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Xiang J, Fan C, Dong H, Ma Y, Xu P. A CRISPR-based rapid DNA repositioning strategy and the early intranuclear life of HSV-1. eLife 2023; 12:e85412. [PMID: 37702383 PMCID: PMC10522339 DOI: 10.7554/elife.85412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/12/2023] [Indexed: 09/14/2023] Open
Abstract
The relative positions of viral DNA genomes to the host intranuclear environment play critical roles in determining virus fate. Recent advances in the application of chromosome conformation capture-based sequencing analysis (3 C technologies) have revealed valuable aspects of the spatiotemporal interplay of viral genomes with host chromosomes. However, to elucidate the causal relationship between the subnuclear localization of viral genomes and the pathogenic outcome of an infection, manipulative tools are needed. Rapid repositioning of viral DNAs to specific subnuclear compartments amid infection is a powerful approach to synchronize and interrogate this dynamically changing process in space and time. Herein, we report an inducible CRISPR-based two-component platform that relocates extrachromosomal DNA pieces (5 kb to 170 kb) to the nuclear periphery in minutes (CRISPR-nuPin). Based on this strategy, investigations of herpes simplex virus 1 (HSV-1), a prototypical member of the human herpesvirus family, revealed unprecedently reported insights into the early intranuclear life of the pathogen: (I) Viral genomes tethered to the nuclear periphery upon entry, compared with those freely infecting the nucleus, were wrapped around histones with increased suppressive modifications and subjected to stronger transcriptional silencing and prominent growth inhibition. (II) Relocating HSV-1 genomes at 1 hr post infection significantly promoted the transcription of viral genes, termed an 'Escaping' effect. (III) Early accumulation of ICP0 was a sufficient but not necessary condition for 'Escaping'. (IV) Subnuclear localization was only critical during early infection. Importantly, the CRISPR-nuPin tactic, in principle, is applicable to many other DNA viruses.
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Affiliation(s)
- Juan Xiang
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen UniversityShenzhenChina
| | - Chaoyang Fan
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen UniversityShenzhenChina
| | - Hongchang Dong
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen UniversityShenzhenChina
| | - Yilei Ma
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen UniversityShenzhenChina
| | - Pei Xu
- The Centre for Infection and Immunity Studies, School of Medicine, Sun Yat-sen UniversityShenzhenChina
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2
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Tian W, Hao X, Nie R, Ling Y, Zhang B, Zhang H, Wu C. Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens. Animals (Basel) 2022; 12:1099. [PMID: 35565526 PMCID: PMC9101879 DOI: 10.3390/ani12091099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/11/2022] [Accepted: 04/21/2022] [Indexed: 11/24/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are implicated in mammalian adipogenesis and obesity. However, their genome-wide distribution, expression profiles, and regulatory mechanisms during chicken adipogenesis remain rarely understood. In the present study, lncRNAs associated with adipogenesis were identified from chicken abdominal adipocytes at multiple differentiation stages using Ribo-Zero RNA-seq. A total of 15,179 lncRNAs were identified and characterized by stage-specific expression patterns. Of these, 840 differentially expressed lncRNAs were detected, and their cis- and trans-target genes were significantly enriched in multiple lipid-related pathways. Through weighted gene co-expression network analysis (WGCNA) and time-series expression profile clustering analysis, 14 key lncRNAs were identified as candidate regulatory lncRNAs in chicken adipogenic differentiation. The cis- and trans-regulatory interactions of key lncRNAs were constructed based on their differentially expressed cis- and trans-target genes, respectively. We also constructed a competing endogenous RNA (ceRNA) network based on the key lncRNAs, differentially expressed miRNAs, and differentially expressed mRNAs. MSTRG.25116.1 was identified as a potential regulator of chicken abdominal preadipocyte adipogenic differentiation by acting as a transcriptional trans-regulator of fatty acid amide hydrolase (FAAH) gene expression and/or a ceRNA that post-transcriptionally mediates FAAH gene expression by sponging gga-miR-1635.
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Affiliation(s)
| | | | | | | | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (W.T.); (X.H.); (R.N.); (Y.L.); (C.W.)
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (W.T.); (X.H.); (R.N.); (Y.L.); (C.W.)
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3
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Mozolewski P, Jeziorek M, Schuster CM, Bading H, Frost B, Dobrowolski R. The role of nuclear Ca2+ in maintaining neuronal homeostasis and brain health. J Cell Sci 2021; 134:jcs254904. [PMID: 33912918 PMCID: PMC8084578 DOI: 10.1242/jcs.254904] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nuclear Ca2+ has emerged as one of the most potent mediators of the dialogue between neuronal synapses and the nucleus that regulates heterochromatin states, transcription factor activity, nuclear morphology and neuronal gene expression induced by synaptic activity. Recent studies underline the importance of nuclear Ca2+ signaling in long-lasting, activity-induced adaptation and maintenance of proper brain function. Diverse forms of neuroadaptation require transient nuclear Ca2+ signaling and cyclic AMP-responsive element-binding protein (CREB1, referred to here as CREB) as its prime target, which works as a tunable switch to drive and modulate specific gene expression profiles associated with memory, pain, addiction and neuroprotection. Furthermore, a reduction of nuclear Ca2+ levels has been shown to be neurotoxic and a causal factor driving the progression of neurodegenerative disorders, as well as affecting neuronal autophagy. Because of its central role in the brain, deficits in nuclear Ca2+ signaling may underlie a continuous loss of neuroprotection in the aging brain, contributing to the pathophysiology of Alzheimer's disease. In this Review, we discuss the principles of the 'nuclear calcium hypothesis' in the context of human brain function and its role in controlling diverse forms of neuroadaptation and neuroprotection. Furthermore, we present the most relevant and promising perspectives for future studies.
