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Cover 封面
Pub Date : 2024-11-08 DOI: 10.1016/S2772-8927(24)00070-1
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引用次数: 0
Phase-separated chromatin compartments: Orchestrating gene expression through condensation 相分离的染色质区室:通过凝集协调基因表达
Pub Date : 2024-10-12 DOI: 10.1016/j.cellin.2024.100213
Xin Li , Chengzhi Liu , Zhichao Lei , Huan Chen , Liang Wang
Eukaryotic genomes are organized into distinct chromatin compartments, some of which exhibit properties of biomolecular condensates. These condensates primarily form due to chromatin-associated proteins/complexes (CAPs). CAPs play a crucial role in gene expression, functioning as either transcriptional repressors or activators. Phase separation, a well-established biophysical phenomenon, is a key driver of chromatin condensate formation by CAPs. Notably, multivalent CAPs with the ability to engage in diverse interactions promote chromatin compaction, leading to the formation of transcriptionally repressed compartments. Conversely, interactions between intrinsically disordered region (IDR)-containing transcriptional regulators, mediated by their multivalent IDRs, lead to the formation of protein-rich, transcriptionally active droplets on decondensed genomic regions. Interestingly, both repressive heterochromatin and activating euchromatin condensates exhibit spontaneous phase separation and selectively enrich components with concordant transcriptional functions. This review delves into the mechanisms by which transcriptionally repressive CAPs orchestrate the formation of repressed chromatin domains. We further explore how a diverse array of transcription-related CAPs or core histone variants, via phase separation, influence gene expression by inducing erroneous transcription events, regulating expression levels, and facilitating the interconversion of transcriptionally repressed and active regions.
真核生物基因组被组织成不同的染色质区室,其中一些表现出生物分子凝聚物的特性。这些凝聚体主要是由染色质相关蛋白/复合物(CAPs)形成的。CAPs 在基因表达中起着至关重要的作用,可作为转录抑制因子或激活因子发挥作用。相分离是一种公认的生物物理现象,是 CAPs 形成染色质凝聚物的关键驱动因素。值得注意的是,能够参与多种相互作用的多价 CAP 可促进染色质的压实,从而形成转录抑制区。与此相反,含有内在紊乱区(IDR)的转录调节因子在多价 IDR 的介导下相互作用,导致在解聚的基因组区域形成富含蛋白质、转录活跃的液滴。有趣的是,抑制性异染色质和激活性超染色质凝集物都表现出自发的相分离,并选择性地富集具有一致转录功能的成分。本综述深入探讨了转录抑制性 CAP 协调形成抑制性染色质域的机制。我们将进一步探讨各种与转录相关的 CAP 或核心组蛋白变体如何通过相分离,诱导错误的转录事件、调节表达水平以及促进转录抑制区和活性区的相互转换,从而影响基因表达。
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引用次数: 0
Transcripts derived from the neocortical enhancer of Ctnnb1 promote the enhancer-promoter interaction and maintain Ctnnb1 transcription 源自 Ctnnb1 新皮质增强子的转录本促进增强子与启动子之间的相互作用并维持 Ctnnb1 的转录
Pub Date : 2024-10-11 DOI: 10.1016/j.cellin.2024.100212
Chen Zhao , Liang Wang , Junbao Wang, Kuan Tian, Xiaojiao Hua, Fangyu Wang, Yan Zhou
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引用次数: 0
APC orchestrates microtubule dynamics by acting as a positive regulator of KIF2A and a negative regulator of CLASPs APC 通过充当 KIF2A 的正调控因子和 CLASPs 的负调控因子来协调微管动力学
Pub Date : 2024-10-11 DOI: 10.1016/j.cellin.2024.100210
Yong Wang , Xinping Liu , Zheng Liu , Shasha Hua , Kai Jiang
Tumor suppressor protein Adenomatous polyposis coli protein (APC) is an EB-binding and microtubule (MT) plus end-tracking protein; however, how exactly APC regulates MT dynamics remains elusive. Here, we show that in LLC-PK1 cells, APC and KIF2A, an MT depolymerase, form a complex clustering at the cell edge and destabilize MTs at the MT plus ends. Further biochemical characterization and mutational analysis reveal key residues for the APC-KIF2A interaction. In addition, APC counteracts the major MT-stabilizer CLASPs at MT plus ends and promotes directional cell migration via modulating cell adhesion force. Reconstitution experiments demonstrate that APC potentiates KIF2A-induced MT catastrophes and antagonizes the stabilizing effect of CLASP2 in vitro. In summary, APC functions as a positive regulator of MT-destabilizer and a negative regulator of MT-stabilizer to orchestrate MT dynamics.
