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Bridging spatial and temporal scales of developmental gene regulation 连接发育基因调控的时空尺度
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-06-01 Epub Date: 2025-03-12 DOI: 10.1016/j.gde.2025.102328
Andrés H Cardona , Márcia M Peixoto , Tohn Borjigin , Thomas Gregor
{"title":"Bridging spatial and temporal scales of developmental gene regulation","authors":"Andrés H Cardona ,&nbsp;Márcia M Peixoto ,&nbsp;Tohn Borjigin ,&nbsp;Thomas Gregor","doi":"10.1016/j.gde.2025.102328","DOIUrl":"10.1016/j.gde.2025.102328","url":null,"abstract":"<div><div>The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue organization during development is crucial for explaining the remarkable reproducibility of complex organisms. This review explores how chromatin-encoded information is transduced from localized transcriptional events to global gene expression patterns, highlighting the challenge of bridging these scales. We discuss recent experimental findings and theoretical frameworks, emphasizing polymer physics as a tool for describing the relationship between chromatin structure and dynamics across scales. By integrating these perspectives, we aim to clarify how gene regulation is coordinated across levels of biological organization and suggest strategies for future experimental approaches.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"92 ","pages":"Article 102328"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143601607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
To splice or not to splice: pseudoexons in neurological disease and opportunities for intervention 剪接或不剪接：神经系统疾病中的假外显子及其干预机会
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-06-01 Epub Date: 2025-03-29 DOI: 10.1016/j.gde.2025.102343
Sue Fletcher , Niall P Keegan , Rita Mejzini , Ianthe L Pitout
{"title":"To splice or not to splice: pseudoexons in neurological disease and opportunities for intervention","authors":"Sue Fletcher ,&nbsp;Niall P Keegan ,&nbsp;Rita Mejzini ,&nbsp;Ianthe L Pitout","doi":"10.1016/j.gde.2025.102343","DOIUrl":"10.1016/j.gde.2025.102343","url":null,"abstract":"<div><div>Accurate exon selection and processing of pre-messenger RNA are crucial for normal gene expression. Mutations that alter splicing disrupt pre-mRNA processing and can have diverse effects on transcript structure, making the consequences of many such mutations difficult to predict. While next-generation sequencing technologies have transformed genetic diagnosis for many patients, deep intronic variants generally evade detection and characterisation. Of all the known types of splicing mutations, the most elusive to predict are those that activate pseudoexons. Because transcripts that contain pseudoexons are otherwise generally intact, exclusion (or ‘skipping’) of the pseudoexon during processing of the pre-mRNA is likely to generate a normal, functional mRNA. Characterisation of pseudoexon mutations will open opportunities for the development of antisense oligonucleotide strategies to overcome these disease-causing mutations.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"92 ","pages":"Article 102343"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143734631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Remodeling, compartmentalization, and degradation: a trifecta for organelle quality control during gametogenesis 重塑、分隔和降解：配子发生过程中细胞器质量控制的三部曲
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-06-01 Epub Date: 2025-04-14 DOI: 10.1016/j.gde.2025.102347
Tianyao Xiao, Elçin Ünal
{"title":"Remodeling, compartmentalization, and degradation: a trifecta for organelle quality control during gametogenesis","authors":"Tianyao Xiao,&nbsp;Elçin Ünal","doi":"10.1016/j.gde.2025.102347","DOIUrl":"10.1016/j.gde.2025.102347","url":null,"abstract":"<div><div>The key to healthy offspring production lies in the accurate inheritance of components from progenitor germ cells during gametogenesis. Along with genetic material, precise regulation of organelle inheritance is vital for gamete health and embryonic development, especially in aged organisms, where organelle function declines and damage accumulates. In these cases, removing age-related organellar defects in precursor cells is crucial for successful reproduction. The single-celled organism <em>Saccharomyces cerevisiae</em> shares striking similarities with more complex organisms: like metazoan cells, yeast accumulate organelle damage with age, yet can still produce damage-free gametes with a reset lifespan. Recent studies show that organelles undergo significant reorganization during yeast gametogenesis, and similar remodeling occurs in metazoans, suggesting common strategies for maintaining gamete quality. This review summarizes organellar reorganization during gametogenesis in yeast and how it aids in clearing age-related cellular damage. We also explore organellar remodeling in multicellular organisms and discuss the potential mechanisms and biological benefits of meiotic organellar reshaping.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"92 ","pages":"Article 102347"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143829348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Pluripotent stem cell–derived mesenchymal stem cells for therapeutic applications, developmental study, and cancer research 多能干细胞衍生的间充质干细胞用于治疗应用、发育研究和癌症研究
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-06-01 Epub Date: 2025-03-06 DOI: 10.1016/j.gde.2025.102327
Siyi Fu, Cheung K Yeung, Ren-He Xu
