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Rubin et al. report the development of a programmable organism- and locus-specific genome editing approach that can target microorganisms in their native community context, without the need for isolation.
In this Review the authors provide an overview of key algorithmic developments, popular tools and emerging technologies used in the bioinformatic analysis of genomes. They also describe how such analysis can identify point mutations, copy number alterations, structural variations and mutational signatures in cancer genomes.
The authors review the field of mammalian mitochondrial genome engineering, culminating in the recent development of mitochondrially targeted programmable nucleases and base editors. They describe research that led to the development of animal models of mitochondrial disease, as well as the potential for translating these approaches to the clinic.
A study in Science reports the genetic determinants of differences in immune responses to viral infection between individuals of European and African ancestries.
Loci that encode long non-coding RNAs (lncRNAs) can be complex and function through multiple modalities. The authors provide a framework for elucidating the physiological roles of lncRNAs using genetically engineered mouse models, including whole-gene deletion, transcription termination, reporters and transgene rescue strategies.
Machine learning is widely applied in various fields of genomics and systems biology. In this Review, the authors describe how responsible application of machine learning requires an understanding of several common pitfalls that users should be aware of (and mitigate) to avoid unreliable results.
A study in Nature Communications shows that horizontal transfer of bacterial chromosomes by phage-mediated lateral transduction renders them more mobile than many classically defined mobile genetic elements, including plasmids and transposons.
A study in Cell describes how non-coding RNAs can drive the formation of higher-order RNA-chromatin structures in the nucleus, with a role in mediating chromatin conformation and gene expression.
In this Review, the authors discuss explanations for why ultraconserved sequences — which are presumed to be functionally crucial on the basis of strong evolutionary constraint — often result in surprisingly minor phenotypic consequences when experimentally disrupted. They also discuss the wider implications of extreme non-coding conservation for understanding the mechanisms of gene regulation and human variant interpretation.
This Perspective highlights privacy issues related to the sharing of functional genomics data, including genotype and phenotype information leakage from different functional genomics data types and their summarization steps. The authors also review the techniques that will enable broad sharing and analysis while maintaining privacy.
In this Journal Club article, Fowzan Alkuraya describes how a paper outlining the mathematical foundations of homozygosity mapping provided a route to disease gene identification that still benefits his patients in clinical practice today.
Individual cells in the same induced pluripotent stem cell (iPSC)-derived clones can exhibit large heterogeneity. In this Comment, Carelli et al. discuss emerging evidence implicating variants in mitochondrial DNA, and highlight the need for routine screening of iPSCs.
Two recent studies demonstrate that putative nucleases encoded by IS200/IS605 family transposons are programmable RNA-guided DNA endonucleases, which could represent a new source of genome-editing enzymes for biotechnological applications.
Hologenomic studies aim to further our understanding of host–microbiota interactions through the integrated analysis of host genomes and microbiota metagenomes. Here, Alberdi and colleagues discuss key considerations for designing optimal hologenomic studies and outline important biological questions that these studies can address.
A study in Nature Biotechnology describes single-cell genome and epigenome by transposases sequencing (scGET-seq), which generates euchromatin and heterochromatin profiles from the same cell, and Chromatin Velocity, a computational framework capable of predicting future epigenetic cell fate trajectories from scGET-seq data.
Tom Misteli highlights a 2006 study by Shopland et al., which used relatively simple methods to visualize characteristics of chromosome organization. Their conclusions foreshadowed key concepts in the field: topologically associating domains, compartments and cell-to-cell heterogeneity in genome organization.
The authors review overlapping sequences as fundamental features of prokaryotic, eukaryotic and viral genomes, discussing the diverse topologies and functions of overlapping genes, open reading frames and coding sequences. Moreover, they highlight the potential of harnessing sequence overlaps for synthetic biology approaches.
