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Emergence of the circadian clock oscillation during the developmental process in mammals 哺乳动物发育过程中昼夜节律时钟振荡的出现
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-01-23 DOI: 10.1016/j.gde.2024.102152
Kazuhiro Yagita

The circadian clocks are cell-autonomous intrinsic oscillators existing throughout the body to coordinate intracellular and intercellular functions of each organ or tissue. The circadian clock oscillation gradually emerges during mid-to-late gestation in the mammalian developmental process. Recently, it has been revealed that the in vitro differentiation of mouse ES cells recapitulates the circadian clock development. Moreover, reprogramming of the cells results in the redisappearance of the clock, indicating that circadian clocks are tightly coupled with cellular differentiation. Interestingly, before the circadian clock develops, the embryo is governed under ultradian rhythms driven by the segmentation clock. This short review explores these observations, discussing the significance of the emergence of circadian clock oscillation during the mammalian developmental process.

昼夜节律钟是遍布全身的细胞自主固有振荡器,用于协调各器官或组织的细胞内和细胞间功能。在哺乳动物的发育过程中,昼夜节律钟振荡在妊娠中晚期逐渐出现。最近有研究发现,小鼠 ES 细胞的体外分化再现了昼夜节律钟的发育过程。此外,对细胞进行重编程会导致时钟重新出现,这表明昼夜节律钟与细胞分化密切相关。有趣的是,在昼夜节律钟发育之前,胚胎受分割钟驱动的超昼夜节律支配。这篇短文探讨了这些观察结果,讨论了哺乳动物发育过程中出现昼夜节律钟振荡的意义。
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引用次数: 0
What are tethering elements? 什么是系留元素?
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-01-18 DOI: 10.1016/j.gde.2023.102151
Xiao Li , Michael Levine

High-resolution Micro-C maps identified a specialized class of regulatory DNAs termed ‘tethering elements’ (TEs) in Drosophila. These 300–500-bp elements facilitate specific long-range genomic associations or loops. The POZ-containing transcription factor GAF (GAGA-associated factor) contributes to loop formation. Tether–tether interactions accelerate Hox gene activation by distal enhancers, and coordinate transcription of duplicated genes (paralogs) through promoter–promoter associations. Some TEs engage in ultra-long-range enhancer–promoter and promoter–promoter interactions (meta-loops) in the Drosophila brain. We discuss the basis for tether–tether specificity and speculate on the occurrence of similar elements in vertebrate genomes.

高分辨率微C图谱在果蝇中发现了一类专门的调控DNA,称为 "系链元件"(TE)。这些 300-500 bp 的元件有助于特定的长程基因组关联或环路。含 POZ 的转录因子 GAF(GAGA 相关因子)有助于环的形成。系链-系链相互作用通过远端增强子加速 Hox 基因的激活,并通过启动子-启动子关联协调重复基因(旁系基因)的转录。在果蝇大脑中,一些TE参与超长距离的增强子-启动子和启动子-启动子相互作用(元环)。我们讨论了系-系特异性的基础,并推测脊椎动物基因组中也存在类似的元素。
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引用次数: 0
On the edge: how nuclear pore complexes rule genome stability 边缘:核孔复合体如何决定基因组的稳定性。
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-01-12 DOI: 10.1016/j.gde.2023.102150
Marie-Noëlle Simon , Karine Dubrana , Benoit Palancade

Nuclear organization has emerged as a critical layer in the coordination of DNA repair activities. Distinct types of DNA lesions have notably been shown to relocate at the vicinity of nuclear pore complexes (NPCs), where specific repair pathways are favored, ultimately safeguarding genome integrity. Here, we review the most recent progress in this field, notably highlighting the increasingly diverse types of DNA structures undergoing repositioning, and the signaling pathways involved. We further discuss our growing knowledge of the molecular mechanisms underlying the choice of repair pathways at NPCs, and their conservation — or divergences. Intriguingly, a series of recent findings suggest that DNA metabolism may be coupled to NPC biogenesis and specialization, challenging our initial vision of these processes.