{"title":"Pluripotent stem cell–derived mesenchymal stem cells for therapeutic applications, developmental study, and cancer research","authors":"Siyi Fu,&nbsp;Cheung K Yeung,&nbsp;Ren-He Xu","doi":"10.1016/j.gde.2025.102327","DOIUrl":"10.1016/j.gde.2025.102327","url":null,"abstract":"<div><div>Human mesenchymal stem cells (MSCs) have been widely studied and applied for the treatment of various diseases due to their crucial role in tissue repair and regeneration. Compared to MSCs isolated from somatic tissues, MSCs differentiated from human pluripotent stem cells (ps-MSCs) have demonstrated similar therapeutic effects while possessing some advantages in quality control and assurance, given their unlimited and consistent supply of source cells. This makes ps-MSCs highly druggable and promising for therapeutic applications. In this minireview, we introduce the latest progress in ps-MSC research, focusing on the therapeutic properties, origin, <em>in vivo</em> development, and application of ps-MSCs in cancer research. We will also discuss the perspectives and challenges of this relatively new source of MSCs.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"92 ","pages":"Article 102327"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143552879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The human endometrium: atlases, models, and prospects 人类子宫内膜：地图集、模型和前景
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-06-01 Epub Date: 2025-03-27 DOI: 10.1016/j.gde.2025.102341
Frederick CK Wong , Christina E Kim , Luz Garcia-Alonso , Roser Vento-Tormo
{"title":"The human endometrium: atlases, models, and prospects","authors":"Frederick CK Wong ,&nbsp;Christina E Kim ,&nbsp;Luz Garcia-Alonso ,&nbsp;Roser Vento-Tormo","doi":"10.1016/j.gde.2025.102341","DOIUrl":"10.1016/j.gde.2025.102341","url":null,"abstract":"<div><div>Approximately every month, the human endometrium undergoes a cycle of proliferation, differentiation, and, in the absence of pregnancy, shedding and repair. Each cycle relies on intricate interorgan coordination of hormonal secretions. Endometrial dysfunction causes significant health complications, including abnormal menstrual bleeding and endometriosis. However, effective diagnosis and treatments are hampered by understudied aetiology. Recent single-cell profiling has disentangled the diverse and dynamic nature of the endometrium, revealing regulatory roles of WNT, NOTCH, and TGF<em>β</em> signalling. These insights have informed mechanistic studies enabled by advanced <em>in vitro</em> models that capture endometrial cellular heterogeneity and structure. In this review, we outline key single-cell transcriptomics atlases and models that provided new avenues for studying endometrial biology, discuss their limitations, and propose future directions.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"92 ","pages":"Article 102341"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143705922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reshaping transcription and translation dynamics during the awakening of the zygotic genome 在合子基因组觉醒期间重塑转录和翻译动力学
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-06-01 Epub Date: 2025-04-05 DOI: 10.1016/j.gde.2025.102344
Louise Maillard , Pierre Bensidoun , Mounia Lagha
{"title":"Reshaping transcription and translation dynamics during the awakening of the zygotic genome","authors":"Louise Maillard ,&nbsp;Pierre Bensidoun ,&nbsp;Mounia Lagha","doi":"10.1016/j.gde.2025.102344","DOIUrl":"10.1016/j.gde.2025.102344","url":null,"abstract":"<div><div>During the oocyte-to-embryo transition, the transcriptome and proteome are dramatically reshaped. This transition entails a shift from maternally inherited mRNAs to newly synthesized transcripts, produced during the zygotic genome activation (ZGA). Furthermore, a crucial transcription and translation selectivity is required for early embryonic development. Studies across various model organisms have revealed conserved <em>cis-</em> and <em>trans-</em>regulatory mechanisms dictating the regimes by which mRNA and proteins are produced during this critical phase. In this article, we highlight recent technological and conceptual advances that deepen our understanding of how the tuning of both transcription and translation evolves during ZGA.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"92 ","pages":"Article 102344"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143776585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
R-loops in neurodegeneration 神经变性中的 R 环
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-06-01 Epub Date: 2025-04-08 DOI: 10.1016/j.gde.2025.102345
Chiara Beghѐ, Helena Harpham, Yasmine Barberic, Natalia Gromak
{"title":"R-loops in neurodegeneration","authors":"Chiara Beghѐ,&nbsp;Helena Harpham,&nbsp;Yasmine Barberic,&nbsp;Natalia Gromak","doi":"10.1016/j.gde.2025.102345","DOIUrl":"10.1016/j.gde.2025.102345","url":null,"abstract":"<div><div>Neurodegenerative diseases are associated with the progressive loss of neurons. R-loops are non-canonical nucleic acid structures formed during transcription and composed of an RNA/DNA hybrid and a displaced single-stranded DNA. Whilst R-loops are important regulators of cellular processes, they are also associated with the pathologies of multiple disorders, including repeat expansion, motor neuron, inflammatory and ageing diseases. In this review, we discuss how R-loops contribute to pathological mechanisms that underpin neurodegeneration. We highlight the role of R-loops in several hallmarks of neurodegenerative disorders, including RNA and DNA defects, DNA damage, protein aggregation, inflammation, mitochondrial dysfunction, and neuronal cell death. We also discuss the potential role of R-loops as therapeutic targets for neurodegenerative disorders.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"92 ","pages":"Article 102345"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143790942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Totipotency or plenipotency: rethinking stem cell bipotentiality 全能性或全能性：重新思考干细胞的双潜能性
