Research Highlights

  • Research Highlight |

    A study in Cell introduces memory sequencing (MemorySeq), a method for identifying genes that are highly and heritably expressed over multiple cell divisions. These expression patterns can reveal cellular subpopulations with distinct phenotypes, such as drug resistance.

    • Dorothy Clyde
  • 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
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    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
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    Epigenetic clocks translate the DNA methylome into a biological age but usually work only within a species. Now, a study in Cell Systems reports a cross-species epigenetic clock that works across a number of mammals, including humans, dogs and mice.

    • Dorothy Clyde
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    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
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    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
  • Research Highlight |

    A study in Nature describes a new method for studying variation in meiosis. Sperm-seq is a single-cell sequencing approach that enables genome-wide analysis of multiple meiotic phenotypes in thousands of sperm simultaneously.

    • Dorothy Clyde
  • Research Highlight |

    During ageing, many normal human tissues become a patchwork of mutant clones. Colom et al. show that, in mutagenized mouse oesophageal epithelium, this mutational landscape arises through cell competition, with clone fitness determined by the genotype of their neighbours.

    • Dorothy Clyde
  • 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
  • Research Highlight |

    A study in Cell Reports describes a machine learning model, named Xpresso, that uses genomic sequence to predict mRNA steady-state abundance.

    • Linda Koch
  • 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 papers in Nature Chemical Biology describe new methods for transcriptome-mapping of N6-methyladenosine (m6A), a covalent modification of RNA. In m6A-SEAL, modified adenosines can be tagged with different functional groups for different applications, whereas m6A-label-seq uses metabolic labelling to achieve single-nucleotide resolution.

    • Dorothy Clyde
  • 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
  • Research Highlight |

    A study in Science shows that anthropologically informed approaches to genome sequencing can provide a fuller understanding of human genetic variation, including new insights into how past events have led to present-day population structure.

    • Dorothy Clyde
  • 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
  • Research Highlight |

    A study in Cell describes a novel, highly scalable CRISPR–Cas9-based assay and its use in assessing the role of enhancer mutations in mammalian limb development.

    • Joseph Willson
  • Research Highlight |

    A new technology, named PIC-seq, combines cell sorting of physically interacting cells (PICs) with single-cell RNA sequencing and computational modelling to profile cellular interactions and their impact on gene expression.

    • Linda Koch
  • 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
  • Research Highlight |

    Pathogens are wreaking havoc on bee populations. A study in Science describes how bacteria in the guts of bees can be engineered to protect their hosts from two particular pests, deformed wing virus and Varroa mites.

    • Dorothy Clyde
  • Research Highlight |

    Two new studies in Molecular Cell report a role for antisense oligonucleotides in inducing transcriptional termination, with important implications for the interpretation of functional studies of long non-coding RNAs.

    • Darren J. Burgess
  • Research Highlight |

    A Genome Research study reports gene expression and DNA methylation profiles of multiple tissues sampled from the same individuals across humans, chimpanzees and rhesus macaques.

    • Linda Koch
  • Research Highlight |

    Two new studies on snake venom glands have implications for improved anti-venom development. One describes the de novo assembly of an Indian cobra reference genome and venom gland transcriptome; the other describes the derivation of snake venom gland organoids.

    • Dorothy Clyde
  • Research Highlight |

    A study in Nature reveals an epigenetic mechanism that supports the idea of a ‘default’ path of cell differentiation during gastrulation.

    • Joseph Willson
  • Research Highlight |

    A large-scale single-cell genomics study of planktonic bacteria and archaea that inhabit the surface ocean broadens insights into the heterogeneity and genomic composition of this marine microbiome.

    • Linda Koch
  • Research Highlight |

    A study in Cell identifies a mechanism by which exon splicing can increase gene expression through the activation of weak upstream promoters.

    • Joseph Willson
  • Research Highlight |

    A new study in Science has mapped regulatory elements for major cell types of the human brain to help elucidate the transcriptional mechanisms underlying their developmental and functional properties in health and disease.

    • Linda Koch
  • Research Highlight |

    Two new studies report advances for nanopore-based long-read sequencing for characterizing complex human transcriptomes and for analysing human repetitive DNA regions.

    • Darren J. Burgess
  • Research Highlight |

    A new study has identified genetic determinants of mosaic loss of chromosome Y (LOY) in leukocytes that are also associated with increased risk of various non-haematological cancers, suggesting LOY in blood is a biomarker of genome instability in other tissues.

    • Dorothy Clyde
  • Research Highlight |

    Two papers in Nature Plants provide evidence that plants, like mammals, regulate gene expression from long-range cis-regulatory elements (CREs). Plant CREs are widespread and have distinct evolutionarily conserved chromatin characteristics that are predictive of their effect on gene expression.

    • Dorothy Clyde
  • Research Highlight |

    Two studies in Nature Genetics provide high-resolution maps of genetic variation across melon and watermelon species, respectively, and identify candidate loci linked to fruit quality traits through genome-wide association studies and population genomic analyses.

    • Linda Koch
  • Research Highlight |

    A new study provides the largest whole-genome sequence data set in an African population to date and shows that genetic causes of disease might be different in African and European populations.

    • Rebecca Kelsey
  • Research Highlight |

    Mohammadi et al. report the development of ANEVA–ANEVA-DOT, a statistical model that quantifies variation in gene dosage, and demonstrate its potential for identifying genes harbouring rare pathogenic variants.

    • Conor A. Bradley
  • Research Highlight |

    A new study in Cell reports a mammalian genetic screening strategy that combines CRISPR libraries with in situ sequencing to read out both complex cellular phenotypes and genetic perturbations using microscopy.

    • Darren J. Burgess
  • Research Highlight |

    A new genome editing strategy called prime editing uses a catalytically impaired Cas9 fused to an engineered reverse transcriptase to write desired genetic sequence information directly into a target locus.

    • Linda Koch
  • Research Highlight |

    A new study in Cell reports that sense-strand Piwi-interacting RNAs have an important role in protecting the germline genome from invading retroviruses.

    • Dorothy Clyde
  • Research Highlight |

    A study in Nature retraces the convergent evolution of resistance to cardiac glycosides in insects, pinpointing the adaptive alleles and their functional consequences.

    • Linda Koch
  • 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
  • Research Highlight |

    A study in Science describes the generation of a lineage-resolved single-cell transcriptome atlas for Caenorhabditis elegans embryos. This resource provides insight into the transcriptional changes underlying cell fate decisions.

    • Dorothy Clyde
  • Research Highlight |

    A recent study in Nature Microbiology reports metagenomic signatures of early-life antibiotic treatment and hospitalization associated with preterm birth that persist long-term.

    • Linda Koch
  • Research Highlight |

    Two new studies in Science survey diversity in malarial Plasmodium species, assessing genetic diversity across Africa, as well as transcriptomic diversity through the pathogen life cycle.

    • Darren J. Burgess
  • Research Highlight |

    A study in Nature Ecology and Evolution reports the genome sequence of the Komodo dragon and describes genomic features that may underlie its distinct physiology.

    • Dorothy Clyde
  • Research Highlight |

    Two recent studies report innovative RNA base editing tools: adenine editing without the requirement for exogenous enzymes, and a new ability to edit cytosines.

    • Darren J. Burgess