Nucleus (Austin, Tex.)最新文献_第2页

Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts. 通过比较重编码位点与不可编辑的对应位点，缩小有益的 A 到 I RNA 编辑的候选范围。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-01-29 DOI: 10.1080/19491034.2024.2304503

Tianyou Zhao, Ling Ma, Shiwen Xu, Wanzhi Cai, Hu Li, Yuange Duan

{"title":"Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts.","authors":"Tianyou Zhao, Ling Ma, Shiwen Xu, Wanzhi Cai, Hu Li, Yuange Duan","doi":"10.1080/19491034.2024.2304503","DOIUrl":"10.1080/19491034.2024.2304503","url":null,"abstract":"Adar-mediated adenosine-to-inosine (A-to-I) RNA editing mainly occurs in nucleus and diversifies the transcriptome in a flexible manner. It has been a challenging task to identify beneficial editing sites from the sea of total editing events. The functional Ser>Gly auto-recoding site in insect Adar gene has uneditable Ser codons in ancestral nodes, indicating the selective advantage to having an editable status. Here, we extended this case study to more metazoan species, and also looked for all Drosophila recoding events with potential uneditable synonymous codons. Interestingly, in D. melanogaster, the abundant nonsynonymous editing is enriched in the codons that have uneditable counterparts, but the Adar Ser>Gly case suggests that the editable orthologous codons in other species are not necessarily edited. The use of editable versus ancestral uneditable codon is a smart way to infer the selective advantage of RNA editing, and priority might be given to these editing sites for functional studies due to the feasibility to construct an uneditable allele. Our study proposes an idea to narrow down the candidates of beneficial recoding sites. Meanwhile, we stress that the matched transcriptomes are needed to verify the conservation of editing events during evolution.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"15 1","pages":"2304503"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10826634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139577285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sensing the squeeze: nuclear mechanotransduction in health and disease. 感知挤压：健康和疾病中的核机械传导。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-07-01 DOI: 10.1080/19491034.2024.2374854

Luv Kishore Srivastava, Allen J Ehrlicher

引用次数: 0

Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. 长非编码 RNA：在细胞应激反应和调节染色质的表观遗传机制中的作用。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-05-22 DOI: 10.1080/19491034.2024.2350180

Jeffrey A Nickerson, Fatemeh Momen-Heravi

引用次数: 0

PML Nuclear bodies: the cancer connection and beyond. PML 核体：与癌症的联系及其他。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-02-27 DOI: 10.1080/19491034.2024.2321265

Majdouline Abou-Ghali, Valérie Lallemand-Breitenbach

{"title":"PML Nuclear bodies: the cancer connection and beyond.","authors":"Majdouline Abou-Ghali, Valérie Lallemand-Breitenbach","doi":"10.1080/19491034.2024.2321265","DOIUrl":"10.1080/19491034.2024.2321265","url":null,"abstract":"Promyelocytic leukemia (PML) nuclear bodies, membrane-less organelles in the nucleus, play a crucial role in cellular homeostasis. These dynamic structures result from the assembly of scaffolding PML proteins and various partners. Recent crystal structure analyses revealed essential self-interacting domains, while liquid-liquid phase separation contributes to their formation. PML bodies orchestrate post-translational modifications, particularly stress-induced SUMOylation, impacting target protein functions. Serving as hubs in multiple signaling pathways, they influence cellular processes like senescence. Dysregulation of PML expression contributes to diseases, including cancer, highlighting their significance. Therapeutically, PML bodies are promising targets, exemplified by successful acute promyelocytic leukemia treatment with arsenic trioxide and retinoic acid restoring PML bodies. Understanding their functions illuminates both normal and pathological cellular physiology, guiding potential therapies. This review explores recent advancements in PML body biogenesis, biochemical activity, and their evolving biological roles.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"15 1","pages":"2321265"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10900273/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139974906","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Apoptosis-induced translocation of nesprin-2 from the nuclear envelope to mitochondria is associated with mitochondrial dysfunction. 凋亡诱导的 nesprin-2 从核包膜转位到线粒体与线粒体功能障碍有关。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-10-15 DOI: 10.1080/19491034.2024.2413501

Hila Zohar, Liora Lindenboim, Oren Gozlan, Gregg G Gundersen, Howard J Worman, Reuven Stein

{"title":"Apoptosis-induced translocation of nesprin-2 from the nuclear envelope to mitochondria is associated with mitochondrial dysfunction.","authors":"Hila Zohar, Liora Lindenboim, Oren Gozlan, Gregg G Gundersen, Howard J Worman, Reuven Stein","doi":"10.1080/19491034.2024.2413501","DOIUrl":"https://doi.org/10.1080/19491034.2024.2413501","url":null,"abstract":"Accumulating evidence suggests that the nuclear envelope (NE) is not just a target, but also a mediator of apoptosis. We showed recently that the NE protein nesprin-2 has pro-apoptotic activity, which involves its subcellular redistribution and Bcl-2 proteins. Here we further characterize the pro-apoptotic activity of nesprin-2 focusing on its redistribution. We assessed the redistribution kinetics of endogenous nesprin-2 tagged with GFP relative to apoptosis-associated mitochondrial dysfunction. The results show apoptosis-induced GFP-nesprin-2G redistribution occurred by two different modes - complete and partial, both lead to appearance of nesprin-2G near the mitochondria. Moreover, GFP-nesprin-2 redistribution is associated with reduction in mitochondrial membrane potential and mitochondrial outer membrane permeabilization and precedes the appearance of morphological features of apoptosis. Our results show that nesprin-2G redistribution and translocation near mitochondria is an early apoptotic effect associated with mitochondrial dysfunction, which may be responsible for the pro-apoptotic function of nesprin-2.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"15 1","pages":"2413501"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11486236/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Emergent microenvironments of nucleoli. 新出现的核小体微环境

