RNA sequencing articles within Nature

Featured

  • Article |

    Genomics analyses reveal that in vitro culture of CAR T cells can lead to reactivation of a latent herpesvirus, which might be involved in complications in patients receiving associated cell therapies.

    • Caleb A. Lareau
    • , Yajie Yin
    •  & Ansuman T. Satpathy

  • Article
    | Open Access

    In situ spatial transcriptomic analysis of more than 1 million cells are used to create a 200-nm-resolution spatial molecular atlas of the adult mouse central nervous system and identify previously unknown tissue architectures.

    • Hailing Shi
    • , Yichun He
    •  & Xiao Wang

  • Article
    | Open Access

    The authors present two technologies for spatially resolved, genome-wide, joint profiling of the epigenome and transcriptome by cosequencing chromatin accessibility and gene expression, or histone modifications and gene expression on the same tissue section at near-single-cell resolution.

    • Di Zhang
    • , Yanxiang Deng
    •  & Rong Fan

  • 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

    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 |

    To understand the contribution of variants to transcript expression regulation, long-read transcriptome data are generated from the GTEx resource, and a new software package to perform allele-specific analysis is developed.

    • Dafni A. Glinos
    • , Garrett Garborcauskas
    •  & Beryl B. Cummings

  • Article |

    Time-resolved RNA–protein cross-linking with a pulsed femtosecond ultraviolet laser, followed by immunoprecipitation and high-throughput sequencing, enables the determination of binding and dissociation kinetics of the RNA-binding protein DAZL within cells.

    • Deepak Sharma
    • , Leah L. Zagore
    •  & Eckhard Jankowsky

  • Article |

    A method termed ac4C-seq is introduced for the transcriptome-wide mapping of the RNA modification N4-acetylcytidine, revealing widespread temperature-dependent acetylation that facilitates thermoadaptation in hyperthermophilic archaea.

    • Aldema Sas-Chen
    • , Justin M. Thomas
    •  & Schraga Schwartz

  • Article |

    Single-cell RNA sequencing and spatial transcriptomics reveal that the somitogenesis clock is active in mouse gastruloids, which can be induced to generate somites with the correct rostral–caudal patterning.

    • Susanne C. van den Brink
    • , Anna Alemany
    •  & Alexander van Oudenaarden

  • Article |

    Single-cell transcriptomic profiling of fetal liver, skin, kidney and yolk sac reveals the differentiation trajectories of human haematopoietic stem cells and multipotent progenitors, which are validated to produce an integrated map of fetal liver haematopoiesis.

    • Dorin-Mirel Popescu
    • , Rachel A. Botting
    •  & Muzlifah Haniffa

  • 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 |

    One hundred and ten Zika virus genomes from ten countries and territories involved in the Zika virus epidemic reveal rapid expansion of the epidemic within Brazil and multiple introductions to other regions.

    • Hayden C. Metsky
    • , Christian B. Matranga
    •  & Pardis C. Sabeti

  • 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 |

    A translation complex sequencing approach has been developed enabling intermediates of all mRNA-associated processes of translation to be isolated and localized across the transcriptome; the results support longstanding models of initiation and termination and offer new mechanistic insights.

    • Stuart K. Archer
    • , Nikolay E. Shirokikh
    •  & Thomas Preiss

  • Letter |

    Tumours can require certain amino acids for their proliferation, and the diricore method described here helps to identify such restrictive amino acids; using this method in kidney cancer tissue and breast carcinoma cells, the authors observe an association between proline deficiency and upregulation of PYCR1, an enzyme required for proline synthesis.

    • Fabricio Loayza-Puch
    • , Koos Rooijers
    •  & Reuven Agami

  • Letter |

    The mRNAs of higher eukaryotes are extensively modified internally with N6-methyladenosine, but the specific functional role of this modification has been unclear; here this modification on mRNA is shown to be recognized by several proteins, the modification and its recognition serve to regulate the RNA’s lifetime.

    • Xiao Wang
    • , Zhike Lu
    •  & Chuan He

  • Letter |

    Single-cell RNA sequencing is used to investigate the transcriptional response of 18 mouse bone-marrow-derived dendritic cells after lipopolysaccharide stimulation; many highly expressed genes, such as key immune genes and cytokines, show bimodal variation in both transcript abundance and splicing patterns. This variation reflects differences in both cell state and usage of an interferon-driven pathway involving Stat2 and Irf7.

    • Alex K. Shalek
    • , Rahul Satija
    •  & Aviv Regev

  • News |

    High-profile results challenged over statistical analysis of sequence data.

    • Erika Check Hayden

  • Article |

    A novel technique called native elongating transcript sequencing (NET-seq) is described, which can quantify transcription with single nucleotide resolution. It is based on sequencing nascent transcripts associated with RNA polymerase II that are captured directly from live cells, and is used to gain insights into polymerase pausing and backtracking and the directionality of transcription.

    • L. Stirling Churchman
    •  & Jonathan S. Weissman

  • Letter |

    There is much interest in understanding the genetic mechanisms that underlie individual variations in gene expression. Here, RNA sequencing has been used to study gene expression in lymphoblastoid cell lines derived from Nigerian individuals for whom extensive genotype information is known. Numerous genetic determinants of variation in gene expression were identified, including variation in transcription, splicing and allele-specific expression.

    • Joseph K. Pickrell
    • , John C. Marioni
    •  & Jonathan K. Pritchard

  • Letter |

    Here, sequencing has been used to characterize the mRNA fraction of the transcriptome in Caucasian individuals, to provide a fine-scale view of transcriptomes and to identify genetic variants that affect alternative splicing. Measuring allele-specific expression identified rare expression quantitative trait loci (eQTLs) and allelic differences in transcript structure, revealing new properties of genetic effects on the transcriptome.

    • Stephen B. Montgomery
    • , Micha Sammeth
    •  & Emmanouil T. Dermitzakis

  • Article |

    The transcriptome of Helicobacter pylori, an important human pathogen involved in gastric ulcers and cancer, is presented. The approach establishes a model for mapping and annotating the primary transcriptomes of many living species.

    • Cynthia M. Sharma
    • , Steve Hoffmann
    •  & Jörg Vogel

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