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Heterochromatin in plant meiosis Nucleus (IF 3.7) Pub Date : 2024-03-15 Cong Wang, Zhiyu Chen, Gregory P. Copenhaver, Yingxiang Wang
Heterochromatin is an organizational property of eukaryotic chromosomes, characterized by extensive DNA and histone modifications, that is associated with the silencing of transposable elements and...
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Inhibition of chromatin condensation disrupts planar cell migration Nucleus (IF 3.7) Pub Date : 2024-03-11 Jack Forman, Briar Hine, Samantha Kaonis, Soham Ghosh
Cell migration involves the actin cytoskeleton, and recently recognized nuclear involvement. In this study, we explore the impact of chromatin remodeling on cell migration using NIH 3T3 cells and a...
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Emergent microenvironments of nucleoli Nucleus (IF 3.7) Pub Date : 2024-03-05 Matthew R. King, Kiersten M. Ruff, Rohit V. Pappu
In higher eukaryotes, the nucleolus harbors at least three sub-phases that facilitate multiple functionalities including ribosome biogenesis. The three prominent coexisting sub-phases are the fibri...
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PML Nuclear bodies: the cancer connection and beyond Nucleus (IF 3.7) Pub Date : 2024-02-27 Majdouline Abou-Ghali, Valérie Lallemand-Breitenbach
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 P...
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Nuclear pore dysfunction and disease: a complex opportunity Nucleus (IF 3.7) Pub Date : 2024-02-21 Charlotte M. Fare, Jeffrey D. Rothstein
The separation of genetic material from bulk cytoplasm has enabled the evolution of increasingly complex organisms, allowing for the development of sophisticated forms of life. However, this comple...
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Nuclear actin filaments – a historical perspective Nucleus (IF 3.7) Pub Date : 2024-02-21 Maria Kristha Fernandez, Molika Sinha, Mia Zidan, Malte Renz
The view on nuclear filaments formed by non-skeletal β-actin has significantly changed over the decades. Initially, filamentous actin was observed in amphibian oocyte nuclei and only under specific...
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Phase separation in nuclear biology Nucleus (IF 3.7) Pub Date : 2024-02-12 Hao Jiang
Published in Nucleus (Vol. 15, No. 1, 2024)
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The genome in space and time comes of age Nucleus (IF 3.7) Pub Date : 2024-02-01 Martin Rey-Millet, Kerstin Bystricky, the International Nucleome Consortium
DNA sequencing is not enough to grasp the complexity of genome organization and function. The four-dimensional (three in space, one in time) configuration of the eukaryotic nucleus varies with cell...
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The perinucleolar compartment: structure, function, and utility in anti-cancer drug development Nucleus (IF 3.7) Pub Date : 2024-01-27 Eugene V. Makeyev, Sui Huang
The perinucleolar compartment (PNC) was initially identified as a nuclear structure enriched for the polypyrimidine tract-binding protein. Since then, the PNC has been implicated in carcinogenesis....
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Narrowing down the candidates of beneficial A-to-I RNA editing by comparing the recoding sites with uneditable counterparts Nucleus (IF 3.7) Pub Date : 2024-01-29 Tianyou Zhao, Ling Ma, Shiwen Xu, Wanzhi Cai, Hu Li, Yuange Duan
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 editin...
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Sculpting nuclear envelope identity from the endoplasmic reticulum during the cell cycle Nucleus (IF 3.7) Pub Date : 2024-01-18 Pallavi Deolal, Julia Scholz, Kaike Ren, Helena Bragulat-Teixidor, Shotaro Otsuka
The nuclear envelope (NE) regulates nuclear functions, including transcription, nucleocytoplasmic transport, and protein quality control. While the outer membrane of the NE is directly continuous w...
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Phase separation in DNA double-strand break response Nucleus (IF 3.7) Pub Date : 2023-12-25 Huan-Lei Liu, Hao Nan, Wan-Wen Zhao, Xiang-Bo Wan, Xin-Juan Fan
DNA double-strand break (DSB) is the most dangerous type of DNA damage, which may lead to cell death or oncogenic mutations. Homologous recombination (HR) and nonhomologous end-joining (NHEJ) are t...
