Biological techniques articles within Nature Reviews Genetics

Featured

  • Review Article |

    Interactions between microorganisms and their hosts are highly context dependent and contribute to both normal tissue function and infectious disease pathology. In this Review, Westermann and Vogel describe how advances in RNA sequencing techniques are providing molecular insights into host–microbe interactions, including advances in cross-species and single-cell transcriptomics.

    • Alexander J. Westermann
    •  & Jörg Vogel

  • Review Article |

    There is a rapidly growing appreciation of the complexities of 3D genome organization, as well as associations with gene expression and wider cellular and organismal phenotypes, including diseases. In this Review, the authors describe diverse experimental methods for manipulating 3D genome organization — from fine-scale control of DNA contacts to large-scale nuclear repositioning — which are facilitating detailed testing of the biological functions of 3D genome organization.

    • Haifeng Wang
    • , Mengting Han
    •  & Lei S. Qi

  • Research Highlight |

    Three new studies identify different types of de novo and somatic mutations associated with autism spectrum disorder (ASD), with potential insights into underlying molecular mechanisms.

    • Darren J. Burgess

  • In Brief |

    In this paper in Nature Genetics, Atkinson et al. describe Tractor, a statistical framework and software package that enables admixed populations to be included in large-scale genomics studies.

    • Dorothy Clyde

  • In Brief |

    In this study in Molecular Cell, Clarke et al. describe a system that enables multiple Cas9-mediated genome edits to be introduced into cells in a defined, sequential order.

    • Dorothy Clyde

  • Research Highlight |

    A report in Science describes in situ genome sequencing (IGS), a method that enables genomes to be simultaneously sequenced and imaged in intact samples, including early mouse embryos. IGS will facilitate insight into the relationship between genome sequence and organization.

    • Dorothy Clyde

  • Review Article |

    MicroRNAs (miRNA) exert essential functions in mammalian development and physiology. The authors review recent insights from the phenotypic analysis of miRNA knockouts in mice that emphasize roles for these non-coding RNAs at different developmental stages and in adults, and illustrate the importance of functional miRNA targets, miRNA dosage, miRNA interactions and cellular context.

    • Brian DeVeale
    • , Jennifer Swindlehurst-Chan
    •  & Robert Blelloch

  • Research Highlight |

    A study in Nature reports that adenine base editors can correct the mutation that causes Hutchinson–Gilford progeria syndrome in a mouse model of this disease, extending lifespan.

    • Katharine H. Wrighton

  • Research Highlight |

    Two new papers in Nature Biotechnology report methods for targeted sequencing of complex DNA samples, achieved in real time during nanopore sequencing runs.

    • Darren J. Burgess

  • In Brief |

    An article in Cell describes a multi-omic analysis of health risks from spaceflights that implicates mitochondrial stress and dysregulation as key drivers.

    • Dorothy Clyde

  • In Brief |

    A study in Genome Biology uses EpiGo-KRAB to analyse the roles of H3K9me3 in genome organization and transcriptional repression and reveals the two functions may be distinct.

    • Dorothy Clyde

  • In Brief |

    Jin et al. describe a barcoding approach for analysing metastasis, which they used to generate an organ-specific metastasis map for 500 cancer cell lines.

    • Dorothy Clyde

  • In Brief |

    Fozouni et al. describe a CRISPR–Cas13a-based approach for rapid, accurate and portable detection of SARS-CoV-2 in infected individuals.

    • Dorothy Clyde

  • Review Article |

    The ability to reprogramme cellular translation and genomes to produce non-canonical biopolymers has wide-ranging applications, including in therapeutics, but has yet to be fully realized. In this Review, de la Torre and Chin discuss recent advances towards achieving this goal.

    • Daniel de la Torre
    •  & Jason W. Chin

  • In Brief |

    The CRISPR–Cas13 system can be used to knock down circular RNAs (circRNAs) without any impact on related mRNAs, reports a study in Nature Methods.

    • Linda Koch

  • In Brief |

    Corley et al. report fSHAPE, a simplified strategy for in vivo transcriptome-wide footprinting with SHAPE structure-probing techniques.