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Affiliation(s)
- Pawel Mozolewski
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Maciej Jeziorek
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Christoph M. Schuster
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, INF 345 and INF 366, 69120 Heidelberg, Germany
| | - Hilmar Bading
- Department of Neurobiology, Interdisciplinary Center for Neurosciences (IZN), Heidelberg University, INF 345 and INF 366, 69120 Heidelberg, Germany
| | - Bess Frost
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health, San Antonio, San Antonio, TX 78229, USA
- Sam and Ann Barshop Institute for Longevity and Aging Studies, Department of Cell Systems and Anatomy, University of Texas Health, San Antonio, San Antonio, TX 78229, USA
| | - Radek Dobrowolski
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health, San Antonio, San Antonio, TX 78229, USA
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4
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Imperador CHL, Rodrigues VLCC, Mello MLS. The Topological Distribution of the Chromocenter in Panstrongylus megistus (Burmeister) Malpighian Tubule Cells Examined by Confocal Microscopy. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | - Maria Luiza S. Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp)
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5
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Abstract
Cancers and developmental disorders are associated with alterations in the 3D genome architecture in space and time (the fourth dimension). Mammalian 3D genome organization is complex and dynamic and plays an essential role in regulating gene expression and cellular function. To study the causal relationship between genome function and its spatio-temporal organization in the nucleus, new technologies for engineering and manipulating the 3D organization of the genome have been developed. In particular, CRISPR-Cas technologies allow programmable manipulation at specific genomic loci, enabling unparalleled opportunities in this emerging field of 3D genome engineering. We review advances in mammalian 3D genome engineering with a focus on recent manipulative technologies using CRISPR-Cas and related technologies.
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6
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Shear Stress Modulates Osteoblast Cell and Nucleus Morphology and Volume. Int J Mol Sci 2020; 21:ijms21218361. [PMID: 33171812 PMCID: PMC7664694 DOI: 10.3390/ijms21218361] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Mechanical loading preserves bone mass and function—yet, little is known about the cell biological basis behind this preservation. For example, cell and nucleus morphology are critically important for cell function, but how these morphological characteristics are affected by the physiological mechanical loading of bone cells is under-investigated. This study aims to determine the effects of fluid shear stress on cell and nucleus morphology and volume of osteoblasts, and how these effects relate to changes in actin cytoskeleton and focal adhesion formation. Mouse calvaria 3T3-E1 (MC3T3-E1) osteoblasts were treated with or without 1 h pulsating fluid flow (PFF). Live-cell imaging was performed every 10 min during PFF and immediately after PFF. Cytoskeletal organization and focal adhesions were visualized, and gene and protein expression quantified. Two-dimensional (2D) and three-dimensional (3D) morphometric analyses were made using MeasureStack and medical imaging interaction toolkit (MITK) software. 2D-images revealed that 1 h PFF changed cell morphology from polygonal to triangular, and nucleus morphology from round to ellipsoid. PFF also reduced cell surface area (0.3-fold), cell volume (0.3-fold), and nucleus volume (0.2-fold). During PFF, the live-cell volume gradually decreased from 6000 to 3000 µm3. After PFF, α-tubulin orientation was more disorganized, but F-actin fluorescence intensity was enhanced, particularly around the nucleus. 3D-images obtained from Z-stacks indicated that PFF increased F-actin fluorescence signal distribution around the nucleus in the XZ and YZ direction (2.3-fold). PFF increased protein expression of phospho-paxillin (2.0-fold) and integrin-α5 (2.8-fold), but did not increase mRNA expression of paxillin-a (PXNA), paxillin-b (PXNB), integrin-α5 (ITGA51), or α-tubulin protein expression. In conclusion, PFF induced substantial changes in osteoblast cytoskeleton, as well as cell and nucleus morphology and volume, which was accompanied by elevated gene and protein expression of adhesion and structural proteins. More insights into the mechanisms whereby mechanical cues drive morphological changes in bone cells, and thereby, possibly in bone cell behavior, will aid the guidance of clinical treatment, particularly in the field of orthodontics, (oral) implantology, and orthopedics.
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Imperador CHL, Bardella VB, Dos Anjos EHM, Rodrigues VLCC, Cabral-de-Mello DC, Mello MLS. Spatial Distribution of Heterochromatin Bodies in the Nuclei of Triatoma infestans (Klug). MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:567-574. [PMID: 32393416 DOI: 10.1017/s143192762000149x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Constitutive heterochromatin typically exhibits low gene density and is commonly found adjacent or close to the nuclear periphery, in contrast to transcriptionally active genes concentrated in the innermost nuclear region. In Triatoma infestans cells, conspicuous constitutive heterochromatin forms deeply stained structures named chromocenters. However, to the best of our knowledge, no information exists regarding whether these chromocenters acquire a precise topology in the cell nuclei or whether their 18S rDNA, which is important for ribosome function, faces the nuclear center preferentially. In this work, the spatial distribution of fluorescent Feulgen-stained chromocenters and the distribution of their 18S rDNA was analyzed in Malpighian tubule cells of T. infestans using confocal microscopy. The chromocenters were shown to be spatially positioned relatively close to the nuclear periphery, though not adjacent to it. The variable distance between the chromocenters and the nuclear periphery suggests mobility of these bodies within the cell nuclei. The distribution of 18S rDNA at the edge of the chromocenters was not found to face the nuclear interior exclusively. Because the genome regions containing 18S rDNA in the chromocenters also face the nuclear periphery, the proximity of the chromocenters to this nuclear region is not assumed to be associated with overall gene silencing.