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CiRS-7 Enhances the Liquid-liquid Phase Separation of miRISC and Promotes DNA Damage Repair Nucleus (IF 3.7) Pub Date : 2023-12-17 Yun-Long Wang, Li-Li Feng, Jie Shi, Wan-Ying Chen, Shu-Ying Bie, Shao-Mei Bai, Guang-Dong Zeng, Rui-Zhi Wang, Jian Zheng, Xiang-Bo Wan, Xin-Juan Fan
Noncoding RNAs have been found to play important roles in DNA damage repair, whereas the participation of circRNA remains undisclosed. Here, we characterized ciRS-7, a circRNA containing over 70 pu...
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Histone locus bodies: a paradigm for how nuclear biomolecular condensates control cell cycle regulated gene expression Nucleus (IF 3.7) Pub Date : 2023-12-14 Mark S. Geisler, James P. Kemp Jr., Robert J. Duronio
Histone locus bodies (HLBs) are biomolecular condensates that assemble at replication-dependent (RD) histone genes in animal cells. These genes produce unique mRNAs that are not polyadenylated and ...
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The farnesyl transferase inhibitor (FTI) lonafarnib improves nuclear morphology in ZMPSTE24-deficient fibroblasts from patients with the progeroid disorder MAD-B Nucleus (IF 3.7) Pub Date : 2023-12-05 Kamsi O. Odinammadu, Khurts Shilagardi, Kelsey Tuminelli, Daniel P. Judge, Leslie B. Gordon, Susan Michaelis
Several related progeroid disorders are caused by defective post-translational processing of prelamin A, the precursor of the nuclear scaffold protein lamin A, encoded by LMNA. Prelamin A undergoes...
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Beyond ribosome biogenesis: noncoding nucleolar RNAs in physiology and tumor biology Nucleus (IF 3.7) Pub Date : 2023-10-31 Nuray Böğürcü-Seidel, Nadja Ritschel, Till Acker, Attila Németh
The nucleolus, the largest subcompartment of the nucleus, stands out from the nucleoplasm due to its exceptionally high local RNA and low DNA concentrations. Within this central hub of nuclear RNA ...
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Prelamin A and ZMPSTE24 in premature and physiological aging Nucleus (IF 3.7) Pub Date : 2023-10-26 Howard J. Worman, Susan Michaelis
As human longevity increases, understanding the molecular mechanisms that drive aging becomes ever more critical to promote health and prevent age-related disorders. Premature aging disorders or pr...
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Revisiting the truncated lamin A produced by a commonly used strain of Lmna knockout mice Nucleus (IF 3.7) Pub Date : 2023-09-27 Joonyoung R. Kim, Paul H. Kim, Ashley Presnell, Yiping Tu, Stephen G. Young
The Lmna knockout mouse (Lmna–/–) created by Sullivan and coworkers in 1999 has been widely used to examine lamin A/C function. The knockout allele contains a deletion of Lmna intron 7–exon 11 sequ...