核组织已成为协调 DNA 修复活动的关键层。研究表明,不同类型的 DNA 病变会迁移到核孔复合体(NPC)附近,而特定的修复途径会在这些地方受到青睐,最终保护基因组的完整性。在此,我们回顾了这一领域的最新进展,特别强调了发生重新定位的 DNA 结构日益多样化的类型,以及所涉及的信号通路。我们还进一步讨论了我们对 NPC 修复途径选择的分子机制及其保护或分歧的日益增长的知识。耐人寻味的是,最近的一系列发现表明,DNA 新陈代谢可能与 NPC 的生物发生和特化相关联,这对我们最初对这些过程的看法提出了挑战。
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引用次数: 0
The stem cell zoo for comparative studies of developmental tempo 用于发育节奏比较研究的干细胞动物园
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-01-09 DOI: 10.1016/j.gde.2023.102149
Jorge Lázaro , Jaroslaw Sochacki , Miki Ebisuya

The rate of development is highly variable across animal species. However, the mechanisms regulating developmental tempo have remained elusive due to difficulties in performing direct interspecies comparisons. Here, we discuss how pluripotent stem cell-based models of development can be used to investigate cell- and tissue-autonomous temporal processes. These systems enable quantitative comparisons of different animal species under similar experimental conditions. Moreover, the constantly growing stem cell zoo collection allows the extension of developmental studies to a great number of unconventional species. We argue that the stem cell zoo constitutes a powerful platform to perform comparative studies of developmental tempo, as well as to study other forms of biological time control such as species-specific lifespan, heart rate, and circadian clocks.

不同动物物种的发育速度差异很大。然而,由于难以进行种间直接比较,调节发育速度的机制一直难以捉摸。在此,我们讨论了如何利用基于多能干细胞的发育模型来研究细胞和组织自主的时间过程。这些系统可在相似的实验条件下对不同动物物种进行定量比较。此外,不断扩大的干细胞动物群使发育研究扩展到大量非常规物种。我们认为,干细胞动物园是进行发育节奏比较研究的强大平台,也是研究其他生物时间控制形式(如物种特异性寿命、心率和昼夜节律钟)的强大平台。
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引用次数: 0
Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation 循环、串扰和区隔:DNA 甲基化需要多层调控
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-01-04 DOI: 10.1016/j.gde.2023.102147
Guanghui Xu , Julie A Law

DNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on plants, this review provides an update on the aforementioned self-reinforcing loops, highlights recent advances in understanding how DNA methylation pathways are restricted to prevent encroachment on genes, and discusses the roles of histone variants in compartmentalizing epigenetic pathways within the genome. This multilayered approach facilitates two essential, yet opposing functions, the ability to maintain heritable DNA methylation patterns while retaining the flexibility to modify these patterns during development.

DNA 甲基化是一种保守的表观遗传修饰,与转座子沉默和基因调控有关。这种修饰的稳定性依赖于 DNA 和组蛋白修饰之间的密切联系,这种联系会产生自我强化循环,其中一个标记的存在会促进另一个标记的存在。然而,人们越来越清楚地认识到,这些环路的效率受到途径之间的交叉对话和染色质可及性的影响,而染色质可及性则受到组蛋白变体的严重影响。本综述主要以植物为研究对象,介绍了上述自我强化循环的最新进展,重点介绍了在理解 DNA 甲基化途径如何受到限制以防止侵占基因方面的最新进展,并讨论了组蛋白变体在基因组内表观遗传途径分区中的作用。这种多层次的方法有助于实现两种基本但又相互对立的功能,即维持遗传 DNA 甲基化模式的能力,同时保持在发育过程中修改这些模式的灵活性。
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引用次数: 0
Deciphering microglia phenotypes in health and disease 解密健康和疾病中的小胶质细胞表型
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2024-01-03 DOI: 10.1016/j.gde.2023.102146
Christopher D Balak , Claudia Z Han , Christopher K Glass

