Genome-wide analysis of gene expression articles within Nature Communications

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  • Article
    | Open Access

    The cereal endosperm constitutes most of the grain by volume. Here the authors use single-cell analysis of maize developing endosperm to decode gene regulatory networks that likely control endosperm growth and offer a framework for crop improvement.

    • Yue Yuan
    • , Qiang Huo
    •  & Zeyang Ma

  • Article
    | Open Access

    Long-read single-cell RNA isoform sequencing can elucidate the intricate landscape of alternative RNA splicing in individual cells, but it suffers from a low read throughput. Here, the authors develop circular consensus sequencing methods to allow high-throughput and high-accuracy single-cell RNA isoform sequencing.

    • Zhuo-Xing Shi
    • , Zhi-Chao Chen
    •  & Yi-Zhi Liu

  • Article
    | Open Access

    Here the authors present their method ‘regulon identification by in vitro transcription-sequencing’ (RIViT-seq), which enables systematic identification of target genes of transcription factors of interest. They applied RIViT-seq to 13 sigma factors from Streptomyces coelicolor A3(2) and successfully identified target genes of 11 of these, expanding the regulatory characterisation in this organism.

    • Hiroshi Otani
    •  & Nigel J. Mouncey

  • Article
    | Open Access

    Global transcriptional differences across lobular units in the liver remain unknown. Here the authors perform spatial transcriptomics of liver tissue to delineate transcriptional differences in physical space, confirm lobular zonation along transcriptional gradients and suggest the presence of previously uncharacterized structures within liver tissue.

    • Franziska Hildebrandt
    • , Alma Andersson
    •  & Johan Ankarklev

  • Article
    | Open Access

    Early stages of embryogenesis are known to depend on subcellular localization and transport of maternal mRNA, but systematic analyses have been hindered by a lack of methods for tracking of RNA. Here the authors combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development, revealing insights into this process.

    • Karoline Holler
    • , Anika Neuschulz
    •  & Jan Philipp Junker

  • Article
    | Open Access

    Glucocorticoid receptors (GR) are thought to bind DNA as dimers or monomers, to regulate different transcription pathways. Here, the authors perform genome-wide studies on GRs with mutations that impair dimerization and provide evidence that monomeric GRs do not play a significant physiologic role.

    • Thomas A. Johnson
    • , Ville Paakinaho
    •  & Diego M. Presman

  • Article
    | Open Access

    Droplet-based high throughput single cell sequencing techniques can often lose information on transcript splicing and heterogenity. Here the authors introduce ScNaUmi-seq, which uses Oxford Nanopore sequencing and barcoding to generate high accuracy full length sequences.

    • Kevin Lebrigand
    • , Virginie Magnone
    •  & Rainer Waldmann

  • Article
    | Open Access

    Early life exposure to environmental stressors, including endocrine disrupting chemicals (EDCs), can impact health later in life. Here, the authors show that neonatal EDC exposure in rats causes epigenetic reprogramming in the liver, which is transcriptionally silent until animals are placed on a Western-style diet.

    • Lindsey S. Treviño
    • , Jianrong Dong
    •  & Cheryl Lyn Walker

  • Article
    | Open Access

    In Drosophila the Male-Specific Lethal complex (MSLc) mediates upregulation of the single male X chromosome. Here the authors provide evidence that MSL2 also targets autosomal genes required for proper development and that MSL2 binds and similarly regulates mouse orthologues.

    • Claudia Isabelle Keller Valsecchi
    • , M. Felicia Basilicata
    •  & Asifa Akhtar

  • Article
    | Open Access

    Single-cell RNA-barcoding and sequencing is an efficient, genome-wide method to characterize cellular identities. Here the authors systematically evaluate the protocol and develop molecular crowding SCRB-seq with improved sensitivity and cost-efficiency.

    • Johannes W. Bagnoli
    • , Christoph Ziegenhain
    •  & Wolfgang Enard

  • Article
    | Open Access

    Neutrophils are abundant immune cells important for antimicrobial defence and in autoimmunity. Here, by mapping expression quantitative trait loci (eQTL) in neutrophils of Chinese ethnicity from Singapore, Andiappan et al.provide a resource for understanding immune-related trait associated genetic variants.

    • Anand Kumar Andiappan
    • , Rossella Melchiotti
    •  & Olaf Rotzschke

  • Article |

    Genes are often transcribed in random bursts followed by long periods of inactivity. Here the authors show, by a light-inducible transcription system in Neurospora, that refractory promoters carry a physical memory of their previous transcription history.

    • François Cesbron
    • , Michael Oehler
    •  & Michael Brunner

  • Article |

    As important post-transcriptional regulators of gene expression, microRNAs play a key role in the generation of complex phenotypes. Here, Huan et al.identify miR-eQTLs in whole blood samples to create a roadmap linking regulation of microRNA expression to complex diseases.

    • Tianxiao Huan
    • , Jian Rong
    •  & Jane E. Freedman

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