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Coilin and Cajal bodies Nucleus (IF 3.7) Pub Date : 2023-09-08 David Staněk
ABSTRACT The nucleus of higher eukaryotes contains a number of structures that concentrate specific biomolecules and play distinct roles in nuclear metabolism. In recent years, the molecular mechanisms controlling their formation have been intensively studied. In this brief review, I focus on coilin and Cajal bodies. Coilin is a key scaffolding protein of Cajal bodies that is evolutionarily conserved
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Interdependent changes of nuclear lamins, nuclear pore complexes, and ploidy regulate cellular regeneration and stress response in the heart Nucleus (IF 3.7) Pub Date : 2023-08-22 Yao Li, Alberto Bertozzi, Mellissa RW Mann, Bernhard Kühn
ABSTRACT In adult mammals, many heart muscle cells (cardiomyocytes) are polyploid, do not proliferate (post-mitotic), and, consequently, cannot contribute to heart regeneration. In contrast, fetal and neonatal heart muscle cells are diploid, proliferate, and contribute to heart regeneration. We have identified interdependent changes of the nuclear lamina, nuclear pore complexes, and DNA-content (ploidy)
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A survey of the specificity and mechanism of 1,6 hexanediol-induced disruption of nuclear transport Nucleus (IF 3.7) Pub Date : 2023-07-27 Elizabeth C. Riquelme Barrientos, Tegan A. Otto, Sara N. Mouton, Anton Steen, Liesbeth M. Veenhoff
ABSTRACT Selective transport through the nuclear pore complex (NPC) depends on the dynamic binding of FG-repeat containing nucleoporins, the FG-nups, with each other and with Karyopherins (Kaps). Here, we assessed the specificity and mechanism by which the aliphatic alcohol 1,6-hexanediol (1,6HD) disrupts the permeability barrier of NPCs in live baker’s yeast cells. After a 10-minute exposure to 5%
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Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes Nucleus (IF 3.7) Pub Date : 2023-07-19 Clare S.K. Lee, Matthias Weiβ, Stephan Hamperl
ABSTRACT In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive
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Transcriptional condensates and phase separation: condensing information across scales and mechanisms Nucleus (IF 3.7) Pub Date : 2023-05-22 Justin Demmerle, Siyuan Hao, Danfeng Cai
ABSTRACT Transcription is the fundamental process of gene expression, which in eukaryotes occurs within the complex physicochemical environment of the nucleus. Decades of research have provided extreme detail in the molecular and functional mechanisms of transcription, but the spatial and genomic organization of transcription remains mysterious. Recent discoveries show that transcriptional components
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The interplay between viral molecular mimicry and host chromatin dynamics Nucleus (IF 3.7) Pub Date : 2023-05-22 Shumin Xiao, Yajing Wang, Shan Shan, Zheng Zhou
ABSTRACT Molecular mimicry is a commonly used mechanism by viruses to manipulate host cellular machinery and coordinate their life cycles. While histone mimicry is well studied, viruses also employ other mimicry strategies to affect chromatin dynamics. However, the relationship between viral molecular mimicry and host chromatin regulation is not well understood. This review summarizes recent advances
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Transcription factor condensates and signaling driven transcription Nucleus (IF 3.7) Pub Date : 2023-05-02 Rajat Mann, Dimple Notani
ABSTRACT Transcription Factor (TF) condensates are a heterogenous mix of RNA, DNA, and multiple co-factor proteins capable of modulating the transcriptional response of the cell. The dynamic nature and the spatial location of TF-condensates in the 3D nuclear space is believed to provide a fast response, which is on the same pace as the signaling cascade and yet ever-so-specific in the crowded environment
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Lamin B1 overexpression alters chromatin organization and gene expression Nucleus (IF 3.7) Pub Date : 2023-04-18 Jeanae M. Kaneshiro, Juliana S. Capitanio, Martin W. Hetzer
ABSTRACT Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through
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Differential contributions of nuclear lamina association and genome compartmentalization to gene regulation Nucleus (IF 3.7) Pub Date : 2023-04-05 Priyojit Das, Rebeca San Martin, Rachel Patton McCord
