Trends in Genetics最新文献

The current nomenclatural rules regulating the naming of microorganisms are too conservative from the perspective of recent developments in molecular genetics tools and organism discovery. The taxonomy of microorganisms would greatly benefit from a conceptual shift toward DNA-based approaches. Current informal practices of DNA-based taxonomy include the use of DNA sequences for species description and type material. Here, we analyze the pros and cons of DNA-based taxonomic approaches and propose guidelines and examples for their appropriate use in descriptions of species and higher-ranking taxa. To facilitate taxon description and communication, we call for a broader use of DNA samples, genome and genetic marker sequences in typifying and diagnosing species and higher-ranking taxa if physical voucher strains or specimens are unavailable.

De-extinction critiques focus on animal welfare, ecosystem disruption, threats to traditional conservation, and anxiety about human hubris. Respondents argue that humanity is obligated to reverse damage to species (natural or human-caused) and to pursue the benefits for conservation science and human health generated by the research.

AlphaGenome, recently announced in a preprint by Avsec et al., is Google DeepMind's powerful 'Swiss army knife' for predicting molecular effects from non-coding DNA. Remarkably, it does so with base-pair resolution while maintaining long-range context. Here, we discuss AlphaGenome's promise and limitations in prioritizing and functionally interpreting non-coding variants underlying human traits and diseases.

Germ cell development involves extensive remodeling of the 3D genome architecture, which is tightly coupled to transcriptional programs, meiotic chromosome dynamics, and re-establishment of totipotency in the next generation. Recent advances in chromosome conformation capture methods have uncovered stage-specific alterations in chromosome organization during spermatogenesis and oogenesis, including germline-specific 3D genome features. These distinctive nuclear configurations orchestrate gene expression programs essential for each developmental stage and meiosis, contribute to epigenetic inheritance, and shape genome evolution. In this review, we synthesize recent progress in understanding 3D genome organization in male and female germlines, and highlight emerging principles, unresolved questions, and innovative approaches that will advance our understanding of germline biology and the principles of genome architecture.

It has been well-established that the vast majority of human genes are expressed not as a single mRNA transcript but rather as a series of many distinct mRNAs due to processes including alternative splicing, promoter use, and polyadenylation. When these transcripts differ in their coding sequences, they can be translated into alternative protein isoforms. Despite known examples of alternative isoforms that are functionally important, whether they diversify the human proteome en masse has long been debated. Recent technological advances, including long-read RNA sequencing, more sensitive proteomics, and high-throughput methods to perturb individual isoforms suggest that most alternative isoforms are expressed at the protein level, are biochemically distinct from each other, and can be associated with disease. It is therefore important to move 'beyond the gene' toward more complex, isoform-aware characterization of molecular processes.

Investigative genetic genealogy (IGG) has helped to resolve over 1300 cases since its advent in 2018. To continue providing justice and answers in the nearly 700 000 cases that could benefit from IGG in the USA, training, funding, and better public understanding of IGG are necessary.

Autism genetics research has the capacity to improve the quality of life of autistic community members, but research priorities vary widely across stakeholders. We summarize key points from our discussion series on autism genetics, highlighting diverse perspectives. Working together, we aim to encourage healthy engagement in autism genetics research.

Circular RNAs (circRNAs) are natural outputs of transcription and RNA processing in eukaryotes. Four subclasses of circRNAs have been identified in animal cells, and most circRNAs are generated via backsplicing. The intricate formation of circRNAs is orchestrated by various cis-regulatory elements and trans-acting factors. Previous studies have gained insights into the general factors and elements involved in backsplicing. Recently, modulation of circRNA biogenesis to generate tissue-specific expression patterns is coming into focus. We summarize various mechanisms involved in the biogenesis of distinct circRNA subclasses across multiple cell types. We also discuss the involvement of relevant mechanisms in human diseases and potential biomedical interventions that target circRNA pathways.

Interruptions within expanded tandem repeats reduce somatic expansion and alter the severity of the resulting diseases. Consequently, much has been done to identify interruptions in the human population and assess their clinical impact. However, how interruptions are gained and lost is unknown. Here, we propose that synthesis-dependent microhomology-mediated end joining (SD-MMEJ) can account for most, if not all, the dynamic changes in interruptions within expanded repeats. SD-MMEJ explains the locus specificity of interruptions, why they appear near the 5' and 3' ends of expanded tracts, and how complex alleles arise within a single generation. Understanding interruption dynamics is fundamental to repeat expansion disease aetiology and therapeutic development.

As the field of spatial omics continues to expand, the spatially resolved profiling of microRNA (miRNA) expression in tissues, or 'spatial miRNomics,' remains in its infancy, with only a few initial pioneering studies to date. MiRNA expression exhibits distinct spatial, temporal, and cell type-specific patterns, and the dysregulation of these patterns is associated with numerous pathological conditions. This highlights the potential of miRNAs as targets for spatial transcriptomic studies in translational and clinical research. In this review, we examine the current landscape of spatial technologies for miRNA detection, from foundational methods to cutting-edge innovations, and we discuss conceptual and technical challenges. We also outline the biomedical implications of spatial miRNA profiling and set out future directions for exploring the spatial dimension of gene regulation.