Current Opinion in Genetics & Development最新文献

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Evolutionary genetics meets ecological immunology: insights into the evolution of immune systems 进化遗传学满足生态免疫学：洞察免疫系统的进化。

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-10-29 DOI: 10.1016/j.gde.2025.102411

Alexander E Downie , Jenny Tung

Immune genes show remarkably consistent evidence of selection, modification, and diversification across the tree of life. Parasites are a key force in this process, but many questions remain about the genetic and phenotypic targets of parasite-mediated selection and how these connect to each other. Ecological immunology — the study of immune variation in natural settings — can complement genetic inference by providing an organismal perspective on immune evolution, including how immune adaptation may be explained or constrained by host life history and ecological context. In this review, we outline key questions in immune evolution where ecological immunology offers insights for evolutionary geneticists, and we explore the value of evolutionary genetic approaches for testing fundamental assumptions in ecological immunology.

免疫基因在整个生命树中表现出显著一致的选择、修饰和多样化证据。寄生虫是这一过程中的关键力量，但关于寄生虫介导的选择的遗传和表型目标以及这些目标如何相互联系仍然存在许多问题。生态免疫学——对自然环境中免疫变异的研究——可以通过提供免疫进化的有机视角来补充遗传推断，包括免疫适应如何被宿主生活史和生态环境所解释或限制。在这篇综述中，我们概述了免疫进化中的关键问题，其中生态免疫学为进化遗传学家提供了见解，我们探讨了进化遗传学方法在检验生态免疫学基本假设方面的价值。

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Editorial Overview: Developmental mechanisms patterning and evolution (2025) 编辑概述：发展机制、模式和进化（2025）

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-10-25 DOI: 10.1016/j.gde.2025.102410

Saher S Hammoud, Yukiko Yamashita

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Human gut evolution: insights from stem cell models and single-cell genomics 人类肠道进化：来自干细胞模型和单细胞基因组学的见解。

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-09-24 DOI: 10.1016/j.gde.2025.102398

Rubén López-Sandoval , Stefano Secchia , Joep Beumer , Jarrett Gray Camp

The gastrointestinal (GI) tract evolved in response to dietary changes and pathogen exposures that varied throughout history. As a major interface between the host and environment, the GI epithelia have evolved specialized barrier and immune functions while optimizing nutrient processing and absorption. Recent technological breakthroughs in modeling human biology in vitro and comparative single-cell genomics are providing novel insights into the genetic, cellular, and ontogenic basis of human evolution. In this review, we provide a broad overview of human-specific gut changes and how GI organoids and single-cell technologies can offer a mechanistic understanding of the specific features of human GI tract physiology.

在整个历史中，胃肠道随着饮食变化和病原体暴露而进化。胃肠道上皮作为宿主和环境之间的主要接口，在优化营养物质加工和吸收的同时，进化出了专门的屏障和免疫功能。最近在体外模拟人类生物学和比较单细胞基因组学方面的技术突破，为人类进化的遗传、细胞和个体基础提供了新的见解。在这篇综述中，我们提供了人类特异性肠道变化的广泛概述，以及胃肠道类器官和单细胞技术如何提供对人类胃肠道生理学特定特征的机制理解。

引用次数: 0

Behavioral evolution by diverging cell type composition 分化细胞类型组成的行为进化

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-09-03 DOI: 10.1016/j.gde.2025.102397

Andres Bendesky

Recent advances in single-cell genomics are propelling a flurry of discoveries about the cellular composition of the brain and other organs across species. These discoveries, coupled with experimental manipulations, have begun to reveal how variation between species in the proportion of cell types, including the outright disappearance of some cell types and the emergence of new ones, contributes to the evolution of behavior. This review highlights these emerging findings in the context of more traditional approaches to study the evolution of behavior and discusses important outstanding questions in this field.

单细胞基因组学的最新进展推动了一系列关于大脑和其他器官的细胞组成的跨物种发现。这些发现，加上实验操作，已经开始揭示物种之间细胞类型比例的差异，包括一些细胞类型的彻底消失和新细胞类型的出现，如何促进行为的进化。这篇综述强调了在研究行为进化的更传统方法的背景下这些新发现，并讨论了该领域的重要突出问题。

引用次数: 0

Polygenic prediction of human complex traits using ancient DNA 利用古代DNA进行人类复杂性状的多基因预测

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-08-30 DOI: 10.1016/j.gde.2025.102396

Iain Mathieson

Ancient DNA has revolutionized our understanding of human history and clarified many aspects of human evolution on a molecular level. In this article, I describe recent efforts to translate this into descriptions of phenotypic change over time and to predict phenotypes of ancient groups and individuals. I do not discuss the more challenging problem of distinguishing between adaptive and neutral evolution and instead focus entirely on whether phenotypes and their evolution can be accurately reconstructed. I begin by describing the conceptual and technical limitations of current approaches, and then discuss efforts to reconstruct various phenotypes and the extent to which they are reliable.