ABSTRACT Chromatin regions that interact with the nuclear lamina are often heterochromatic, repressed in gene expression, and in the spatial B compartment. However, exceptions to this trend allow us to examine the relative impact of lamin association and spatial compartment on gene regulation. Here, we compared lamin association, gene expression, Hi-C, and histone mark datasets from cell lines representing
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Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies Nucleus (IF 3.7) Pub Date : 2023-03-06 Sofie S. Schmøkel, Iver Nordentoft, Sia V. Lindskrog, Philippe Lamy, Michael Knudsen, Jørgen Bjerggaard Jensen, Lars Dyrskjøt
ABSTRACT This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times
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Through the lens of phase separation: intrinsically unstructured protein and chromatin looping Nucleus (IF 3.7) Pub Date : 2023-02-23 Ling Cai, Gang Greg Wang
ABSTRACT The establishment, maintenance and dynamic regulation of three-dimensional (3D) chromatin structures provide an important means for partitioning of genome into functionally distinctive domains, which helps to define specialized gene expression programs associated with developmental stages and cell types. Increasing evidence supports critical roles for intrinsically disordered regions (IDRs)
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Nuclear envelope budding and its cellular functions Nucleus (IF 3.7) Pub Date : 2023-02-22 Katharina S. Keuenhof, Verena Kohler, Filomena Broeskamp, Dimitra Panagaki, Sean D. Speese, Sabrina Büttner, Johanna L. Höög
ABSTRACT The nuclear pore complex (NPC) has long been assumed to be the sole route across the nuclear envelope, and under normal homeostatic conditions it is indeed the main mechanism of nucleo-cytoplasmic transport. However, it has also been known that e.g. herpesviruses cross the nuclear envelope utilizing a pathway entitled nuclear egress or envelopment/de-envelopment. Despite this, a thread of
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The lamin A/C Ig-fold undergoes cell density-dependent changes that alter epitope binding Nucleus (IF 3.7) Pub Date : 2023-02-21 Melanie Wallace, Gregory R. Fedorchak, Richa Agrawal, Rachel M. Gilbert, Jineet Patel, Sangwoo Park, Matthew Paszek, Jan Lammerding
ABSTRACT Lamins A/C are nuclear intermediate filament proteins that are involved in diverse cellular mechanical and biochemical functions. Here, we report that recognition of Lamins A/C by a commonly used antibody (JOL-2) that binds the Lamin A/C Ig-fold and other antibodies targeting similar epitopes is highly dependent on cell density, even though Lamin A/Clevels do not change. We propose that the
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Plant nuclear envelope as a hub connecting genome organization with regulation of gene expression Nucleus (IF 3.7) Pub Date : 2023-02-16 Yu Tang
ABSTRACT Eukaryotic cells organize their genome within the nucleus with a double-layered membrane structure termed the nuclear envelope (NE) as the physical barrier. The NE not only shields the nuclear genome but also spatially separates transcription from translation. Proteins of the NE including nucleoskeleton proteins, inner nuclear membrane proteins, and nuclear pore complexes have been implicated
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Heterochromatin organization and phase separation Nucleus (IF 3.7) Pub Date : 2023-01-29 Hui Zhang, Weihua Qin, Hector Romero, Heinrich Leonhardt, M. Cristina Cardoso
ABSTRACT The eukaryotic nucleus displays a variety of membraneless compartments with distinct biomolecular composition and specific cellular activities. Emerging evidence indicates that protein-based liquid–liquid phase separation (LLPS) plays an essential role in the formation and dynamic regulation of heterochromatin compartmentalization. This feature is especially conspicuous at the pericentric
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Mechanism of action of the SWI/SNF family complexes Nucleus (IF 3.7) Pub Date : 2023-01-12 Kangjing Chen, Junjie Yuan, Youyang Sia, Zhucheng Chen
Published in Nucleus (Vol. 14, No. 1, 2023)
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PRR14 organizes H3K9me3-modified heterochromatin at the nuclear lamina Nucleus (IF 3.7) Pub Date : 2023-01-12 Anna A. Kiseleva, Yu-Chia Cheng, Cheryl L. Smith, Richard A. Katz, Andrey Poleshko
ABSTRACT The eukaryotic genome is organized in three dimensions within the nucleus. Transcriptionally active chromatin is spatially separated from silent heterochromatin, a large fraction of which is located at the nuclear periphery. However, the mechanisms by which chromatin is localized at the nuclear periphery remain poorly understood. Here we demonstrate that Proline Rich 14 (PRR14) protein organizes
