Sequence annotation articles within Nature

Featured

  • Perspective |

    Although the catalogue of human protein-coding genes is nearing completion, the number of non-coding RNA genes remains highly uncertain, and for all genes much work remains to be done to understand their functions.

    • Paulo Amaral
    • , Silvia Carbonell-Sala
    •  & Steven L. Salzberg

  • Article
    | Open Access

    Conditional genetic ferret models enable ionocyte lineage tracing, ionocyte ablation and ionocyte-specific deletion of CFTR to elucidate the roles of pulmonary ionocyte biology and function during human health and disease.

    • Feng Yuan
    • , Grace N. Gasser
    •  & John F. Engelhardt

  • Article
    | Open Access

    The extent to which the AlphaFold database has structurally illuminated proteins that are challenging to annotate for function or putative biological role using standard homology-based approaches at high predicted accuracy is investigated.

    • Janani Durairaj
    • , Andrew M. Waterhouse
    •  & Joana Pereira

  • Article |

    A computational system termed MetaWIBELE (workflow to identify novel bioactive elements in the microbiome) is used to identify microbial gene products that are potentially bioactive and have a functional role in the pathogenesis of inflammatory bowel disease.

    • Yancong Zhang
    • , Amrisha Bhosle
    •  & Eric A. Franzosa

  • Article |

    A comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin structure, the methylome and 3D genome organization in the zebrafish (Danio rerio) enables identification of species-specific and evolutionarily conserved regulatory features, and provides a foundation for modelling studies on human disease and development.

    • Hongbo Yang
    • , Yu Luan
    •  & Feng Yue

  • Letter |

    Highly conserved recursive splice sites are identified in vertebrates, particularly within long genes encoding proteins that are involved in neuronal development; analysis of the splicing mechanism reveals that such recursive splicing sites can be used to dictate different mRNA isoforms.

    • Christopher R. Sibley
    • , Warren Emmett
    •  & Jernej Ule

  • Article |

    A study comparing the Y chromosome across mammalian species reveals that selection to maintain the ancestral dosage of homologous X–Y gene pairs preserved a handful of genes on the Y chromosome while the rest were lost; the survival of broadly expressed dosage-sensitive regulators of gene expression suggest that the human Y chromosome is essential for male viability.

    • Daniel W. Bellott
    • , Jennifer F. Hughes
    •  & David C. Page

  • Letter |

    As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans, this study created a map of the regulatory part of the fruitfly genome. On the basis of the developmental dynamics of chromatin modifications, polymerase and transcription factor occupancy this work defines a vast array of putative regulatory elements, such as enhancers, promoters, insulators and silencers. This resource represents the first attempt at a comprehensive annotation of cis-regulatory elements in a metazoan genome.

    • Nicolas Nègre
    • , Christopher D. Brown
    •  & Kevin P. White

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