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-03-05 DOI: 10.1080/19491034.2024.2319957

Matthew R King, Kiersten M Ruff, Rohit V Pappu

引用次数: 0

Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus. 细胞核聚合物模型中染色质相分离与核形状波动相关。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-05-16 DOI: 10.1080/19491034.2024.2351957

Ali Goktug Attar, Jaroslaw Paturej, Edward J Banigan, Aykut Erbaş

{"title":"Chromatin phase separation and nuclear shape fluctuations are correlated in a polymer model of the nucleus.","authors":"Ali Goktug Attar, Jaroslaw Paturej, Edward J Banigan, Aykut Erbaş","doi":"10.1080/19491034.2024.2351957","DOIUrl":"10.1080/19491034.2024.2351957","url":null,"abstract":"Abnormal cell nuclear shapes are hallmarks of diseases, including progeria, muscular dystrophy, and many cancers. Experiments have shown that disruption of heterochromatin and increases in euchromatin lead to nuclear deformations, such as blebs and ruptures. However, the physical mechanisms through which chromatin governs nuclear shape are poorly understood. To investigate how heterochromatin and euchromatin might govern nuclear morphology, we studied chromatin microphase separation in a composite coarse-grained polymer and elastic shell simulation model. By varying chromatin density, heterochromatin composition, and heterochromatin-lamina interactions, we show how the chromatin phase organization may perturb nuclear shape. Increasing chromatin density stabilizes the lamina against large fluctuations. However, increasing heterochromatin levels or heterochromatin-lamina interactions enhances nuclear shape fluctuations by a \"wetting\"-like interaction. In contrast, fluctuations are insensitive to heterochromatin's internal structure. Our simulations suggest that peripheral heterochromatin accumulation could perturb nuclear morphology, while nuclear shape stabilization likely occurs through mechanisms other than chromatin microphase organization.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"15 1","pages":"2351957"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11407394/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140961039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cytoplasmic nucleoporin assemblage: the cellular artwork in physiology and disease. 细胞质核蛋白组合：生理学和疾病中的细胞艺术品。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-08-12 DOI: 10.1080/19491034.2024.2387534

Junyan Lin, Izabela Sumara

引用次数: 0

eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production. eIF4E 可协调 mRNA 处理、RNA 输出和翻译，从而改变特定蛋白质的生成。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-06-16 DOI: 10.1080/19491034.2024.2360196

Jean-Clément Mars, Biljana Culjkovic-Kraljacic, Katherine L B Borden

{"title":"eIF4E orchestrates mRNA processing, RNA export and translation to modify specific protein production.","authors":"Jean-Clément Mars, Biljana Culjkovic-Kraljacic, Katherine L B Borden","doi":"10.1080/19491034.2024.2360196","DOIUrl":"10.1080/19491034.2024.2360196","url":null,"abstract":"The eukaryotic translation initiation factor eIF4E acts as a multifunctional factor that simultaneously influences mRNA processing, export, and translation in many organisms. Its multifactorial effects are derived from its capacity to bind to the methyl-7-guanosine cap on the 5'end of mRNAs and thus can act as a cap chaperone for transcripts in the nucleus and cytoplasm. In this review, we describe the multifactorial roles of eIF4E in major mRNA-processing events including capping, splicing, cleavage and polyadenylation, nuclear export and translation. We discuss the evidence that eIF4E acts at two levels to generate widescale changes to processing, export and ultimately the protein produced. First, eIF4E alters the production of components of the mRNA processing machinery, supporting a widescale reprogramming of multiple mRNA processing events. In this way, eIF4E can modulate mRNA processing without physically interacting with target transcripts. Second, eIF4E also physically interacts with both capped mRNAs and components of the RNA processing or translation machineries. Further, specific mRNAs are sensitive to eIF4E only in particular mRNA processing events. This selectivity is governed by the presence of cis-acting elements within mRNAs known as USER codes that recruit relevant co-factors engaging the appropriate machinery. In all, we describe the molecular bases for eIF4E's multifactorial function and relevant regulatory pathways, discuss the basis for selectivity, present a compendium of ~80 eIF4E-interacting factors which play roles in these activities and provide an overview of the relevance of its functions to its oncogenic potential. Finally, we summarize early-stage clinical studies targeting eIF4E in cancer.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"15 1","pages":"2360196"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11185188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141332695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In remembrance: Joseph Gall. 纪念：约瑟夫·加尔。

Nucleus (Austin, Tex.) Pub Date : 2024-12-01 Epub Date: 2024-11-10 DOI: 10.1080/19491034.2024.2426552

Thoru Pederson

引用次数: 0