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The chromatin signatures of enhancers and their dynamic regulation Nucleus (IF 3.7) Pub Date : 2023-01-05 Amandine Barral, Jérôme Déjardin
ABSTRACT Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified
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Nucleus-wide analysis of coherent RNA pol II movement in the context of chromatin dynamics in living cancer cells Nucleus (IF 3.7) Pub Date : 2022-12-13 Haitham A. Shaban
ABSTRACT Activation of transcription results in coordinated movement of chromatin over a range of micrometers. To investigate how transcriptional regulation affects the mobility of RNA Pol II molecules and whether this movement response depends on the coordinated movement of chromatin, we used our Dense Flow reConstruction and Correlation (DFCC) method. Using DFCC, we studies the nucleus-wide coherent
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Aberrant chromatin organization at the nexus of laminopathy disease pathways Nucleus (IF 3.7) Pub Date : 2022-12-11 Garrett T. Santini, Parisha P. Shah, Ashley Karnay, Rajan Jain
Published in Nucleus (Vol. 13, No. 1, 2022)
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Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes Nucleus (IF 3.7) Pub Date : 2022-11-29 Ricardo S Randall, Claire Jourdain, Anna Nowicka, Kateřina Kaduchová, Michaela Kubová, Mohammad A. Ayoub, Veit Schubert, Christophe Tatout, Isabelle Colas, Kalyanikrishna, Sophie Desset, Sarah Mermet, Aurélia Boulaflous-Stevens, Ivona Kubalová, Terezie Mandáková, Stefan Heckmann, Martin A. Lysak, Martina Panatta, Raffaella Santoro, Daniel Schubert, Ales Pecinka, Devin Routh, Célia Baroux
ABSTRACT Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel
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Chromatin accessibility: methods, mechanisms, and biological insights Nucleus (IF 3.7) Pub Date : 2022-11-20 Andrés R. Mansisidor, Viviana I. Risca
ABSTRACT Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a
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A-type lamins involvement in transport and implications in cancer? Nucleus (IF 3.7) Pub Date : 2022-09-15 Nicholas R. Scott, Sapun H. Parekh
ABSTRACT Nuclear lamins and transport are intrinsically linked, but their relationship is yet to be fully unraveled. A multitude of complex, coupled interactions between lamins and nucleoporins (Nups), which mediate active transport into and out of the nucleus, combined with well documented dysregulation of lamins in many cancers, suggests that lamins and nuclear transport may play a pivotal role in
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Cell cycle control of kinetochore assembly Nucleus (IF 3.7) Pub Date : 2022-08-29 Qianhua Dong, Fei Li
ABSTRACT The kinetochore is a large proteinaceous structure assembled on the centromeres of chromosomes. The complex machinery links chromosomes to the mitotic spindle and is essential for accurate chromosome segregation during cell division. The kinetochore is composed of two submodules: the inner and outer kinetochore. The inner kinetochore is assembled on centromeric chromatin and persists with
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Autophagy regulates rRNA synthesis Nucleus (IF 3.7) Pub Date : 2022-08-21 Yinfeng Xu, Wei Wan
ABSTRACT Autophagy has emerged as a key regulator of cell metabolism. Recently, we have demonstrated that autophagy is involved in RNA metabolism by regulating ribosomal RNA (rRNA) synthesis. We found that autophagy-deficient cells display much higher 47S precursor rRNA level, which is caused by the accumulation of SQSTM1/p62 (sequestosome 1) but not other autophagy receptors. Mechanistically, SQSTM1
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Spatially coherent diffusion of human RNA Pol II depends on transcriptional state rather than chromatin motion Nucleus (IF 3.7) Pub Date : 2022-06-19 Roman Barth, Haitham A. Shaban
ABSTRACT Gene transcription by RNA polymerase II (RNAPol II) is a tightly regulated process in the genomic, temporal, and spatial context. Recently, we have shown that chromatin exhibits spatially coherently moving regions over the entire nucleus, which is enhanced by transcription. Yet, it remains unclear how the mobility of RNA Pol II molecules is affected by transcription regulation and whether
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Spelling out the roles of individual nucleoporins in nuclear export of mRNA Nucleus (IF 3.7) Pub Date : 2022-05-20 Mark Tingey, Yichen Li, Wenlan Yu, Albert Young, Weidong Yang