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Affiliation(s)
- Carlos Henrique L Imperador
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Rua Monteiro Lobato 255, 13083-862Campinas, SP, Brazil
| | - Vanessa B Bardella
- Department of Biology, Institute of Biosciences, State University of São Paulo (Unesp), Avenida 24-A, 1515, 13506-900Rio Claro, SP, Brazil
| | - Eli Heber M Dos Anjos
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Rua Monteiro Lobato 255, 13083-862Campinas, SP, Brazil
| | - Vera L C C Rodrigues
- Superintendence for Control of Endemic Diseases (SUCEN), Rua Afonso Pessini, 86, 13845-206Mogi-Guaçu, SP, Brazil
| | - Diogo C Cabral-de-Mello
- Department of Biology, Institute of Biosciences, State University of São Paulo (Unesp), Avenida 24-A, 1515, 13506-900Rio Claro, SP, Brazil
| | - Maria Luiza S Mello
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas (Unicamp), Rua Monteiro Lobato 255, 13083-862Campinas, SP, Brazil
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8
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Anselme K, Wakhloo NT, Rougerie P, Pieuchot L. Role of the Nucleus as a Sensor of Cell Environment Topography. Adv Healthc Mater 2018; 7:e1701154. [PMID: 29283219 DOI: 10.1002/adhm.201701154] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/06/2017] [Indexed: 12/25/2022]
Abstract
The proper integration of biophysical cues from the cell vicinity is crucial for cells to maintain homeostasis, cooperate with other cells within the tissues, and properly fulfill their biological function. It is therefore crucial to fully understand how cells integrate these extracellular signals for tissue engineering and regenerative medicine. Topography has emerged as a prominent component of the cellular microenvironment that has pleiotropic effects on cell behavior. This progress report focuses on the recent advances in the understanding of the topography sensing mechanism with a special emphasis on the role of the nucleus. Here, recent techniques developed for monitoring the nuclear mechanics are reviewed and the impact of various topographies and their consequences on nuclear organization, gene regulation, and stem cell fate is summarized. The role of the cell nucleus as a sensor of cell-scale topography is further discussed.
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Affiliation(s)
- Karine Anselme
- University of Haute‐AlsaceUniversity of Strasbourg CNRS UMR7361, IS2M 68057 Mulhouse France
| | - Nayana Tusamda Wakhloo
- University of Haute‐AlsaceUniversity of Strasbourg CNRS UMR7361, IS2M 68057 Mulhouse France
| | - Pablo Rougerie
- Institute of Biomedical SciencesFederal University of Rio de Janeiro Rio de Janeiro RJ 21941‐902 Brazil
| | - Laurent Pieuchot
- University of Haute‐AlsaceUniversity of Strasbourg CNRS UMR7361, IS2M 68057 Mulhouse France
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9
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Automated 3D Gene Position Analysis Using a Customized Imaris Plugin: XTFISHInsideNucleus. Methods Mol Biol 2018; 1675:591-613. [PMID: 29052213 DOI: 10.1007/978-1-4939-7318-7_32] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Fluorescence in situ hybridization (FISH) is commonly used to visualize chromosomal regions or genomic loci within the nucleus, and can largely contribute to unraveling the link between structure and function in the nucleus. Three-dimensional (3D) analyses are required to best capture the nucleus' organizing principles, but the experimental setup and computational analyses are far from trivial. Here, we present a robust workflow for 3D FISH against repeats and single copy loci in embedded intact nuclei from Arabidopsis leaves. We then describe in detail the image acquisition, subsequent image deconvolution before 3D image processing, and the image reconstruction. We developed an automated batch image processing pipeline using a customized, open source plugin implemented in the Imaris environment.
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10
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Zeller P, Gasser SM. The Importance of Satellite Sequence Repression for Genome Stability. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:15-24. [PMID: 29133300 DOI: 10.1101/sqb.2017.82.033662] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Up to two-thirds of eukaryotic genomes consist of repetitive sequences, which include both transposable elements and tandemly arranged simple or satellite repeats. Whereas extensive progress has been made toward understanding the danger of and control over transposon expression, only recently has it been recognized that DNA damage can arise from satellite sequence transcription. Although the structural role of satellite repeats in kinetochore function and end protection has long been appreciated, it has now become clear that it is not only these functions that are compromised by elevated levels of transcription. RNA from simple repeat sequences can compromise replication fork stability and genome integrity, thus compromising germline viability. Here we summarize recent discoveries on how cells control the transcription of repeat sequence and the dangers that arise from their expression. We propose that the link between the DNA damage response and the transcriptional silencing machinery may help a cell or organism recognize foreign DNA insertions into an evolving genome.
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Affiliation(s)
- Peter Zeller
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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11
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Pueschel R, Coraggio F, Meister P. From single genes to entire genomes: the search for a function of nuclear organization. Development 2016; 143:910-23. [PMID: 26980791 DOI: 10.1242/dev.129007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The existence of different domains within the nucleus has been clear from the time, in the late 1920s, that heterochromatin and euchromatin were discovered. The observation that heterochromatin is less transcribed than euchromatin suggested that microscopically identifiable structures might correspond to functionally different domains of the nucleus. Until 15 years ago, studies linking gene expression and subnuclear localization were limited to a few genes. As we discuss in this Review, new genome-wide techniques have now radically changed the way nuclear organization is analyzed. These have provided a much more detailed view of functional nuclear architecture, leading to the emergence of a number of new paradigms of chromatin folding and how this folding evolves during development.
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Affiliation(s)
- Ringo Pueschel
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Francesca Coraggio
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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12
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13
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Kilinc S, Meredith DT, Lane RP. Sequestration within nuclear chromocenters is not a requirement for silencing olfactory receptor transcription in a placode-derived cell line. Nucleus 2014; 5:318-30. [PMID: 25482121 PMCID: PMC4152346 DOI: 10.4161/nucl.29343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/20/2014] [Accepted: 05/23/2014] [Indexed: 02/03/2023] Open
Abstract
Mouse olfaction depends on specialized olfactory sensory neurons (OSNs) that each express only one olfactory receptor protein from among a family of >1000 olfactory receptor (OR) genes encoded in the genome. To investigate epigenetic mechanisms underlying monogenic OR expression, we characterized the nuclear organization of OR loci in an olfactory placode-derived cell line (OP6) derived from a pre-neuronal cell along the OSN lineage. OR loci are significantly enriched within nuclear chromocenters in these cells as compared with control loci tested. However, we observe variability in chromocenter occupancy among different OR loci and from cell-to-cell, suggesting that these associations are transient or context dependent. The lamin B receptor (LBR), whose downregulation is necessary for aggregation of chromocenters and OR genes in mature OSNs, exhibits an unusual non-peripheral expression pattern in OP6 nuclei; upon further OP6 cell differentiation, LBR expression is lost and chromocenters begin to aggregate. However, neither undifferentiated nor differentiated OP6 cells sequester OR genes within the chromocenters, despite the establishment of monogenic OR expression in these cells. These results indicate that sequestration of competing OR loci is not a requirement for monogenic OR expression in OP6 cells, and could indicate that the initial establishment of monogenic OR expression during OSN differentiation in vivo occurs prior to recruitment of OR genes into chromocenters.
