Gene expression analysis articles within Nature Reviews Genetics

Featured

  • Journal Club |

    Mustafa Mir reflects on a 1976 paper by McKnight and Miller, in which they developed a technique to directly visualize gene regulatory dynamics.

    • Mustafa Mir

  • Research Highlight |

    The Farm Animal GTEx project introduces a new resource for pigs, in which they map genetic variation to differences in gene expression across thousands of samples.

    • Henry Ertl

  • Review Article |

    In this Review, Zhang et al. discuss how recent advances in computational methods are helping to reveal the multiscale features involved in genome folding within the nucleus and how the resulting 3D genome organization relates to genome function.

    • Yang Zhang
    • , Lorenzo Boninsegna
    •  & Jian Ma

  • Journal Club |

    Roser Vento-Tormo highlights the synergy of single-cell omics and organoids by Camp et al., who used single-cell RNA sequencing to characterize the cell–cell communication events driving tissue formation in human liver organoids.

    • Roser Vento-Tormo

  • Review Article |

    In this Review, the authors describe the emerging field of single-cell genetics, which lies at the intersection of single-cell genomics and human genetics. They review the first single-cell expression quantitative trait loci studies, which combine single-cell information with genotype data at the population scale and thereby link genetic variation to the cellular processes underpinning key aspects of human biology and disease.

    • Anna S. E. Cuomo
    • , Aparna Nathan
    •  & Joseph E. Powell

  • Review Article |

    In this Review, the authors discuss the latest advances in profiling multiple molecular modalities from single cells, including genomic, transcriptomic, epigenomic and proteomic information. They describe the diverse strategies for separately analysing different modalities, how the data can be computationally integrated, and approaches for obtaining spatially resolved data.

    • Katy Vandereyken
    • , Alejandro Sifrim
    •  & Thierry Voet

  • Research Highlight |

    Two new studies in Nature Biotechnology describe cellular recording systems that incorporate time-resolved optical signals into self-assembling protein filaments.

    • Darren J. Burgess

  • Research Highlight |

    A new study in Cell describes how topologically associating domains (TADs) of chromosomes can restructure to resolve the regulatory conflict that arises when a new gene incorporates into an ancestral TAD.

    • Darren J. Burgess

  • In Brief |

    In a paper in Nature, Hua et al. report the Micro-Capture-C method for near-base-pair resolution characterization of chromosomal interactions in mammalian cells.

    • Darren Burgess

  • Research Highlight |

    The GTEx consortium reports results from its third and final phase in several new papers. They provide unprecedented detail of human gene expression regulation across tissues.

    • Darren J. Burgess

  • Research Highlight |

    A study in Cell presents a new approach that increases resolution and throughput compared with existing imaging methods and provides insights into the relationship between transcription and the 3D genome.

    • Linda Koch

  • Research Highlight |

    A new study in Nature Methods presents the ‘ZipSeq’ spatial transcriptomics approach, whereby patterned illumination is used to print barcodes onto chosen tissue regions.

    • Darren J. Burgess

  • Research Highlight |

    A new study in Cell describes the CRISPR array repair lineage tracing (CARLIN) engineered mouse line that genomically encodes all the components for CRISPR-based lineage tracking at single-cell resolution.

    • Darren J. Burgess

  • Research Highlight |

    Two studies in Molecular Cell report fine-scale structural profiles of mammalian genomes using Micro-C, indicating that fine chromosomal structure is regulated by diverse transcription-related features.

    • Darren J. Burgess

  • Research Highlight |

    A study in Nature provides new insights into chromatin dynamics and allele-specific gene expression regulation during early mouse embryogenesis.

    • Linda Koch

  • Review Article |

    Understanding developmental trajectories has recently been enabled by progress in modern lineage-tracing methods that combine genetic lineage analysis with omics-based characterization of cell states (particularly transcriptomes). In this Review, Wagner and Klein discuss the conceptual underpinnings, experimental strategies and analytical considerations of these approaches, as well as the biological insights gained.

    • Daniel E. Wagner
    •  & Allon M. Klein

  • Research Highlight |

    Two new studies in Science combine single-cell RNA sequencing with either lineage tracing or a computational framework to link transcriptomes to future developmental trajectories.

    • Darren J. Burgess

  • Review Article |

    How chromosomes are positioned and folded within the nucleus has implications for gene regulation. In this Review, Kempfer and Pombo describe and evaluate methods for studying chromosome architecture and outline the insights they are providing about nuclear organization.

    • Rieke Kempfer
    •  & Ana Pombo

  • Review Article |

    Advances in sequencing- and imaging-based techniques for chromosome structure analysis have led to a mature understanding of bacterial chromosome structure and dynamics. In this Review, Dame, Rashid and Grainger discuss the hierarchical nature of bacterial chromosome structure and how it is influenced by diverse types of nucleoid-associated proteins. Furthermore, they describe roles for nucleoid-associated proteins and chromosome structure, including in gene expression, chromosome segregation and cell cycle regulation.