ABSTRACT The Nuclear Pore Complex (NPC) represents a critical passage through the nuclear envelope for nuclear import and export that impacts nearly every cellular process at some level. Recent technological advances in the form of Auxin Inducible Degron (AID) strategies and Single-Point Edge-Excitation sub-Diffraction (SPEED) microscopy have enabled us to provide new insight into the distinct functions
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Workshop on RanBP2/Nup358 and acute necrotizing encephalopathy Nucleus (IF 3.7) Pub Date : 2022-04-29 Alexander F. Palazzo, Jomon Joseph, Ming Lim, Kiran T. Thakur
ABSTRACT Dominant missense mutations in RanBP2/Nup358 cause Acute Necrotizing Encephalopathy (ANE), a pediatric disease where seemingly healthy individuals develop a cytokine storm that is restricted to the central nervous system in response to viral infection. Untreated, this condition leads to seizures, coma, long-term neurological damage and a high rate of mortality. The exact mechanism by which
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Dictyostelium spastin is involved in nuclear envelope dynamics during semi-closed mitosis Nucleus (IF 3.7) Pub Date : 2022-03-17 Ulrike Schweigel, Petros Batsios, Annette Müller-Taubenberger, Ralph Gräf, Marianne Grafe
ABSTRACT Dictyostelium amoebae perform a semi-closed mitosis, in which the nuclear envelope is fenestrated at the insertion sites of the mitotic centrosomes and around the central spindle during karyokinesis. During late telophase the centrosome relocates to the cytoplasmic side of the nucleus, the central spindle disassembles and the nuclear fenestrae become closed. Our data indicate that Dictyostelium
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Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate Nucleus (IF 3.7) Pub Date : 2022-03-16 Charlotte R. Pfeifer, Michael P. Tobin, Sangkyun Cho, Manasvita Vashisth, Lawrence J. Dooling, Lizeth Lopez Vazquez, Emma G. Ricci-De Lucca, Keiann T. Simon, Dennis E. Discher
ABSTRACT Nuclear rupture has long been associated with deficits or defects in lamins, with recent results also indicating a role for actomyosin stress, but key physical determinants of rupture remain unclear. Here, lamin-B filaments stably interact with the nuclear membrane at sites of low Gaussian curvature yet dilute at high curvature to favor rupture, whereas lamin-A depletion requires high strain-rates
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In situ nuclear matrix preparation in Drosophila melanogaster embryos/tissues and its use in studying the components of nuclear architecture Nucleus (IF 3.7) Pub Date : 2022-03-03 Rashmi U Pathak, Ashish Bihani, Rahul Sureka, Parul Varma, Rakesh K Mishra
ABSTRACT The study of nuclear matrix (NuMat) over the last 40 years has been limited to either isolated nuclei from tissues or cells grown in culture. Here, we provide a protocol for NuMat preparation in intact Drosophila melanogaster embryos and its use in dissecting the components of nuclear architecture. The protocol does not require isolation of nuclei and therefore maintains the three-dimensional
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Mammalian nuclear speckles exhibit stable association with chromatin: a biochemical study Nucleus (IF 3.7) Pub Date : 2022-02-27 Komal Raina, Basuthkar J Rao
ABSTRACT Nuclear Speckles (NS) are phase-separated condensates of protein and RNA whose components dynamically coordinate RNA transcription, splicing, transport and DNA repair. NS, probed largely by imaging studies, remained historically well known as Interchromatin Granule Clusters, and biochemical properties, especially their association with Chromatin have been largely unexplored. In this study
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Mechanical determinants of chromatin topology and gene expression Nucleus (IF 3.7) Pub Date : 2022-02-27 Rajiv Kumar Jha, David Levens, Fedor Kouzine
ABSTRACT The compaction of linear DNA into micrometer-sized nuclear boundaries involves the establishment of specific three-dimensional (3D) DNA structures complexed with histone proteins that form chromatin. The resulting structures modulate essential nuclear processes such as transcription, replication, and repair to facilitate or impede their multi-step progression and these contribute to dynamic
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Uip4p modulates nuclear pore complex function in Saccharomyces cerevisiae Nucleus (IF 3.7) Pub Date : 2022-02-16 Pallavi Deolal, Imlitoshi Jamir, Krishnaveni Mishra
ABSTRACT A double membrane bilayer perforated by nuclear pore complexes (NPCs) governs the shape of the nucleus, the prominent distinguishing organelle of a eukaryotic cell. Despite the absence of lamins in yeasts, the nuclear morphology is stably maintained and shape changes occur in a regulated fashion. In a quest to identify factors that contribute to regulation of nuclear shape and function in