    • Linda Koch

  • Research Highlight |

    Two new reports in Cell use genome-wide CRISPR screens to uncover host determinants of coronavirus infection, identifying potential leads for antiviral therapeutics.

    • Darren J. Burgess

  • Research Highlight |

    SHARE-seq, a new high-throughput, high-resolution multi-omics method described in Cell, measures chromatin accessibility and gene expression in the same cell and enables future potential gene expression (and therefore lineage choices) to be inferred from chromatin profiles.

    • Dorothy Clyde

  • Perspective |

    This Perspective reviews efforts to map six different RNA modifications — pseudouridine (Ψ), 5-methylcytidine (m5C), N 1-methyladenosine (m1A), N 4-acetylcytidine (ac4C), ribose methylations (Nm) and N 7-methylguanosine (m7G) — and how they differ from N 6-methyladenosine (m6A). The authors discuss the technical and analytical challenges of characterizing the epitranscriptome and provide their own conclusions on the abundance and distribution of these modifications.

    • David Wiener
    •  & Schraga Schwartz

  • Review Article |

    Cell–cell interactions and communication can be inferred from RNA sequencing data of, for example, ligand–receptor pairs. The authors review insights gained and the methods and tools used in studies of cell–cell interactions based on transcriptomic data.

    • Erick Armingol
    • , Adam Officer
    •  & Nathan E. Lewis

  • Research Highlight |

    A recent study re-casts proteomic analyses as a DNA sequencing problem; by fusing in vivo-expressed proteins to their encoding mRNA, molecular interactions can be identified and quantified through high-throughput nucleic-acid sequencing.

    • Linda Koch

  • 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

  • Comment |

    In Africa, there is a disparity in ethics and permission requirements for molecular research on samples from living people versus ancient DNA. At the precipice of the archaeogenomics revolution, heritage agencies require updated policies and procedures for genetic and genomic research on African ancient DNA.

    • Victoria E. Gibbon

  • 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

  • Review Article |

    In this Review, Suhre, McCarthy and Schwenk describe how combining genetics with plasma proteomics is providing notable insights into human disease. As changes in the circulating proteome are often an intermediate molecular readout between a genetic variant and its organismal effect, proteomics can enable a deeper understanding of disease mechanisms, clinical biomarkers and therapeutic opportunities.

    • Karsten Suhre
    • , Mark I. McCarthy
    •  & Jochen M. Schwenk

  • Viewpoint |

    To celebrate the first 20 years of Nature Reviews Genetics, we asked 12 leading scientists to reflect on the key challenges and opportunities faced by the field of genetics and genomics.

    • Amy L. McGuire
    • , Stacey Gabriel
    •  & Jin-Soo Kim

  • Research Highlight |

    A recent study combines CRISPR-based perturbation with single-cell RNA sequencing to characterize the roles of epigenome regulator proteins in controlling cell fate and identity during embryonic development.

    • Darren J. Burgess

  • Research Highlight |

    A new study in Science uses chromatin accessibility profiles to reveal gene regulatory alterations associated with genetic variants in neuropsychiatric disease.

    • Darren J. Burgess

  • Review Article |

    Both genetic and non-genetic factors underlie the intratumoural heterogeneity that fuels cancer evolution. This Review discusses the application of single-cell multi-omics technologies to the study of cancer evolution, which capture and integrate the different layers of heritable information and reveal their complex interplay.

    • Anna S. Nam
    • , Ronan Chaligne
    •  & Dan A. Landau

  • Comment |

    Thirty years on from the launch of the Human Genome Project, Richard Gibbs reflects on the promisesthat this voyage of discovery bore. Its success should be measured by how this project transformed the rules of research, the way of practising biological discovery and the ubiquitous digitization of biological science.

    • Richard A. Gibbs

  • Research Highlight |

    A study in Nature describes the assembly of a human genome with greater continuity than the current reference genome, as well as the assembly of a complete human X chromosome. These assemblies were achieved by combining data generated by different long-read sequencing technologies.