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Affiliation(s)
- Seda Kilinc
- Department of Molecular Biology and Biochemistry; Wesleyan University; Middletown, CT USA
| | - Diane T Meredith
- Department of Molecular Biology and Biochemistry; Wesleyan University; Middletown, CT USA
| | - Robert P Lane
- Department of Molecular Biology and Biochemistry; Wesleyan University; Middletown, CT USA
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14
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Malhas AN, Vaux DJ. Nuclear envelope invaginations and cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 773:523-35. [PMID: 24563364 DOI: 10.1007/978-1-4899-8032-8_24] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The nuclear envelope (NE) surrounds the nucleus and separates it from the cytoplasm. The NE is not a passive structural component, but rather contributes to various cellular processes such as genome organization, transcription, signaling, and stress responses. Although the NE is mostly a smooth surface, it also forms invaginations that can reach deep into the nucleoplasm and may even traverse the nucleus completely. Cancer cells are generally characterized by irregularities and invaginations of the NE that are of diagnostic and prognostic significance. In the current chapter, we describe the link between nuclear invaginations and irregularities with cancer and explore possible mechanistic roles they might have in tumorigenesis.
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Affiliation(s)
- Ashraf N Malhas
- Sir William Dunn School of Pathology, South Parks Road, Oxford, OX1 3RE, UK,
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15
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Belan E. LINEs of evidence: noncanonical DNA replication as an epigenetic determinant. Biol Direct 2013; 8:22. [PMID: 24034780 PMCID: PMC3868326 DOI: 10.1186/1745-6150-8-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 09/06/2013] [Indexed: 12/17/2022] Open
Abstract
LINE-1 (L1) retrotransposons are repetitive elements in mammalian genomes. They are
capable of synthesizing DNA on their own RNA templates by harnessing reverse
transcriptase (RT) that they encode. Abundantly expressed full-length L1s and their
RT are found to globally influence gene expression profiles, differentiation state,
and proliferation capacity of early embryos and many types of cancer, albeit by yet
unknown mechanisms. They are essential for the progression of early development and
the establishment of a cancer-related undifferentiated state. This raises important
questions regarding the functional significance of L1 RT in these cell systems.
Massive nuclear L1-linked reverse transcription has been shown to occur in mouse
zygotes and two-cell embryos, and this phenomenon is purported to be DNA replication
independent. This review argues against this claim with the goal of understanding the
nature of this phenomenon and the role of L1 RT in early embryos and cancers.
Available L1 data are revisited and integrated with relevant findings accumulated in
the fields of replication timing, chromatin organization, and epigenetics, bringing
together evidence that strongly supports two new concepts. First, noncanonical
replication of a portion of genomic full-length L1s by means of L1 RNP-driven reverse
transcription is proposed to co-exist with DNA polymerase-dependent replication of
the rest of the genome during the same round of DNA replication in embryonic and
cancer cell systems. Second, the role of this mechanism is thought to be epigenetic;
it might promote transcriptional competence of neighboring genes linked to
undifferentiated states through the prevention of tethering of involved L1s to the
nuclear periphery. From the standpoint of these concepts, several hitherto
inexplicable phenomena can be explained. Testing methods for the model are
proposed.
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Affiliation(s)
- Ekaterina Belan
- Genetics Laboratory, Royal University Hospital, Saskatoon, SK S7N 0W8, Canada.
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16
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Steglich B, Sazer S, Ekwall K. Transcriptional regulation at the yeast nuclear envelope. Nucleus 2013; 4:379-89. [PMID: 24021962 DOI: 10.4161/nucl.26394] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The spatial organization of the genome inside the nucleus affects many nuclear processes, such as DNA replication, DNA repair, and gene transcription. In metazoans, the nuclear periphery harbors mainly repressed genes that associate with the nuclear lamina. This review discusses how peripheral positioning is connected to transcriptional regulation in yeasts. Tethering of reporter genes to the nuclear envelope was found to result in transcriptional silencing. Similarly, repression of the silent mating type loci and subtelomeric genes is influenced by their position close to the nuclear envelope. In contrast, active genes are bound by nucleoporins and inducible genes associate with the nuclear pore complex upon activation. Taken together, these results portray the nuclear envelope as a platform for transcriptional regulation, both through activation at nuclear pores and silencing at the nuclear envelope.
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Affiliation(s)
- Babett Steglich
- Department of Biosciences and Nutrition; Center for Biosciences; Karolinska Institutet; Huddinge, Sweden; Verna and Marrs McLean Department of Biochemistry and Molecular Biology; Baylor College of Medicine; Houston, TX USA; Department of Molecular and Cellular Biology; Baylor College of Medicine; Houston, TX USA
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17
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Directing nuclear deformation on micropillared surfaces by substrate geometry and cytoskeleton organization. Biomaterials 2013; 34:2991-3001. [PMID: 23357373 DOI: 10.1016/j.biomaterials.2013.01.018] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 01/04/2013] [Indexed: 12/21/2022]
Abstract
We have recently demonstrated strong nuclear deformation of SaOs-2 osteosarcoma cells on poly-L-lactic acid (PLLA) micropillar substrates. In the present study, we first demonstrated that chemical and mechanical properties of the micropillar substrates have no dominant effect on deformation. However, SaOs-2 nucleus deformation could be strongly modulated by varying the pillar size and spacing, highlighting the importance of geometric constraints for shaping the nucleus. Furthermore, comparing the capacity for nuclear deformation in three different osteosarcoma cell lines (SaOs-2, MG-63 and OHS-4) revealed strong cell-type specific differences. Surprisingly, the highly-deformable SaOs-2 cell line displayed the highest cell stiffness as assessed by AFM-based colloidal force spectroscopy and featured a more prominent array of actin fibres above the nucleus, suggesting a link between actin-mediated cell stiffness and cell nucleus deformation. In contrast, in MG-63 and OHS-4 cells dense microtubule and vimentin networks seem to facilitate some nuclear deformation even in the absence of a prominent actin cytoskeleton. Together these results suggest that an interaction of all three cytoskeletal elements is needed for efficient nuclear deformation. In conclusion, the dominant parameters influencing nuclear deformation on micropillar substrates are not their material properties but the substrate geometry together with cell phenotype and cytoskeleton organization.