肿瘤抑制蛋白腺瘤性息肉病大肠杆菌蛋白(APC)是一种EB结合蛋白和微管(MT)加端追踪蛋白;然而,APC究竟是如何调节MT动态的仍然令人费解。在这里,我们发现在 LLC-PK1 细胞中,APC 和 MT 解聚酶 KIF2A 在细胞边缘形成一个复合体,并在 MT 加端破坏 MT 的稳定性。进一步的生化鉴定和突变分析揭示了 APC-KIF2A 相互作用的关键残基。此外,APC 还能抵消 MT 加端的主要 MT 稳定剂 CLASPs,并通过调节细胞粘附力促进细胞定向迁移。重组实验证明,APC 能增强 KIF2A 诱导的 MT 灾难,并在体外拮抗 CLASP2 的稳定作用。总之,APC 可作为 MT 失稳器的正调控因子和 MT 稳定器的负调控因子协调 MT 动态。
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引用次数: 0
Just a SNP away: The future of in vivo massively parallel reporter assay 只差一个 SNP体内大规模并行报告分析的未来
Pub Date : 2024-10-10 DOI: 10.1016/j.cellin.2024.100214
Katherine N. Degner , Jessica L. Bell , Sean D. Jones , Hyejung Won
The human genome is largely noncoding, yet the field is still grasping to understand how noncoding variants impact transcription and contribute to disease etiology. The massively parallel reporter assay (MPRA) has been employed to characterize the function of noncoding variants at unprecedented scales, but its application has been largely limited by the in vitro context. The field will benefit from establishing a systemic platform to study noncoding variant function across multiple tissue types under physiologically relevant conditions. However, to date, MPRA has been applied to only a handful of in vivo conditions. Given the complexity of the central nervous system and its widespread interactions with all other organ systems, our understanding of neuropsychiatric disorder-associated noncoding variants would be greatly advanced by studying their functional impact in the intact brain. In this review, we discuss the importance, technical considerations, and future applications of implementing MPRA in the in vivo space with the focus on neuropsychiatric disorders.
人类基因组在很大程度上是非编码的,但该领域仍在努力了解非编码变异如何影响转录并导致疾病的发生。大规模并行报告测定(MPRA)已被用于以前所未有的规模描述非编码变异体的功能,但其应用在很大程度上受到体外环境的限制。建立一个系统平台,在生理相关条件下研究多种组织类型的非编码变体功能,将使该领域受益匪浅。然而,迄今为止,MPRA 仅应用于少数体内条件。鉴于中枢神经系统的复杂性及其与所有其他器官系统的广泛相互作用,通过研究神经精神障碍相关非编码变异体在完整大脑中的功能影响,将极大地促进我们对这些变异体的理解。在这篇综述中,我们将以神经精神疾病为重点,讨论在体内空间实施 MPRA 的重要性、技术考虑因素和未来应用。
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引用次数: 0
Roles of core fucosylation modification in immune system and diseases 核心岩藻糖基化修饰在免疫系统和疾病中的作用
Pub Date : 2024-10-09 DOI: 10.1016/j.cellin.2024.100211
Qiu Pan , Xiao-Lian Zhang
Core fucosylation, catalyzed by α1,6-fucosyltransferase (FUT8), is an important N-glycosylation modification process that attaches a fucose residue via an α1,6-linkage to the core N-acetylglucosamine of N-glycans in mammals. Research over the past three decades has revealed the critical role of FUT8-mediated core fucosylation modification in various physiological and pathological processes, including cell growth, adhesion, receptor activation, antibody-dependent cellular cytotoxicity (ADCC), tumor metastasis and infections. This review discusses the immune system function involving FUT8 and the mechanisms by which core fucosylation regulates immunity and contributes to disease. A deeper understanding of these mechanisms can provide insights into cellular biology and suggest new therapeutic approaches and targets for related diseases.