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Pericentromeric repetitive ncRNA regulates chromatin interaction and inflammatory gene expression Nucleus (IF 3.7) Pub Date : 2022-02-15 Kenichi Miyata, Akiko Takahashi
ABSTRACT Cellular senescence provokes a dramatic alteration of chromatin organization and gene expression profile of proinflammatory factors, thereby contributing to various age-related pathologies via the senescence-associated secretory phenotype (SASP). Chromatin organization and global gene expression are maintained through the CCCTC-binding factor (CTCF). However, the molecular mechanism underlying
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MeCP2-induced heterochromatin organization is driven by oligomerization-based liquid–liquid phase separation and restricted by DNA methylation Nucleus (IF 3.7) Pub Date : 2022-02-13 Hui Zhang, Hector Romero, Annika Schmidt, Katalina Gagova, Weihua Qin, Bianca Bertulat, Anne Lehmkuhl, Manuela Milden, Malte Eck, Tobias Meckel, Heinrich Leonhardt, M. Cristina Cardoso
ABSTRACT Heterochromatin is the highly compacted form of chromatin with various condensation levels hallmarked by high DNA methylation. MeCP2 is mostly known as a DNA methylation reader but has also been reported as a heterochromatin organizer. Here, we combine liquid–liquid phase separation (LLPS) analysis and single-molecule tracking with quantification of local MeCP2 concentrations in vitro and
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Architectural control of mesenchymal stem cell phenotype through nuclear actin Nucleus (IF 3.7) Pub Date : 2022-02-08 Janet Rubin, Andre J. van Wijnen, Gunes Uzer
ABSTRACT There is growing appreciation that architectural components of the nucleus regulate gene accessibility by altering chromatin organization. While nuclear membrane connector proteins link the mechanosensitive actin cytoskeleton to the nucleoskeleton, actin’s contribution to the inner architecture of the nucleus remains enigmatic. Control of actin transport into the nucleus, plus the presence
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Filament assembly of the C. elegans lamin in the absence of helix 1A Nucleus (IF 3.7) Pub Date : 2022-02-07 Rebecca de Leeuw, Rafael Kronenberg-Tenga, Matthias Eibauer, Ohad Medalia
ABSTRACT Lamins are the major constituent of the nuclear lamina, a protein meshwork underlying the inner nuclear membrane. Nuclear lamins are type V intermediate filaments that assemble into ~3.5 nm thick filaments. To date, only the conditions for the in vitro assembly of Caenorhabditis elegans lamin (Ce-lamin) are known. Here, we investigated the assembly of Ce-lamin filaments by cryo-electron microscopy
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Nuclear envelope mechanobiology: linking the nuclear structure and function Nucleus (IF 3.7) Pub Date : 2021-08-30
ABSTRACT The nucleus, central to cellular activity, relies on both direct mechanical input as well as its molecular transducers to sense external stimuli and respond by regulating intra-nuclear chromatin organization that determines cell function and fate. In mesenchymal stem cells of musculoskeletal tissues, changes in nuclear structures are emerging as a key modulator of their differentiation and
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Modeling the 3D genome of plants Nucleus (IF 3.7) Pub Date : 2021-05-31 Marco Di Stefano, Hans-Wilhelm Nützmann
ABSTRACT Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the transcription machinery, histone modifications, and their three-dimensional folding. The synergistic application of experimental approaches and computer
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In vitro assembly of nuclear envelope in tobacco cultured cells Nucleus (IF 3.7) Pub Date : 2021-05-25 Kentaro Tamura, Haruko Ueda, Ikuko Hara-Nishimura
ABSTRACT The coordinated regulation of the nucelar envelope (NE) reassembly during cell division is an essential event. However, there is little information on the molecular components involved in NE assembly in plant cells. Here we developed an in vitro assay of NE assembly using tobacco BY-2 cultured cells. To start the NE assembly reaction, the demembranated nuclei and the S12 fraction (cytosol
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4DNvestigator: time series genomic data analysis toolbox Nucleus (IF 3.7) Pub Date : 2021-04-14 Stephen Lindsly, Can Chen, Sijia Liu, Scott Ronquist, Samuel Dilworth, Michael Perlman, Indika Rajapakse
ABSTRACT Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the ‘4DNvestigator’, a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression