Nucleus (Austin, Tex.)最新文献_第2页

Closing the loops: chromatin loop dynamics after DNA damage. 闭合环：DNA损伤后染色质环动力学。

Nucleus (Austin, Tex.) Pub Date : 2025-12-01 Epub Date: 2024-12-25 DOI: 10.1080/19491034.2024.2438633

Pierre-Alexandre Vidi, Jing Liu, Keith Bonin, Kerry Bloom

引用次数: 0

Correction. 修正。

Nucleus (Austin, Tex.) Pub Date : 2025-12-01 Epub Date: 2025-01-21 DOI: 10.1080/19491034.2024.2443274

引用次数: 0

Constitutive heterochromatin controls nuclear mechanics, morphology, and integrity through H3K9me3 mediated chromocenter compaction. 本构异染色质通过H3K9me3介导的染色质压实控制核力学、形态和完整性。

IF 4.5

Nucleus (Austin, Tex.) Pub Date : 2025-12-01 Epub Date: 2025-04-09 DOI: 10.1080/19491034.2025.2486816

Gianna Manning, Andy Li, Nebiyat Eskndir, Marilena Currey, Andrew D Stephens

{"title":"Constitutive heterochromatin controls nuclear mechanics, morphology, and integrity through H3K9me3 mediated chromocenter compaction.","authors":"Gianna Manning, Andy Li, Nebiyat Eskndir, Marilena Currey, Andrew D Stephens","doi":"10.1080/19491034.2025.2486816","DOIUrl":"10.1080/19491034.2025.2486816","url":null,"abstract":"Aberrant nuclear morphology is a hallmark of human disease and causes nuclear dysfunction. Perturbed nuclear mechanics via reduced heterochromatin weakens the nucleus resulting in nuclear blebbing and rupture. While the role of heterochromatin is known, the separate roles of constitutive heterochromatin methylation states remains elusive. Using MEF and HT1080 cells, we isolated the individual contribution of constitutive heterochromatin H3K9 methylation states through histone methyltransferase inhibitors. Inhibition of SUV39H1 via Chaetocin downregulates H3K9 trimethylation (me3), while inhibition of G9a via BIX01294 downregulates H3K9 dimethylation (me2). Overall, the loss of H3K9me3 increased nuclear blebbing and rupture in interphase nuclei due to decreased nuclear rigidity from decompaction of chromocenters. Oppositely, loss of H3K9me2 decreased nuclear blebbing and rupture with increased nuclear rigidity and more compact chromocenters. We show that facultative heterochromatin and HP1α are non-essential for chromocenter compaction. Constitutive heterochromatin provides essential nuclear mechanical support to maintain nuclear shape and integrity through chromocenter compaction.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"16 1","pages":"2486816"},"PeriodicalIF":4.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11988277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144735915","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

Bridging-mediated compaction of mitotic chromosomes. 桥接介导的有丝分裂染色体的压实。

IF 4.5

Nucleus (Austin, Tex.) Pub Date : 2025-12-01 Epub Date: 2025-05-09 DOI: 10.1080/19491034.2025.2497765

Giada Forte, Lora Boteva, Nick Gilbert, Peter R Cook, Davide Marenduzzo

引用次数: 0

Interplay of replication timing, DNA repair, and translesion synthesis in UV mutagenesis in yeast. 酵母紫外诱变中复制时间、DNA修复和翻译合成的相互作用。

Nucleus (Austin, Tex.) Pub Date : 2025-12-01 Epub Date: 2025-03-13 DOI: 10.1080/19491034.2025.2476935

Allysa Sewell, John J Wyrick

{"title":"Interplay of replication timing, DNA repair, and translesion synthesis in UV mutagenesis in yeast.","authors":"Allysa Sewell, John J Wyrick","doi":"10.1080/19491034.2025.2476935","DOIUrl":"10.1080/19491034.2025.2476935","url":null,"abstract":"Replication timing during S-phase impacts mutation rates in yeast and human cancers; however, the exact mechanism involved remains unclear. Here, we analyze the impact of replication timing on UV mutagenesis in Saccharomyces cerevisiae. Our analysis indicates that UV mutations are enriched in early-replicating regions of the genome in wild-type cells, but in cells deficient in global genomic-nucleotide excision repair (GG-NER), mutations are enriched in late-replicating regions. Analysis of UV damage maps revealed that cyclobutane pyrimidine dimers are enriched in late-replicating regions, but this enrichment is almost entirely due to repetitive ribosomal DNA. Complex mutations typically associated with TLS activity are also elevated in late-replicating regions in GG-NER deficient cells. We propose that UV mutagenesis is higher in early-replicating regions in repair-competent cells because there is less time to repair the lesion prior to undergoing replication. However, in the absence of GG-NER, increased TLS activity promotes UV mutagenesis in late-replicating regions.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"16 1","pages":"2476935"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11913381/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143617679","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