由α1,6-岩藻糖基转移酶(FUT8)催化的核心岩藻糖基化是一种重要的N-糖基化修饰过程,它通过α1,6-连接将岩藻糖残基连接到哺乳动物体内N-聚糖的核心N-乙酰葡糖胺上。过去三十年的研究揭示了 FUT8 介导的核心岩藻糖基化修饰在细胞生长、粘附、受体激活、抗体依赖性细胞毒性(ADCC)、肿瘤转移和感染等各种生理和病理过程中的关键作用。这篇综述讨论了涉及 FUT8 的免疫系统功能以及核心岩藻糖基化调节免疫和导致疾病的机制。加深对这些机制的了解可以深入了解细胞生物学,并为相关疾病提出新的治疗方法和靶点。
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引用次数: 0
Cover 封面
Pub Date : 2024-10-01 DOI: 10.1016/S2772-8927(24)00057-9
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引用次数: 0
Spontaneous and environment induced genomic alterations in yeast model 酵母模型中自发和环境诱导的基因组变化
Pub Date : 2024-09-26 DOI: 10.1016/j.cellin.2024.100209
Ke-Jing Li , Lei Qi , Ying-Xuan Zhu , Min He , Qian Xiang , Dao-Qiong Zheng
While genomic alterations are fundamental to biological evolution, enabling adaptation and diversity, they can also result in detrimental outcomes, such as the development of genetic diseases including cancer. The budding yeast Saccharomyces cerevisiae serves as an exemplary model for investigating the mechanisms behind various genomic alterations, including point mutations, chromosomal rearrangements, and whole-chromosome aneuploidy. In this review, we highlight the application of genetic screening systems to assess the mutagenic effects of physical and chemical agents efficiently. Additionally, we discuss the utilization of high-throughput sequencing technologies to uncover comprehensive genomic alterations and rare genetic events. We provide a detailed summary of the features of genomic alterations and discuss the genetic mechanisms driving these changes under both spontaneous and stress-induced conditions. Given the high conservation of DNA replication and repair machinery across different organisms, the insights gained from studies on yeast offer valuable perspectives for understanding the delicate balance between genome plasticity and integrity in other species.
虽然基因组改变是生物进化的基础,能促进生物的适应性和多样性,但它们也可能导致有害的结果,如发展成包括癌症在内的遗传疾病。芽殖酵母是研究点突变、染色体重排和全染色体非整倍体等各种基因组改变背后机制的典范。在这篇综述中,我们重点介绍了基因筛选系统在有效评估物理和化学试剂诱变效应方面的应用。此外,我们还讨论了如何利用高通量测序技术来发现全面的基因组改变和罕见遗传事件。我们详细总结了基因组改变的特征,并讨论了在自发和应激诱导条件下驱动这些改变的遗传机制。鉴于不同生物的 DNA 复制和修复机制高度一致,从酵母研究中获得的见解为理解其他物种基因组可塑性和完整性之间的微妙平衡提供了宝贵的视角。
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引用次数: 0
Modeling respiratory tract diseases for clinical translation employing conditionally reprogrammed cells 利用条件重编程细胞建立呼吸道疾病模型,促进临床转化
Pub Date : 2024-09-18 DOI: 10.1016/j.cellin.2024.100201
Danyal Daneshdoust , Kai He , Qi-En Wang , Jenny Li , Xuefeng Liu
Preclinical models serve as indispensable tools in translational medicine. Specifically, patient-derived models such as patient-derived xenografts (PDX), induced pluripotent stem cells (iPSC), organoids, and recently developed technique of conditional reprogramming (CR) have been employed to reflect the host characteristics of diseases. CR technology involves co-culturing epithelial cells with irradiated Swiss-3T3-J2 mouse fibroblasts (feeder cells) in the presence of a Rho kinase (ROCK) inhibitor, Y-27632. CR technique facilitates the rapid conversion of both normal and malignant cells into a “reprogrammed stem-like” state, marked by robust in vitro proliferation. This is achieved without reliance on exogenous gene expression or viral transfection, while maintaining the genetic profile of the parental cells. So far, CR technology has been used to study biology of diseases, targeted therapies (precision medicine), regenerative medicine, and noninvasive diagnosis and surveillance. Respiratory diseases, ranking as the third leading cause of global mortality, pose a significant burden to healthcare systems worldwide. Given the substantial mortality and morbidity rates of respiratory diseases, efficient and rapid preclinical models are imperative to accurately recapitulate the diverse spectrum of respiratory conditions. In this article, we discuss the applications and future potential of CR technology in modeling various respiratory tract diseases, including lung cancer, respiratory viral infections (such as influenza and Covid-19 and etc.), asthma, cystic fibrosis, respiratory papillomatosis, and upper aerodigestive track tumors. Furthermore, we discuss the potential utility of CR in personalized medicine, regenerative medicine, and clinical translation.