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Meister P, Taddei A. Building silent compartments at the nuclear periphery: a recurrent theme. Curr Opin Genet Dev 2013; 23:96-103. [PMID: 23312840 DOI: 10.1016/j.gde.2012.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/29/2012] [Accepted: 12/05/2012] [Indexed: 01/12/2023]
Abstract
In eukaryotes, the genetic material is stored in the nucleus, which is enclosed in a double lipid bilayer, the nuclear envelope (NE). It protects the genome from physical stress and separates it from the rest of the cell. On top of this physical function, growing evidence shows that the nuclear periphery contributes to the 3D organization of the genome. In turn, tridimensional organization of chromatin in the nuclear space influences genome expression. Here we review recent findings on the function of this physical barrier in gene repression and latest models on how silent subnuclear compartments at the NE are built in yeast as well as in the nematode C. elegans and mammalian cells; trying to draw parallels between the three systems.
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Affiliation(s)
- Peter Meister
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland.
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19
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Graumann K, Bass HW, Parry G. SUNrises on the International Plant Nucleus Consortium: SEB Salzburg 2012. Nucleus 2013; 4:3-7. [PMID: 23324458 DOI: 10.4161/nucl.23385] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The nuclear periphery is a dynamic, structured environment, whose precise functions are essential for global processes-from nuclear, to cellular, to organismal. Its main components-the nuclear envelope (NE) with inner and outer nuclear membranes (INM and ONM), nuclear pore complexes (NPC), associated cytoskeletal and nucleoskeletal components as well as chromatin are conserved across eukaryotes (Fig. 1). In metazoans in particular, the structure and functions of nuclear periphery components are intensely researched partly because of their involvement in various human diseases. While far less is known about these in plants, the last few years have seen a significant increase in research activity in this area. Plant biologists are not only catching up with the animal field, but recent findings are pushing our advances in this field globally. In recognition of this developing field, the Annual Society of Experimental Biology Meeting in Salzburg kindly hosted a session co-organized by Katja Graumann and David E. Evans (Oxford Brookes University) highlighting new insights into plant nuclear envelope proteins and their interactions. This session brought together leading researchers with expertise in topics such as epigenetics, meiosis, nuclear pore structure and functions, nucleoskeleton and nuclear envelope composition. An open and friendly exchange of ideas was fundamental to the success of the meeting, which resulted in founding the International Plant Nucleus Consortium. This review highlights new developments in plant nuclear envelope research presented at the conference and their importance for the wider understanding of metazoan, yeast and plant nuclear envelope functions and properties.
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Affiliation(s)
- Katja Graumann
- Plant Nuclear Envelope Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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20
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Gissot M, Walker R, Delhaye S, Huot L, Hot D, Tomavo S. Toxoplasma gondii chromodomain protein 1 binds to heterochromatin and colocalises with centromeres and telomeres at the nuclear periphery. PLoS One 2012; 7:e32671. [PMID: 22427862 PMCID: PMC3302879 DOI: 10.1371/journal.pone.0032671] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/02/2012] [Indexed: 01/11/2023] Open
Abstract
Background Apicomplexan parasites are responsible for some of the most deadly parasitic diseases afflicting humans, including malaria and toxoplasmosis. These obligate intracellular parasites exhibit a complex life cycle and a coordinated cell cycle-dependant expression program. Their cell division is a coordinated multistep process. How this complex mechanism is organised remains poorly understood. Methods and Findings In this study, we provide evidence for a link between heterochromatin, cell division and the compartmentalisation of the nucleus in Toxoplasma gondii. We characterised a T. gondii chromodomain containing protein (named TgChromo1) that specifically binds to heterochromatin. Using ChIP-on-chip on a genome-wide scale, we report TgChromo1 enrichment at the peri-centromeric chromatin. In addition, we demonstrate that TgChromo1 is cell-cycle regulated and co-localised with markers of the centrocone. Through the loci-specific FISH technique for T. gondii, we confirmed that TgChromo1 occupies the same nuclear localisation as the peri-centromeric sequences. Conclusion We propose that TgChromo1 may play a role in the sequestration of chromosomes at the nuclear periphery and in the process of T. gondii cell division.
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Affiliation(s)
- Mathieu Gissot
- Center for Infection and Immunity of Lillle, CNRS UMR 8204, INSERM U 1019, Université Lille Nord de France, Institut Pasteur de Lille, Lille, France
- * E-mail: (MG); (ST)
| | | | | | | | | | - Stanislas Tomavo
- Center for Infection and Immunity of Lillle, CNRS UMR 8204, INSERM U 1019, Université Lille Nord de France, Institut Pasteur de Lille, Lille, France
- * E-mail: (MG); (ST)
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21
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Abstract
Because of the association between aberrant nuclear structure and tumour grade, nuclear morphology is an indispensible criterion in the current pathological assessment of cancer. Components of the nuclear envelope environment have central roles in many aspects of cell function that affect tumour development and progression. As the roles of the nuclear envelope components, including nuclear pore complexes and nuclear lamina, are being deciphered in molecular detail there are opportunities to harness this knowledge for cancer therapeutics and biomarker development. In this Review, we summarize the progress that has been made in our understanding of the nuclear envelope and the implications of changes in this environment for cancer biology.