Microglia are the major immune cells of the central nervous system (CNS) that perform numerous adaptive functions required for normal CNS development and homeostasis but are also linked to neurodegenerative and behavioral diseases. Microglia development and function are strongly influenced by brain environmental signals that are integrated at the level of transcriptional enhancers to drive specific programs of gene expression. Here, we describe a conceptual framework for how lineage-determining and signal-dependent transcription factors interact to select and regulate the ensembles of enhancers that determine microglia development and function. We then highlight recent findings that advance these concepts and conclude with a consideration of open questions that represent some of the major hurdles to be addressed in the future.

小胶质细胞是中枢神经系统(CNS)的主要免疫细胞,可发挥中枢神经系统正常发育和平衡所需的多种适应性功能,但也与神经退行性疾病和行为疾病有关。小胶质细胞的发育和功能受到脑环境信号的强烈影响,这些信号在转录增强子水平上整合在一起,驱动特定的基因表达程序。在这里,我们描述了一个概念框架,说明了系谱决定和信号依赖性转录因子如何相互作用,选择和调控决定小胶质细胞发育和功能的增强子组合。然后,我们重点介绍了推进这些概念的最新发现,最后考虑了代表未来需要解决的一些主要障碍的开放性问题。
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引用次数: 0
Exploring new roles for RNA-binding proteins in epigenetic and gene regulation 探索 RNA 结合蛋白在表观遗传和基因调控中的新作用。
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2023-12-20 DOI: 10.1016/j.gde.2023.102136
Pedro Avila-Lopez , Shannon M Lauberth

A significant portion of the human proteome comprises RNA-binding proteins (RBPs) that play fundamental roles in numerous biological processes. In the last decade, there has been a staggering increase in RBP identification and classification, which has fueled interest in the evolving roles of RBPs and RBP-driven molecular mechanisms. Here, we focus on recent insights into RBP-dependent regulation of the epigenetic and transcriptional landscape. We describe advances in methodologies that define the RNA-protein interactome and machine-learning algorithms that are streamlining RBP discovery and predicting new RNA-binding regions. Finally, we present how RBP dysregulation leads to alterations in tumor-promoting gene expression and discuss the potential for targeting these RBPs for the development of new cancer therapeutics.

人类蛋白质组中有很大一部分是 RNA 结合蛋白(RBPs),它们在许多生物过程中发挥着重要作用。在过去的十年中,RBP 的鉴定和分类有了惊人的增长,这激发了人们对 RBP 不断演变的作用和 RBP 驱动的分子机制的兴趣。在此,我们重点介绍最近对 RBP 依赖性调控表观遗传和转录格局的深入研究。我们介绍了定义 RNA 蛋白相互作用组的方法学进展,以及简化 RBP 发现和预测新 RNA 结合区的机器学习算法。最后,我们介绍了 RBP 失调如何导致肿瘤促进基因表达的改变,并讨论了靶向这些 RBPs 开发癌症新疗法的潜力。
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引用次数: 0
Polycomb repressive complex 2 accessory factors: rheostats for cell fate decision? 多聚胞抑制复合体 2 辅助因子:细胞命运决定的调节器?
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2023-12-12 DOI: 10.1016/j.gde.2023.102137
Hina Bharti , Sungwook Han , Han-Wen Chang , Danny Reinberg

Epigenetic reprogramming during development is key to cell identity and the activities of the Polycomb repressive complexes are vital for this process. We focus on polycomb repressive complex 2 (PRC2), which catalyzes H3K27me1/2/3 and safeguards cellular integrity by ensuring proper gene repression. Notably, various accessory factors associate with PRC2, strongly influencing cell fate decisions, and their deregulation contributes to various illnesses. Yet, the exact role of these factors during development and carcinogenesis is not fully understood. Here, we present recent progress toward addressing these points and an analysis of the expression levels of PRC2 accessory factors in various tissues and developmental stages to highlight their abundance and roles. Last, we evaluate their contribution to cancer-specific phenotypes, providing insight into novel anticancer therapies.

发育过程中的表观遗传重编程是细胞特性的关键,而多聚核抑制复合体的活动对这一过程至关重要。我们重点研究多聚核抑制复合体2(PRC2),它催化H3K27me1/2/3,通过确保适当的基因抑制来保障细胞的完整性。值得注意的是,各种附属因子与 PRC2 相关联,对细胞命运的决定有很大影响,它们的失调会导致各种疾病。然而,这些因子在发育和癌变过程中的确切作用还不完全清楚。在此,我们介绍了解决这些问题的最新进展,并分析了 PRC2 辅助因子在不同组织和发育阶段的表达水平,以突出它们的丰度和作用。最后,我们评估了它们对癌症特异性表型的贡献,从而为新型抗癌疗法提供启示。
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引用次数: 0
Topical section: embryonic models (2023) for Current Opinion in Genetics & Development 遗传学与发育当前观点》的专题部分:胚胎模型(2023)。
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2023-12-05 DOI: 10.1016/j.gde.2023.102134
Charlotte E Handford , Sergi Junyent , Victoria Jorgensen , Magdalena Zernicka-Goetz

Stem cell-based mammalian embryo models facilitate the discovery of developmental mechanisms because they are more amenable to genetic and epigenetic perturbations than natural embryos. Here, we highlight exciting recent advances that have yielded a plethora of models of embryonic development. Imperfections in these models highlight gaps in our current understanding and outline future research directions, ushering in an exciting new era for embryology.

与自然胚胎相比,基于干细胞的哺乳动物胚胎模型更容易受到遗传和表观遗传扰动的影响,因此有助于发现发育机制。在此,我们重点介绍最近取得的令人兴奋的进展,这些进展产生了大量胚胎发育模型。这些模型的缺陷凸显了我们目前认识的不足,并勾勒出未来的研究方向,为胚胎学开创了一个激动人心的新时代。
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引用次数: 0
Human blastoid as an in vitro model of human blastocysts 作为人类囊胚体外模型的人类囊胚。
IF 4 2区 生物学 Q2 CELL BIOLOGY Pub Date : 2023-12-04 DOI: 10.1016/j.gde.2023.102135
Xiaodong Liu , Jose M Polo

Human development is a highly coordinated process, with any abnormalities during the early embryonic stages that can often have detrimental consequences. The complexity and nuances of human development underpin its significance in embryo research. However, this research is often hindered by limited availability and ethical considerations associated with the use of donated blastocysts from in vitro fertilization (IVF) surplus. Human blastoids offer promising alternatives as they can be easily generated and manipulated in the laboratory while preserving key characteristics of human blastocysts. In this way, they hold the potential to serve as a scalable and ethically permissible resource in embryology research. By utilizing such human embryo models, we can establish a transformative platform that complements the study with IVF embryos, ultimately enhancing our understanding of human embryogenesis.

人类发育是一个高度协调的过程,胚胎早期阶段的任何异常都可能造成有害后果。人类发育的复杂性和细微差别决定了胚胎研究的重要性。然而,由于使用体外受精(IVF)剩余捐赠囊胚的可用性有限且存在伦理方面的考虑,这项研究往往受到阻碍。人类囊胚提供了很有前景的替代品,因为它们可以很容易地在实验室中生成和操作,同时保留人类囊胚的主要特征。因此,它们有可能成为胚胎学研究中可扩展且符合伦理要求的资源。通过利用这种人类胚胎模型,我们可以建立一个变革性平台,对体外受精胚胎研究进行补充,最终提高我们对人类胚胎发生的认识。
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引用次数: 0
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Current Opinion in Genetics & Development
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