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-06-01 Epub Date: 2025-03-19 DOI: 10.1016/j.gde.2025.102342
Duancheng Wen , Jianlong Wang
{"title":"Totipotency or plenipotency: rethinking stem cell bipotentiality","authors":"Duancheng Wen ,&nbsp;Jianlong Wang","doi":"10.1016/j.gde.2025.102342","DOIUrl":"10.1016/j.gde.2025.102342","url":null,"abstract":"<div><div>The term ‘totipotency’ has often been misapplied in stem cell research to describe cells with embryonic and extraembryonic bipotentiality, despite a lack of evidence that they can generate an entire organism from a single cell. Additionally, no specific term currently distinguishes bipotential stem cells from pluripotent cells, which contribute poorly to extraembryonic tissues. This review examines the developmental continuum from totipotency to pluripotency in early embryos and revisits the previously proposed concept of plenipotency in preimplantation development. We evaluate emerging stem cell models that exhibit bipotentiality but have lost the ability to autonomously initiate and sustain the sequential fate decisions necessary to develop into a complete organism. Unlike totipotent embryonic cells, which retain the information required to initiate fate decisions at the correct timing and cell numbers, these stem cells have lost that capacity. This loss of critical developmental information distinguishes totipotency from plenipotency, with bipotential stem cells aligning more closely with the latter. By distinguishing plenipotency from totipotency and pluripotency, we aim to refine terminology, enhance our understanding of early embryonic development, and address ethical considerations in human research.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"92 ","pages":"Article 102342"},"PeriodicalIF":3.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143644513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Recent insights into the in vitro culture systems for mammalian embryos 哺乳动物胚胎体外培养系统的最新进展。
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-01-18 DOI: 10.1016/j.gde.2025.102309
Zhiyuan Guo , Wentao Zhao , Hongmei Wang , Jinglei Zhai
{"title":"Recent insights into the in vitro culture systems for mammalian embryos","authors":"Zhiyuan Guo ,&nbsp;Wentao Zhao ,&nbsp;Hongmei Wang ,&nbsp;Jinglei Zhai","doi":"10.1016/j.gde.2025.102309","DOIUrl":"10.1016/j.gde.2025.102309","url":null,"abstract":"<div><div>Mammalian early embryonic development is the cornerstone for a healthy life. Any aberrations during early embryonic development may lead to adverse pregnancy outcomes. Therefore, the comprehensive study of embryonic developmental events is essential for understanding biological and pathological pregnancy. However, due to mammalian embryo development taking place in the uterus, it is hard to directly observe the developing embryos that are undergoing dramatic and complex morphologies, proliferation, and differentiation. The <em>in vitro</em> culture (IVC) of mammalian embryos is a pivotal model for studying developmental events. Recent advancements in establishing long-term culture systems for early mammalian embryos have allowed researchers to culture human embryos up to the embryonic day (E) 14 ethical limitations and extend mouse and macaque embryos to early organogenesis. Here, we review the development of IVC systems for mammalian embryos, emphasize the important improvements in culture elements, and offer our perspectives on potential future optimizations of IVC systems.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102309"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Modeling forebrain regional development and connectivity by human brain organoids 用人脑类器官模拟前脑区域发育和连通性
IF 3.7 2区 生物学
Current Opinion in Genetics & Development Pub Date : 2025-04-01 Epub Date: 2025-02-20 DOI: 10.1016/j.gde.2025.102324
Mu Seog Choe , Cynthia Lo , In-Hyun Park
{"title":"Modeling forebrain regional development and connectivity by human brain organoids","authors":"Mu Seog Choe ,&nbsp;Cynthia Lo ,&nbsp;In-Hyun Park","doi":"10.1016/j.gde.2025.102324","DOIUrl":"10.1016/j.gde.2025.102324","url":null,"abstract":"<div><div>The forebrain is one of the most important brain structures for modern human existence, which houses the uniquely sophisticated social and cognitive functions that distinguish our species. Therefore, modeling the forebrain development by using human cells is especially critical for our understanding of the intricacies of human development and devising treatments for related diseases. Recent advancements in brain organoid fields have offered unprecedented tools to investigate forebrain development from studies on specific regions to exploring tract formation and connectivity between different regions of the forebrain. In this review, we discuss the developmental biology of the forebrain and diverse methods for modeling its development by using organoids.</div></div>","PeriodicalId":50606,"journal":{"name":"Current Opinion in Genetics & Development","volume":"91 ","pages":"Article 102324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143454829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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