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Affiliation(s)
- Kin-Hoe Chow
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
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22
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Udagawa K, Kimura H, Tanabe H, Ohyama T. Nuclear localization of reporter genes activated by curved DNA. J Biosci Bioeng 2011; 113:431-7. [PMID: 22197431 DOI: 10.1016/j.jbiosc.2011.11.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/17/2011] [Accepted: 11/18/2011] [Indexed: 10/14/2022]
Abstract
Curved DNA structures with a left-handed superhelical conformation can activate eukaryotic transcription. Mechanistically, these structures favor binding to histone cores and can function as a docking site for sliding nucleosomes. Thus, promoters with this kind of curved DNA can adopt a more open structure, facilitating transcription initiation. However, whether the curved DNA segment can affect localization of a reporter gene is an open question. Localization of a gene in the nucleus often plays an important role in its expression and this phenomenon may also have a curved DNA-dependent mechanism. We examined this issue in transient and stable assay systems using a 180-bp synthetic curved DNA with a left-handed superhelical conformation. The results clearly showed that curved DNA of this kind does not have a property to deliver reporter constructs to nuclear positions that are preferable for transcription. We also identify the spatial location to which electroporation delivers a reporter plasmid in the nucleus.
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Affiliation(s)
- Koji Udagawa
- Graduate School of Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
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23
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García-Oliver E, García-Molinero V, Rodríguez-Navarro S. mRNA export and gene expression: the SAGA-TREX-2 connection. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:555-65. [PMID: 22178374 DOI: 10.1016/j.bbagrm.2011.11.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/29/2011] [Accepted: 11/30/2011] [Indexed: 01/07/2023]
Abstract
In the gene expression field, different steps have been traditionally viewed as discrete and unconnected events. Nowadays, genetic and functional studies support the model of a coupled network of physical and functional connections to carry out mRNA biogenesis. Gene expression is a coordinated process that comprises different linked steps like transcription, RNA processing, export to the cytoplasm, translation and degradation of mRNAs. Its regulation is essential for cellular survival and can occur at many different levels. Transcription is the central function that occurs in the nucleus, and RNAPII plays an essential role in mRNA biogenesis. During transcription, nascent mRNA is associated with the mRNA-binding proteins involved in processing and export of the mRNA particle. Cells have developed a network of multi-protein complexes whose functions regulate the different factors involved both temporally and spatially. This coupling mechanism acts as a quality control to solve some of the organization problems of gene expression in vivo, where all the factors implicated ensure that mRNAs are ready to be exported and translated. In this review, we focus on the functional coupling of gene transcription and mRNA export, and place particular emphasis on the relationship between the NPC-associated complex, TREX2, and the transcription co-activator, SAGA. We have pinpointed the experimental evidence for Sus1's roles in transcription initiation, transcription elongation and mRNA export. In addition, we have reviewed other NPC-related processes such as gene gating to the nuclear envelope, the chromatin structure and the cellular context in which these processes take place. This article is part of a Special Issue entitled: Nuclear Transport and RNA Processing.
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Affiliation(s)
- Encar García-Oliver
- Centro de Investigación Príncipe Felipe (CIPF), Gene Expression coupled with RNA Transport Laboratory, Valencia, Spain
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24
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Specific positioning of the casein gene cluster in active nuclear domains in luminal mammary epithelial cells. Chromosome Res 2011; 19:979-97. [PMID: 22033805 DOI: 10.1007/s10577-011-9249-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 10/05/2011] [Accepted: 10/08/2011] [Indexed: 12/15/2022]
Abstract
The nuclear organization of mammary epithelial cells has been shown to be sensitive to the three-dimensional microenvironment in several models of cultured cells. However, the relationships between the expression and position of genes have not often been explored in animal tissues. We therefore studied the localization of milk protein genes in the nuclei of luminal mammary epithelial cells during lactation as well as in two non-expressing cells, i.e., hepatocytes and the less differentiated embryonic fibroblasts. We compared the position of a cluster of co-regulated genes, encoding caseins (CSN), with that of the whey acidic protein (WAP) gene which is surrounded by genes displaying different expression profiles. We show that the position of the CSN cluster relative to various nuclear compartments is correlated with its activity. In luminal cells, the CSN cluster loops out from its chromosome territory and is positioned in the most euchromatic regions, and frequently associated with elongating RNA polymerase II-rich zones. In hepatocytes and embryonic fibroblasts, the cluster is found preferentially closer to the nuclear periphery. Interestingly, we had previously observed a very peripheral position of the CSN locus in the nuclei of HC11 mammary epithelial cells weakly expressing milk protein genes. We thus show that cultured cell lines are not fully representative of the nuclear organization of genes in a complex and highly organized tissue such as the mammary gland and propose that the spatial positioning of the locus is important to ensuring the optimum control of CSN gene activity observed in the mammary tissue.
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25
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Roy AL, Sen R, Roeder RG. Enhancer-promoter communication and transcriptional regulation of Igh. Trends Immunol 2011; 32:532-9. [PMID: 21855411 DOI: 10.1016/j.it.2011.06.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/23/2011] [Accepted: 06/23/2011] [Indexed: 12/18/2022]
Abstract
Transcriptional regulation of eukaryotic protein-coding genes requires the participation of site-specific transcription factors that bind distal regulatory elements, as well as factors that, together with RNA polymerase II, form the basal transcription machinery at the core promoter. Gene regulation requires proper communication between promoters and enhancers, often over great distances. Therefore, it is important to understand the potentially inter-related transcription factor interactions at both of these elements. How this is achieved on tissue-specific genes, such as the immunoglobulin heavy chain (IgH) in B cells remains unclear. Here, we review known interactions at the Igh variable region (V(H)) promoters and present our perspective on promoter-enhancer interactions that are likely important for Ig gene regulation in B cells.