古代DNA彻底改变了我们对人类历史的理解，并在分子水平上阐明了人类进化的许多方面。在这篇文章中，我描述了最近的努力，将其转化为表型变化随时间的描述，并预测古代群体和个体的表型。我不讨论区分适应性进化和中性进化这一更具挑战性的问题，而是完全关注表型及其进化是否可以精确地重建。我首先描述当前方法的概念和技术限制，然后讨论重建各种表型的努力以及它们的可靠程度。

引用次数: 0

Genome instability in mammalian embryos implications for genome editing, development, and evolution 哺乳动物胚胎基因组不稳定性对基因组编辑、发育和进化的影响

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-08-16 DOI: 10.1016/j.gde.2025.102395

Xiangyi Liu , Shuangyi Xu , Dieter Egli

Genomic instability is a significant challenge in early mammalian development and a cause for developmental failure and abnormalities, particularly in humans. Here, we review our knowledge and explore its significance of genome instability in early embryos across multiple mammalian species, including humans, rhesus macaques, mice, bovines, equines, and porcine. All these species but mice share one feature: frequent chromosomal aberrations, aneuploidy, and developmental failure. We discuss the impact of genome instability on embryonic development, the applicability of gene editing using Cas9, and potential evolutionary implications. We also explore the role of germ cell and early embryo mutations and the bottleneck effect in mammals in comparison to lower vertebrates. Understanding genome stability in mammalian embryos can contribute to our understanding of genetic variation in development and evolution.

基因组不稳定是哺乳动物早期发育的重大挑战，也是导致发育失败和异常的原因，特别是在人类中。在这里，我们回顾了我们的知识，并探讨了其在多种哺乳动物物种早期胚胎基因组不稳定性的意义，包括人类、恒河猴、小鼠、牛、马和猪。除了老鼠之外，所有这些物种都有一个共同的特征：染色体畸变、非整倍体和发育失败。我们讨论了基因组不稳定性对胚胎发育的影响，使用Cas9进行基因编辑的适用性，以及潜在的进化意义。与低等脊椎动物相比，我们还探讨了生殖细胞和早期胚胎突变的作用以及哺乳动物的瓶颈效应。了解哺乳动物胚胎基因组的稳定性有助于我们理解发育和进化过程中的遗传变异。

引用次数: 0

Genetic disruption of nonsense-mediated mRNA decay in neurodevelopmental disorders 神经发育障碍中无义介导的mRNA衰变的遗传破坏

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-08-06 DOI: 10.1016/j.gde.2025.102394

Saba Montazaribarforoushi , Lachlan A Jolly

Nonsense-mediated mRNA decay (NMD) is a translation-dependent mRNA decay mechanism that serves the purpose of controlling both mRNA quality and quantity. As a quality control mechanism, NMD protects organisms against the deleterious effects of mRNAs that encode premature termination codons, which arise through either transcriptional errors or genetic variation. NMD is also employed as a major regulator of physiological gene expression levels, and complete knockouts of multiple NMD genes are embryonic lethal in model organisms. The identification of genes that contribute to human Mendelian disease has now highlighted that gene variants that impact NMD function contribute to a spectrum of neurodevelopmental disorders (NDDs). Here, we capture the current landscape of NMD genes and gene variants implicated in NDDs with a focus on recent discoveries. The survey highlighted the involvement of more than half of all NMD and NMD-related genes in NDDs, representing a significant enrichment. That compromised NMD is a likely convergent pathogenic mechanism across multiple genetic causes of NDDs warrants ongoing investigation into the role of NMD in brain development.