临床前模型是转化医学不可或缺的工具。具体来说,患者衍生模型,如患者衍生异种移植(PDX)、诱导多能干细胞(iPSC)、器官组织以及最近开发的条件重编程(CR)技术,都被用来反映疾病的宿主特征。条件重编程技术包括在Rho激酶(ROCK)抑制剂Y-27632的作用下,将上皮细胞与经过辐照的Swiss-3T3-J2小鼠成纤维细胞(饲养细胞)进行共培养。CR技术有助于将正常细胞和恶性细胞快速转化为 "重编程干样 "状态,其特点是体外增殖强劲。实现这一目标无需依赖外源基因表达或病毒转染,同时还能保持亲代细胞的遗传特征。迄今为止,CR 技术已被用于疾病生物学研究、靶向治疗(精准医疗)、再生医学以及无创诊断和监测。呼吸系统疾病是导致全球死亡的第三大原因,给全球医疗系统造成了沉重负担。鉴于呼吸系统疾病的死亡率和发病率都很高,因此必须建立高效、快速的临床前模型,以准确再现各种呼吸系统疾病。本文将讨论 CR 技术在各种呼吸道疾病建模中的应用和未来潜力,包括肺癌、呼吸道病毒感染(如流感和 Covid-19 等)、哮喘、囊性纤维化、呼吸道乳头状瘤病和上消化道肿瘤。此外,我们还讨论了 CR 在个性化医学、再生医学和临床转化方面的潜在用途。
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引用次数: 0
The role of SUMOylation in biomolecular condensate dynamics and protein localization SUMOylation 在生物分子凝聚动态和蛋白质定位中的作用
Pub Date : 2024-09-10 DOI: 10.1016/j.cellin.2024.100199
Emily Gutierrez-Morton, Yanchang Wang
As a type of protein post-translational modification, SUMOylation is the process that attaches a small ubiquitin-like modifier (SUMO) to lysine residues of protein substrates. Not only do SUMO and ubiquitin exhibit structure similarity, but the enzymatic cascades for SUMOylation and ubiquitination are also similar. It is well established that protein ubiquitination triggers proteasomal degradation, but the function of SUMOylation remains poorly understood compared to ubiquitination. Recent studies reveal the role of SUMOylation in regulating protein localization, stability, and interaction networks. SUMO can be covalently attached to substrates either as an individual monomer (monoSUMOylation) or as a polymeric SUMO chain (polySUMOylation). Strikingly, mono- and polySUMOylation likely play distinct roles in protein subcellular localization and the assembly/disassembly of biomolecular condensates, which are membraneless cellular compartments with concentrated biomolecules. In this review, we summarize the recent advances in the understanding of the function and regulation of SUMOylation, which could reveal potential therapeutic targets in disease pathogenesis.
作为蛋白质翻译后修饰的一种,SUMOylation 是一种将小型泛素样修饰物(SUMO)连接到蛋白质底物赖氨酸残基上的过程。SUMO 和泛素不仅结构相似,而且 SUMOylation 和泛素化的酶级联也很相似。蛋白质泛素化会引发蛋白酶体降解,这一点已得到公认,但与泛素化相比,人们对 SUMOylation 的功能仍然知之甚少。最近的研究揭示了 SUMOylation 在调节蛋白质定位、稳定性和相互作用网络中的作用。SUMO 可以以单个单体(单SUMOylation)或聚合 SUMO 链(聚 SUMOylation)的形式共价连接到底物上。令人震惊的是,单SUMO酰化和多SUMO酰化可能在蛋白质亚细胞定位和生物分子凝聚体的组装/解组装过程中发挥着不同的作用。在这篇综述中,我们总结了对 SUMOylation 功能和调控的最新认识进展,这些进展可能揭示了疾病发病机制中的潜在治疗靶点。
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引用次数: 0
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Cell insight
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