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Affiliation(s)
- Ananda L Roy
- Program in Immunology, Department of Pathology, Tufts University School of Medicine, Boston, MA, USA.
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26
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Woodwark C, Bateman A. The characterisation of three types of genes that overlie copy number variable regions. PLoS One 2011; 6:e14814. [PMID: 21637334 PMCID: PMC3102654 DOI: 10.1371/journal.pone.0014814] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2010] [Accepted: 09/07/2010] [Indexed: 12/21/2022] Open
Abstract
Background Due to the increased accuracy of Copy Number Variable region (CNV) break point mapping, it is now possible to say with a reasonable degree of confidence whether a gene (i) falls entirely within a CNV; (ii) overlaps the CNV or (iii) actually contains the CNV. We classify these as type I, II and III CNV genes respectively. Principal Findings Here we show that although type I genes vary in copy number along with the CNV, most of these type I genes have the same expression levels as wild type copy numbers of the gene. These genes must, therefore, be under homeostatic dosage compensation control. Looking into possible mechanisms for the regulation of gene expression we found that type I genes have a significant paucity of genes regulated by miRNAs and are not significantly enriched for monoallelically expressed genes. Type III genes, on the other hand, have a significant excess of genes regulated by miRNAs and are enriched for genes that are monoallelically expressed. Significance Many diseases and genomic disorders are associated with CNVs so a better understanding of the different ways genes are associated with normal CNVs will help focus on candidate genes in genome wide association studies.
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Affiliation(s)
- Cara Woodwark
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.
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27
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Slomiany A, Slomiany BL. Transformations of phosphatidylinositol phosphates in the outer and inner nuclear membrane are linked to synthesis and restitution of cellular membranes. Health (London) 2011. [DOI: 10.4236/health.2011.34035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Grimaud C, Becker PB. Form and function of dosage-compensated chromosomes--a chicken-and-egg relationship. Bioessays 2010; 32:709-17. [PMID: 20658709 DOI: 10.1002/bies.201000029] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Does the three-dimensional (3D) conformation of interphase chromosomes merely reflect their function or does it actively contribute to gene regulation? The analysis of sex chromosomes that are subject to chromosome-wide dosage compensation processes promises new insight into this question. Chromosome conformations are dynamic and largely determined by association of distant chromosomal loci in the nuclear space or by their anchoring to the nuclear envelope, effectively generating chromatin loops. The type and extent of such interactions depend on chromatin-bound transcription regulators and therefore reflects function. Dosage compensation adjusts the overall transcription activity of X chromosomes to assure balanced expression in the two sexes. Initial analyses of mammalian and Drosophila X chromosomes have led to the hypothesis that their conformations may not only reflect their functional state but may in turn contribute to the coordination of chromosome-wide tuning of transcription.
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Affiliation(s)
- Charlotte Grimaud
- Adolf-Butenandt-Institute and Centre for Integrated Protein Science (CiPSM) Ludwig-Maximilians University, Munich, Germany
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29
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Kubben N, Voncken JW, Misteli T. Mapping of protein- and chromatin-interactions at the nuclear lamina. Nucleus 2010; 1:460-71. [PMID: 21327087 PMCID: PMC3027047 DOI: 10.4161/nucl.1.6.13513] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 08/30/2010] [Accepted: 09/03/2010] [Indexed: 01/07/2023] Open
Abstract
The nuclear envelope and the lamina define the nuclear periphery and are implicated in many nuclear processes including chromatin organization, transcription and DNA replication. Mutations in lamin A proteins, major components of the lamina, interfere with these functions and cause a set of phenotypically diverse diseases referred to as laminopathies. The phenotypic diversity of laminopathies is thought to be the result of alterations in specific protein- and chromatin interactions due to lamin A mutations. Systematic identification of lamin A-protein and -chromatin interactions will be critical to uncover the molecular etiology of laminopathies. Here we summarize and critically discuss recent technology to analyze lamina-protein and-chromatin interactions.
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Affiliation(s)
- Nard Kubben
- Center for Heart Failure Research; Maastricht, The Netherlands
- National Cancer Institute; National Institutes of Health; Bethesda, MD USA
| | - Jan Willem Voncken
- Department of Molecular Genetics; Maastricht University Medical Center; Maastricht, The Netherlands
| | - Tom Misteli
- National Cancer Institute; National Institutes of Health; Bethesda, MD USA
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30
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Nuclear export of mRNA. Trends Biochem Sci 2010; 35:609-17. [PMID: 20719516 DOI: 10.1016/j.tibs.2010.07.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 07/05/2010] [Accepted: 07/07/2010] [Indexed: 01/19/2023]
Abstract
The nuclear export of mRNA, in which Mex67-Mtr2 mediates movement of mature transcripts through nuclear pores, represents the culmination of the nuclear portion of the gene expression pathway. Nuclear export is closely integrated with transcription and processing, and is based on forming a messenger ribonucleoprotein (mRNP) export complex in the nucleus that is able to diffuse back and forth through the pores. Directionality is imposed by remodelling of the mRNP in the cytoplasm, thereby removing key transport-related proteins and preventing its return to the nucleus. The nuclear and cytoplasmic steps of this pathway, in which Mex67-Mtr2 and Nab2 are added and removed, are crucial, and both involve remodelling of the mRNP, which is mediated by DEAD-box helicases together with adaptor and accessory proteins. Recent structural and cell biology results provide key information that should enable development of a detailed understanding of this central cellular process at a molecular level.
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31
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Abstract
Transcriptional enhancers are key determinants of developmentally regulated gene expression. Models of enhancer function must distinguish between analog or digital control of transcription, as well as their requirement to initiate or maintain transcriptional activity of a gene. In light of a recent study by Chong and colleagues (pp. 659-669) providing evidence of a transient requirement of an enhancer associated with the CD4 gene, we discuss possible mechanisms by which transcriptional memory can be propagated in the absence of enhancers.
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Affiliation(s)
- Ranjan Sen
- Laboratory of Cellular and Molecular Biology, National Institute of Aging, Baltimore, Maryland 21224, USA.