无义介导的mRNA衰变（NMD）是一种依赖于翻译的mRNA衰变机制，其目的是控制mRNA的质量和数量。作为一种质量控制机制，NMD保护生物体免受编码过早终止密码子的mrna的有害影响，这些mrna是通过转录错误或遗传变异产生的。NMD还被用作生理基因表达水平的主要调节因子，在模式生物中，多个NMD基因的完全敲除是胚胎致死的。导致人类孟德尔病的基因鉴定现在强调了影响NMD功能的基因变异会导致一系列神经发育障碍（ndd）。在这里，我们捕捉到NMD基因和与ndd相关的基因变异的现状，重点关注最近的发现。该调查强调了ndd中超过一半的NMD和NMD相关基因的参与，这代表了显著的富集。NMD受损可能是ndd的多种遗传原因的趋同致病机制，值得对NMD在大脑发育中的作用进行持续研究。

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引用次数: 0

Evolution of comparative transcriptomics: biological scales, phylogenetic spans, and modeling frameworks 比较转录组学的进化：生物尺度、系统发育跨度和建模框架

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-08-06 DOI: 10.1016/j.gde.2025.102387

Matteo Zambon , Federica Mantica , Mafalda Dias , Jonathan Frazer , Manuel Irimia

Comparative transcriptomic studies are key to understanding how molecular evolution drives phenotypic divergence across the tree of life. Here, we discuss three major directions in which the field of comparative transcriptomics is evolving. The first one is enabled by advances in sequencing technologies. Bulk RNA sequencing emerged two decades ago as a key tool to characterize transcriptomic states, enabling evolutionary comparisons at the tissue and organ levels. However, single-cell and spatial transcriptomics are now driving a shift toward a paradigm centered around cell types. Second, while comparative transcriptomic studies have historically focused on a few key model organisms and on species closely related to humans, recent trends have shifted toward both broader phylogenetic coverage and deeper sampling within clades. In parallel, the growing amount of transcriptomic data, together with the advent of machine learning approaches, are leading to the development of new modeling frameworks. These frameworks range from reconstruction of cell type phylogenies to prediction of RNA coverage from genomic sequence alone and have propelled significant progress in evolutionary biology and its biomedical applications.

比较转录组学研究是理解分子进化如何驱动整个生命之树的表型差异的关键。在这里，我们讨论比较转录组学领域正在发展的三个主要方向。第一个是由于测序技术的进步。大量RNA测序在20年前出现，作为表征转录组状态的关键工具，可以在组织和器官水平上进行进化比较。然而，单细胞和空间转录组学现在正在推动以细胞类型为中心的范式转变。其次，虽然比较转录组学研究历来集中在几个关键的模式生物和与人类密切相关的物种上，但最近的趋势已经转向更广泛的系统发育覆盖范围和在进化枝内更深入的采样。与此同时，越来越多的转录组学数据，以及机器学习方法的出现，正在导致新的建模框架的发展。这些框架的范围从细胞类型系统发育的重建到仅从基因组序列预测RNA覆盖范围，并推动了进化生物学及其生物医学应用的重大进展。

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引用次数: 0

Transcription-coupled repair: protecting genome across generations 转录偶联修复：跨代保护基因组

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-08-05 DOI: 10.1016/j.gde.2025.102385

Bibhusita Pani , Evgeny Nudler

The primary objective of life is to ensure the faithful transmission of genetic material across generations, despite the constant threat posed by DNA-damaging factors. To counter these challenges, life has evolved intricate mechanisms to detect, signal, and repair DNA damage, thereby preventing mutations that can cause developmental abnormalities or diseases. DNA repair is especially vital during development — a period of rapid cell proliferation and differentiation. Failure to repair DNA damage in somatic cells can result in tissue dysfunction, while during embryonic development, it is often fatal. Transcription machinery plays a key role in the mechanisms of DNA repair. This review highlights current insights into DNA repair pathways that are driven or facilitated by transcription and their essential contribution to preserving genome stability.

生命的首要目标是确保遗传物质代代相传，尽管dna破坏因素不断构成威胁。为了应对这些挑战，生命进化出了复杂的机制来检测、发送信号和修复DNA损伤，从而防止可能导致发育异常或疾病的突变。在细胞快速增殖和分化的发育时期，DNA修复尤为重要。体细胞DNA损伤修复失败会导致组织功能障碍，而在胚胎发育过程中，这通常是致命的。转录机制在DNA修复机制中起着关键作用。这篇综述强调了目前对转录驱动或促进的DNA修复途径的见解，以及它们对保持基因组稳定性的重要贡献。

引用次数: 0

Editorial overview: 3Rs update: a new era in cellular identity and therapeutic plasticity 编辑概述：3Rs更新：细胞身份和治疗可塑性的新时代

IF 3.6 2区生物学 Q2 CELL BIOLOGY

Current Opinion in Genetics & Development

Pub Date : 2025-08-05 DOI: 10.1016/j.gde.2025.102386

Peng Du , Jianlong Wang

引用次数: 0

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