H2A.Z-nucleosomes are stabilized by the superhelicity-dependent DNA binding of the C-terminal tail of the histone variant. H2A。z -核小体通过组蛋白变体的c末端末端的超螺旋依赖DNA结合来稳定。

IF 4.5

Nucleus (Austin, Tex.) Pub Date : 2025-12-01 Epub Date: 2025-09-09 DOI: 10.1080/19491034.2025.2557113

Ibtissem Benhamza, Laszlo Imre, Zutao Yu, Peter Nanasi, Pialy Sen, Kata Nora Enyedi, Katalin Goda, György Vamosi, Gabor Szabo

{"title":"H2A.Z-nucleosomes are stabilized by the superhelicity-dependent DNA binding of the C-terminal tail of the histone variant.","authors":"Ibtissem Benhamza, Laszlo Imre, Zutao Yu, Peter Nanasi, Pialy Sen, Kata Nora Enyedi, Katalin Goda, György Vamosi, Gabor Szabo","doi":"10.1080/19491034.2025.2557113","DOIUrl":"10.1080/19491034.2025.2557113","url":null,"abstract":"Using an in situ nucleosome stability assay based on salt extraction, we identified distinct stability features of H2A.Z-containing nucleosomes linked to alternative interactions of the histone variant's C-terminal tail (Imre et al., Nat. Commun., 2024). In DT40 cells expressing either full-length or C-terminally truncated human H2A.Z1, we show that nucleosome stability is tail-dependent also through the spectacles of intercalator sensitivity, raising the possibility that the tail may bind to DNA in a superhelicity-dependent fashion. Supporting this, fluorescence correlation spectroscopy detected binding of a fluorescent H2A.Z-tail nonapeptide to supercoiled-but not relaxed-plasmid DNA, while a scrambled peptide showed negligible binding. The DNA topology-dependent binding of the unstructured H2A.Z C-terminus, by affecting nucleosome stability, may be of functional significance in various roles of the histone variant, demonstrating the strong interplay between DNA topology and nucleosome stability and exemplifying how it may be exploited by the cell for regulatory purposes.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"16 1","pages":"2557113"},"PeriodicalIF":4.5,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12427435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145031309","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

Perinuclear organelle trauma at the nexus of cardiomyopathy pathogenesis arising from loss of function LMNA mutation. 核周细胞器损伤是由功能丧失引起的心肌病发病机制的纽带。

Nucleus (Austin, Tex.) Pub Date : 2025-12-01 Epub Date: 2025-01-09 DOI: 10.1080/19491034.2024.2449500

Jason C Choi

引用次数: 0

Unraveling gene expression: a beginner's guide from chromatin modifications to mRNA export in Saccharomyces cerevisiae. 揭示基因表达：从酿酒酵母的染色质修饰到mRNA出口的初学者指南。

Nucleus (Austin, Tex.) Pub Date : 2025-12-01 Epub Date: 2025-06-13 DOI: 10.1080/19491034.2025.2516909

Joan Serrano-Quílez, Susana Rodriguez-Navarro

{"title":"Unraveling gene expression: a beginner's guide from chromatin modifications to mRNA export in Saccharomyces cerevisiae.","authors":"Joan Serrano-Quílez, Susana Rodriguez-Navarro","doi":"10.1080/19491034.2025.2516909","DOIUrl":"10.1080/19491034.2025.2516909","url":null,"abstract":"Understanding gene expression requires grasping its multi-step processes, from chromatin remodeling to mRNA export. This manuscript provides an accessible entry point for PhD students and junior postdocs beginning research in this area, using yeast as a model organism. We present a beginner-friendly overview of gene expression, emphasizing the dynamic interplay between chromatin modifications, transcription, mRNA processing, and export. Key topics include chromatin organization, with a focus on H2B ubiquitylation and H3 methylation crosstalk; transcriptional control by RNA polymerase II, including initiation, elongation, and termination; and the export of mRNAs via Mex67-Mtr2, adaptor proteins, and the TREX and TREX-2 complexes at the nuclear pore complex. Relevant examples from yeast genetics, biochemistry, and structural biology illustrate each step. This overview aims to equip new researchers with foundational knowledge and provides references to key studies, current challenges, and open questions in the regulation of gene expression.","PeriodicalId":74323,"journal":{"name":"Nucleus (Austin, Tex.)","volume":"16 1","pages":"2516909"},"PeriodicalIF":0.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12169046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144287502","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

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