,886 noncoding variants in the human genome, providing data to improve prediction of the effects of noncoding variants on transcription factor binding and thereby increase understanding of molecular pathways involved in diverse human traits and genetic diseases.

    • Jian Yan
    • , Yunjiang Qiu
    •  & Bing Ren

  • Article |

    An analysis using ribosome-profiling and matched RNA-sequencing data for three organs across five mammalian species and a bird enables the comparison of translatomes and transcriptomes, revealing patterns of co-evolution of these two expression layers.

    • Zhong-Yi Wang
    • , Evgeny Leushkin
    •  & Henrik Kaessmann

  • Article
    | Open Access

    Single-cell and single-nucleus RNA sequencing are used to construct a cellular atlas of the human heart that will aid further research into cardiac physiology and disease.

    • Monika Litviňuková
    • , Carlos Talavera-López
    •  & Sarah A. Teichmann

  • 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 |

    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 |

    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 |

    A genetic atlas of the human plasma proteome, comprising 1,927 genetic associations with 1,478 proteins, identifies causes of disease and potential drug targets.

    • Benjamin B. Sun
    • , Joseph C. Maranville
    •  & Adam S. Butterworth

  • Letter |

    RNA polymerase III is a key evolutionarily conserved regulator of longevity that may have potential as a therapeutic target for age-related conditions.

    • Danny Filer
    • , Maximillian A. Thompson
    •  & Nazif Alic

  • 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 |

    Gene expression analysis in brain tissue from individuals with and without autism spectrum disorder (ASD) suggests that the transcription factor SOX5 contributes to an ASD-associated reduction in transcriptional differences between brain areas and indicates that common transcriptomic changes occur in different forms of ASD.

    • Neelroop N. Parikshak
    • , Vivek Swarup
    •  & Daniel H. Geschwind

  • Letter |

    Atherosclerotic lesions in mice and humans switch on a ‘don’t eat me’ signal—expression of CD47—that prevents effective removal of diseased tissue; anti-CD47 antibody therapy can normalize this defective efferocytosis, with beneficial results in several mouse models of atherosclerosis.

    • Yoko Kojima
    • , Jens-Peter Volkmer
    •  & Nicholas J. Leeper

  • Letter |

    Preclinical evaluation and optimization of mitochondrial replacement therapy reveals that a modified form of pronuclear transfer is likely to give rise to normal pregnancies with a reduced risk of mitochondrial DNA disease, but may need further modification to eradicate the disease in all cases.

    • Louise A. Hyslop
    • , Paul Blakeley
    •  & Mary Herbert

  • Letter |

    Translation termination sequences are occasionally bypassed by the ribosome and the resulting proteins can be detrimental to the cell; here it is shown that cells can prevent such proteins from accumulating through peptides that are encoded within the 3' UTR of genes in both humans and C. elegans.

    • Joshua A. Arribere
    • , Elif S. Cenik
    •  & Andrew Z. Fire

  • Letter |

    Splicing factors such as BUD31 are identified in a synthetic-lethal screen with cells overexpressing the transcription factor MYC; oncogenic MYC leads to an increase in pre-mRNA synthesis, and spliceosome inhibition impairs the growth and tumorigenicity of MYC-dependent breast cancers, suggesting that spliceosome components may be potential therapeutic targets for MYC-driven cancers.

    • Tiffany Y.-T. Hsu
    • , Lukas M. Simon
    •  & Thomas F. Westbrook

  • Letter |

    Quantifying activity of cis-regulatory sequences controlling gene expression shows that selection on expression noise has a greater impact on sequence variation than selection on mean expression level.

    • Brian P. H. Metzger
    • , David C. Yuan
    •  & Patricia J. Wittkopp

  • Letter
    | Open Access

    As part of the Epigenome Roadmap project, this study uses a chromosome-spanning haplotype reconstruction strategy to construct haplotype-resolved epigenomic maps for a diverse set of human tissues; the maps reveal extensive allelic biases in chromatin state and transcription, which vary across individuals due to genetic backgrounds.

    • Danny Leung
    • , Inkyung Jung
    •  & Bing Ren

  • Letter |

    Disruption of lignin biosynthesis has been proposed as a way to improve forage and bioenergy crops, but it can result in stunted growth and developmental abnormalities; here, the undesirable features of one such manipulation are shown to depend on the transcriptional co-regulatory complex Mediator.

    • Nicholas D. Bonawitz
    • , Jeong Im Kim
    •  & Clint Chapple

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