    • Katharine H. Wrighton

  • Research Highlight |

    A study in Nature analysing genome-wide variation in individuals from islands across Polynesia reports evidence of admixture with Native Americans related to Indigenous inhabitants of northern South America.

    • 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 |

    Structural variants have proved difficult to characterize using traditional sequencing approaches. In two new studies in Cell, the authors demonstrate the use of pan-genome approaches to identify and explore the impact of structural variants in crop genomes and reveal variants linked to specific agronomic traits.

    • Joseph Willson

  • Research Highlight |

    Three new studies in Nature Biotechnology combine the adenine and cytosine deaminase activities of single base editors to generate dual base editor systems for combinatorial editing in human cells.

    • Darren J. Burgess

  • Review Article |

    The development of successful anticancer therapies relies on identifying drug targets that are genuine cancer-specific vulnerabilities. In this article, Lin and Sheltzer discuss how the different genetic and pharmacological methods for identifying and characterizing cancer dependencies each have important strengths and limitations. Responsible and orthogonal use of these methods holds promise for maximizing the ability of preclinical research to translate into clinical benefit.

    • Ann Lin
    •  & Jason M. Sheltzer

  • Review Article |

    In this Review, several experts discuss progress in the decade since the development of transposon-based approaches for bacterial genetic screens. They describe how advances in both experimental technologies and analytical strategies are resulting in insights into diverse biological processes.

    • Amy K. Cain
    • , Lars Barquist
    •  & Tim van Opijnen

  • Research Highlight |

    A collection of seven articles from the gnomAD consortium, published in Nature, Nature Medicine and Nature Communications, showcases analyses of global human genetic variation in coding and non-coding genomic regions across this data set.

    • Linda Koch

  • Review Article |

    Genetic recombination is a fundamental biological process generating genetic variation by shuffling combinations of alleles. In this Review, Peñalba and Wolf focus on how sequencing-based approaches are providing diverse insights into recombination rate variation across levels of biological organization and timescales, from individual gametes of single individuals to populations through evolutionary history.

    • Joshua V. Peñalba
    •  & Jochen B. W. Wolf

  • 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 |

    A study reports on the suitability of the yeast Saccharomyces cerevisiae as a platform for the assembly and maintenance of diverse RNA virus genomes, including SARS-CoV-2.

    • Linda Koch

  • 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 |

    Improvements in DNA extraction methods and sequencing technologies have led to the successful sequencing of numerous whole ancient genomes. In this Review, the authors provide an overview of how ancient DNA has informed our understanding of the domestication of various animal species, including dogs, pigs, cattle, goats and chickens.

    • Laurent A. F. Frantz
    • , Daniel G. Bradley
    •  & Ludovic Orlando

  • Perspective |

    In this Perspective article, the authors discuss how Indigenous Peoples' desires for greater involvement and oversight when participating in genomic research projects can be balanced against calls for unrestricted data access. They provide practical recommendations for the handling and sharing of Indigenous genomic data, with the aim of achieving mutual benefit for the research community and participating Indigenous communities.

    • Maui Hudson
    • , Nanibaa’ A. Garrison
    •  & Stephanie Russo Carroll

  • Research Highlight |

    Two new studies in Nature Biotechnology demonstrate the feasibility of functional genomics systems beyond Cas9: a combinatorial DNA editing system involving both Cas9 and Cas12a, and an RNA-targeted system based on Cas13.

    • Darren J. Burgess

  • 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

  • Review Article |

    Electronic health records (EHRs) linked to biobanks provide new opportunities for developing and applying polygenic risk scores in the clinic. The authors review the opportunities and challenges that arise when using EHR data for the systematic evaluation of patient disease susceptibilities.

    • Ruowang Li
    • , Yong Chen
    •  & Jason H. Moore

  • Research Highlight |

    RNA interference screening in Caenorhabditis elegans has identified two repressive epigenetic regulators of age-related behavioural performance that are conserved in mammals.

    • Linda Koch

  • 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

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