    • Remus T. Dame
    • , Fatema-Zahra M. Rashid
    •  & David C. Grainger

  • Research Highlight |

    A new study in Science reports a synthetic biology approach to encode an ultrasound-based gene expression reporter that is applicable to mammalian cells in vitro and in vivo.

    • Darren J. Burgess

  • Review Article |

    This Review provides an overview of different approaches for measuring nascent RNA synthesis. It discusses the complementary strengths of these different methods and how they have contributed to a mechanistic understanding of transcription regulation.

    • Erin M. Wissink
    • , Anniina Vihervaara
    •  & John T. Lis

  • Research Highlight |

    A study in Nature Genetics shows that genomic rearrangements that cause extensive changes to chromatin topology do not alter expression for the majority of genes.

    • Linda Koch

  • Review Article |

    This Review discusses advances in RNA-sequencing technologies and methods over the past decade and outlines adaptations that are enabling a fuller understanding of RNA biology, from when and where an RNA is expressed to the structures it adopts.

    • Rory Stark
    • , Marta Grzelak
    •  & James Hadfield

  • Research Highlight |

    A recent study in Science demonstrates how capturing gene expression over a developmental time course enables the discovery of dynamic expression quantitative trait loci (eQTLs) that would otherwise be challenging to find.

    • Darren J. Burgess

  • Review Article |

    For appropriate control of gene expression, enhancers must communicate with the right target genes at the right time, typically over large genomic distances. In this Review, Schoenfelder and Fraser discuss our latest understanding of long-range enhancer–promoter crosstalk, including target-gene specificity, interaction dynamics, protein and RNA architects of interactions, roles of 3D genome organization and the pathological consequences of regulatory rewiring.

    • Stefan Schoenfelder
    •  & Peter Fraser

  • Research Highlight |

    Two new spatial transcriptomics techniques published in Nature and Science bring us an important step closer to the goal of achieving transcriptome-wide data at single-cell resolution.

    • Darren J. Burgess

  • Review Article |

    The functional interpretation of single-cell RNA sequencing (scRNA-seq) data can be enhanced by integrating additional data types beyond RNA-based gene expression. In this Review, Stuart and Satija discuss diverse approaches for integrative single-cell analysis, including experimental methods for profiling multiple omics types from the same cells, analytical approaches for extracting additional layers of information directly from scRNA-seq data and computational integration of omics data collected across different cell samples.

    • Tim Stuart
    •  & Rahul Satija

  • Review Article |

    Single-cell RNA sequencing (scRNA-seq) enables transcriptome-based characterization of the constituent cell types within a heterogeneous sample. However, reliable analysis and biological interpretation typically require optimal use of clustering algorithms. This Review discusses the multiple algorithmic options for clustering scRNA-seq data, including various technical, biological and computational considerations.

    • Vladimir Yu Kiselev
    • , Tallulah S. Andrews
    •  & Martin Hemberg

  • Research Highlight |

    Proximity-CLIP, a method that combines proximity-based protein biotinylation and UV crosslinking, profiles the transcriptome and ribonucleoproteins in subcellular compartments.

    • Linda Koch

  • Perspective |

    High-resolution studies of chromosome conformation are revealing that the 3D genome is organized into smaller structural features than was previously supposed and is primarily composed of compartmental domains and CTCF loops. In this Perspectives article Rowley and Corces describe the latest views on the organizational drivers and principles of the 3D genome, and the interplay between genome activity and organization.

    • M. Jordan Rowley
    •  & Victor G. Corces

  • Research Highlight |

    A new study reports the ‘Tabula Muris’, an atlas of single-cell RNA sequencing data from >100,000 cells across 20 mouse tissues.

    • Darren J. Burgess

  • Research Highlight |

    A study in Nature describes RNA velocity, which is a computational method to derive dynamic gene expression information from static single-cell RNA sequencing data. It provides valuable insights into developmental trajectories of cells.

    • Darren J. Burgess

  • Review Article |

    Although cancer genome sequencing is becoming routine in cancer research, cancer transcriptome profiling through methods such as RNA sequencing (RNA-seq) provides information not only on mutations but also on their functional cellular consequences. This Review discusses how technical and analytical advances in cancer transcriptomics have provided various clinically valuable insights into gene expression signatures, driver gene prioritization, cancer microenvironments, immuno-oncology and prognostic biomarkers.

    • Marcin Cieślik
    •  & Arul M. Chinnaiyan

  • Review Article |

    As the genetic and phenotypic heterogeneities among cells become more appreciated, there is increasing demand for technologies that facilitate high-throughput and high-efficiency single-cell 'omic' analyses in miniaturized and automated formats. This Review discusses the diverse microfluidic methodologies — with a primary focus on valve-, droplet- and nanowell-based platforms — for characterization of the genomes, epigenomes, transcriptomes and proteomes of single cells, and addresses technical considerations and future opportunities.

    • Sanjay M. Prakadan
    • , Alex K. Shalek
    •  & David A. Weitz

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