Gene regulatory networks articles within Nature

Featured

  • Article |

    A context-aware, attention-based deep learning model pretrained on single-cell transcriptomes enables predictions in settings with limited data in network biology and could accelerate discovery of key network regulators and candidate therapeutic targets.

    • Christina V. Theodoris
    • , Ling Xiao
    •  & Patrick T. Ellinor

  • Article
    | Open Access

    A machine-learning-based strategy called CellOracle combines computational perturbation with modelling of gene-regulatory networks to analyse how cell identity is regulated by transcription factors, and correctly predicts phenotypic changes after transcription factor perturbation in the developing zebrafish.

    • Kenji Kamimoto
    • , Blerta Stringa
    •  & Samantha A. Morris

  • 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 |

    A chromatin accessibility atlas of 240,919 cells in the adult and developing Drosophila brain reveals 95,000 enhancers, which are integrated in cell-type specific enhancer gene regulatory networks and decoded into combinations of functional transcription factor binding sites using deep learning.

    • Jasper Janssens
    • , Sara Aibar
    •  & Stein Aerts

  • Letter |

    Single-nucleus RNA sequencing analysis identifies different subclusters of oligodendroglia in white matter from individuals with multiple sclerosis compared with controls, and these differences may be important for understanding disease progression.

    • Sarah Jäkel
    • , Eneritz Agirre
    •  & Gonçalo Castelo-Branco

  • Letter |

    Embryos in a particular phylum of the animal kingdom tend to most resemble one another at a stage in the middle of embryogenesis known as the phylotypic period; a transcriptional analysis of embryogenesis from single embryos of ten different phyla reveals that the transcripts expressed at the phylotypic stage (or mid-developmental transition) differ greatly between phyla, and a ‘phylum’ may be defined as a set of species sharing the same signals and transcription factor networks during the mid-developmental transition.

    • Michal Levin
    • , Leon Anavy
    •  & Itai Yanai

  • Article |

    Genomic studies of the paediatric brain tumour medulloblastoma have revealed four clinically distinct molecular subgroups; here active gene regulatory elements in 28 primary medulloblastoma tissues are mapped to reveal differentially regulated enhancers across the different subgroups, allowing insights into the transcription factors that characterize subgroup divergence and the cellular origin of the poorly characterized Group 3 and 4 subgroups.

    • Charles Y. Lin
    • , Serap Erkek
    •  & Paul A. Northcott

  • Article
    | Open Access

    An analysis of genome-wide chromatin interactions during human embryonic stem cell differentiation reveals changes in chromatic organization and simultaneously identifies allele-resolved chromatin structure and differences in gene expression during differentiation.

    • Jesse R. Dixon
    • , Inkyung Jung
    •  & Bing Ren

  • Letter
    | Open Access

    A map of genome-wide binding locations of 165 human, 93 worm and 52 fly transcription-regulatory factors (almost 50% presented for the first time) from diverse cell types, developmental stages, or conditions reveals that gene-regulatory properties previously observed for individual factors may be general principles of metazoan regulation that are well preserved.

    • Alan P. Boyle
    • , Carlos L. Araya
    •  & Michael Snyder

  • Article |

    A study from the FANTOM consortium using single-molecule cDNA sequencing of transcription start sites and their usage in human and mouse primary cells, cell lines and tissues reveals insights into the specificity and diversity of transcription patterns across different mammalian cell types.

    • Alistair R. R. Forrest
    • , Hideya Kawaji
    •  & Yoshihide Hayashizaki

  • 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 |

    A novel approach to analyse high-depth Hi-C data provides a comprehensive chromatin interaction map at approximately 5–10 kb resolution in human fibroblasts; this reveals that TNF-α-responsive enhancers are already in contact with target promoters before signalling and that this chromatin looping is a strong predictor of gene induction.

    • Fulai Jin
    • , Yan Li
    •  & Bing Ren

  • Article |

    This study reports a global analysis of binding sites for over 200 RNA-binding proteins (RBPs) from 24 species; conserved RNA-binding motifs are identified, and their analysis allows prediction of interaction sites based on the sequence of the RNA-binding domain alone.

    • Debashish Ray
    • , Hilal Kazan
    •  & Timothy R. Hughes

  • Article |

    Local adaptations are often governed by several interacting genes scattered throughout the genome. Here a novel type of multi–locus genetic variation is described that has been maintained within a species over a vast period of time. A balanced unlinked gene network polymorphism is dissected that involves galactose utilization in a close relative of baker's yeast.

    • Chris Todd Hittinger
    • , Paula Gonçalves
    •  & Antonis Rokas

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