Trends in Genetics最新文献

Transcriptional cis-regulation has emerged as the predominant force underlying the evolution of phenotypic diversity, yet our understanding of it is still rudimentary. While empirical comparative genomic approaches have been quite informative, they also suffer from numerous confounders and limited scalability. Here we propose using machine-learning-based methods that predict cis-regulatory activity from DNA sequence to perform in silico 'genome transplants' to predict cis-regulatory features as if the genome from one species had been transplanted into the nuclei of another species. Inference of natural selection from the resulting genome-wide catalogs of cis-regulatory divergence could be far more powerful, efficient, and widely applicable than current empirical approaches, enabling unprecedented insights into the genetic basis of biodiversity across the tree of life.

Visual representations are indispensable in genetics education; yet, their apparent simplicity can mask deep conceptual challenges for learners. We summarize empirical evidence for this 'illusion of clarity' and describe resources that may help genetic instructors dispel this illusion.

Despite ongoing efforts, no African country is on track to achieve its agricultural transformation goals, as based on the 2014 Malabo Declaration's objective of accelerated agricultural growth and transformation. How can we ensure that locally relevant scientific innovations are adopted? Without co-creation, inclusion, and ethical delivery, science fails to take root socially.

Boundaries of cross-kingdom RNA communication are now being expanded, with recent work showing that plants deliver gene-silencing RNA into bacteria. Ravet et al. report that both extracellular vesicular and nonvesicular RNAs are biologically active, challenging the current models of RNA secretion and delivery during plant-bacterial communication.

N6-methyladenosine (m⁶A) is the most abundant internal modification in mRNA and plays a crucial role in regulating mRNA turnover. This review explores the characteristics of m⁶A sites in the coding sequence (CDS) and their influence on mRNA decay, with a focus on the newly discovered CDS-m⁶A decay (CMD) pathway - a translation-dependent mechanism that promotes rapid and efficient degradation. Further, we examine how splicing-associated factors influence m⁶A deposition and discuss the enrichment of CMD targets in processing bodies (P-bodies). We emphasize the interplay between m⁶A modification and decay, and propose that targeting the CMD pathway could offer novel therapeutic strategies for diseases such as cancer and metabolic disorders.

Variation of mutation rates between species has been documented over decades, but the variation between different regions of a genome has been less often discussed. Recent studies using high-quality sequence data have revealed previously unknown levels of intragenomic heterogeneity of mutation rates and their association with other structural and functional features of DNA sequences. This article reviews accumulating evidence of this intragenomic heterogeneity and speculates its cause and influence on organismal phenotypes.

Clitellate genomes are the result of a profound genome reshaping compared to marine annelids, as if their genomes had exploded into thousands of atomic pieces and were reassembled in a different order by evolution. Recent studies not only revealed widespread gene order shuffling and massive rearrangements but also point to a potential adaptive rationale for this architectural chaos. What triggered such extreme rearrangements, and what molecular logic (if any) underlies their persistence? What is the role of spatial organization and regulatory rewiring in the maintenance of functional integrity in how the genome adjusts to this newly disordered architecture? By synthesizing current discoveries, this review outlines the mechanisms, consequences, and evolutionary paradoxes of genome rearrangement in clitellates, highlighting them as models of extreme yet functional genome plasticity.

Due to its high variation and its diversity of functional roles, animal colouration has long been a fascinating phenotype for geneticists. While the loci underpinning colour are relatively well known, there remain components of unexplained variation. The contribution of DNA and RNA methylation to these molecular mechanisms of colouration is only now being explored. Recent research has shown that DNA (m⁵C) methylation plays a role in plastic colouration change, the development of colour, and adult intra- and interindividual colouration differences. Studies on RNA (m⁶A) methylation are few but suggest that it also contributes to colour differences. Emerging advances in native DNA and RNA sequencing will allow a novel understanding of methylation contributions to colour evolution and development.

For 35 years, the Ethical, Legal, and Social Implications (ELSI) Research Program has addressed the societal implications of genomic research. However, its policy impact remains controversial. Here, we propose practical approaches for enhancing its policy impact by leveraging sociological studies on technology and critical arguments raised by ELSI scholars themselves.