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32
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Nuclear envelope proteins and their role in nuclear positioning and replication. Biochem Soc Trans 2010; 38:741-6. [DOI: 10.1042/bst0380741] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Controlled movement of the nucleus is important in a wide variety of plant cellular events. Positioning involving intact nuclei occurs in cell division, development, tip growing systems such as the root hair and in response to stimuli, including light, touch and infection. Positioning is also essential in the division and replication of nuclear components, ranging from chromosome attachment to the breakdown and reformation of the nuclear envelope. Although description and understanding of the processes involved have advanced rapidly in recent years, significant gaps remain in our knowledge, especially concerning nuclear proteins involved in anchoring and interacting with cytoskeletal and nucleoskeletal elements involved in movement. In the present review, processes involving the movement and positioning of nuclei and nuclear components are described together with novel proteins implicated in nucleoskeletal and cytoskeletal interactions.
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33
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Kress C, Ballester M, Devinoy E, Rijnkels M. Epigenetic modifications in 3D: nuclear organization of the differentiating mammary epithelial cell. J Mammary Gland Biol Neoplasia 2010; 15:73-83. [PMID: 20143138 DOI: 10.1007/s10911-010-9169-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 01/21/2010] [Indexed: 10/19/2022] Open
Abstract
During the development of tissues, complex programs take place to reach terminally differentiated states with specific gene expression profiles. Epigenetic regulations such as histone modifications and chromatin condensation have been implicated in the short and long-term control of transcription. It has recently been shown that the 3D spatial organization of chromosomes in the nucleus also plays a role in genome function. Indeed, the eukaryotic interphase nucleus contains sub-domains that are characterized by their enrichment in specific factors such as RNA Polymerase II, splicing machineries or heterochromatin proteins which render portions of the genome differentially permissive to gene expression. The positioning of individual genes relative to these sub-domains is thought to participate in the control of gene expression as an epigenetic mechanism acting in the nuclear space. Here, we review what is known about the sub-nuclear organization of mammary epithelial cells in connection with gene expression and epigenetics. Throughout differentiation, global changes in nuclear architecture occur, notably with respect to heterochromatin distribution. The positions of mammary-specific genes relative to nuclear sub-compartments varies in response to hormonal stimulation. The contribution of tissue architecture to cell differentiation in the mammary gland is also seen at the level of nuclear organization, which is sensitive to microenvironmental stimuli such as extracellular matrix signaling. In addition, alterations in nuclear organization are concomitant with immortalization and carcinogenesis. Thus, the fate of cells appears to be controlled by complex pathways connecting external signal integration, gene expression, epigenetic modifications and chromatin organization in the nucleus.
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Affiliation(s)
- Clémence Kress
- UR1196 Génomique et Physiologie de la Lactation, INRA, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
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34
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Abstract
Recent progress in understanding the plant NE (nuclear envelope) has resulted from significant advances in identifying and characterizing the protein constituents of the membranes and nuclear pores. Here, we review recent findings on the membrane integral and membrane-associated proteins of the key domains of the NE, the pore domain and inner and outer NEs, together with information on protein targeting and NE function.
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35
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Lu Q, Tang X, Tian G, Wang F, Liu K, Nguyen V, Kohalmi SE, Keller WA, Tsang EWT, Harada JJ, Rothstein SJ, Cui Y. Arabidopsis homolog of the yeast TREX-2 mRNA export complex: components and anchoring nucleoporin. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:259-70. [PMID: 19843313 DOI: 10.1111/j.1365-313x.2009.04048.x] [Citation(s) in RCA: 263] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nuclear pore complexes (NPCs) are vital to nuclear-cytoplasmic communication in eukaryotes. The yeast NPC-associated TREX-2 complex, also known as the Thp1-Sac3-Cdc31-Sus1 complex, is anchored on the NPC via the nucleoporin Nup1, and is essential for mRNA export. Here we report the identification and characterization of the putative Arabidopsis thaliana TREX-2 complex and its anchoring nucleoporin. Physical and functional evidence support the identification of the Arabidopsis orthologs of yeast Thp1 and Nup1. Of three Arabidopsis homologs of yeast Sac3, two are putative TREX-2 components, but, surprisingly, none are required for mRNA export as they are in yeast. Physical association of the two Cdc31 homologs, but not the Sus1 homolog, with the TREX-2 complex was observed. In addition to identification of these TREX-2 components, direct interactions of the Arabidopsis homolog of DSS1, which is an established proteasome component in yeast and animals, with both the TREX-2 complex and the proteasome were observed. This suggests the possibility of a link between the two complexes. Thus this work has identified the putative Arabidopsis TREX-2 complex and provides a foundation for future studies of nuclear export in Arabidopsis.
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Affiliation(s)
- Qing Lu
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, ON N5V 4T3, Canada
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36
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Jungwirth M, Dear ML, Brown P, Holbrook K, Goodchild R. Relative tissue expression of homologous torsinB correlates with the neuronal specific importance of DYT1 dystonia-associated torsinA. Hum Mol Genet 2009; 19:888-900. [DOI: 10.1093/hmg/ddp557] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Barlow CA, Laishram RS, Anderson RA. Nuclear phosphoinositides: a signaling enigma wrapped in a compartmental conundrum. Trends Cell Biol 2009; 20:25-35. [PMID: 19846310 DOI: 10.1016/j.tcb.2009.09.009] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 09/27/2009] [Accepted: 09/28/2009] [Indexed: 01/09/2023]
Abstract
While the presence of phosphoinositides in the nuclei of eukaryotes and the identity of the enzymes responsible for their metabolism have been known for some time, their functions in the nucleus are only now emerging. This is illustrated by the recent identification of effectors for nuclear phosphoinositides. Like the cytosolic phosphoinositide signaling pathway, nuclear phosphatidylinositol 4,5-bisphosphate (PI4,5P(2)) is at the center of the pathway and acts both as a messenger and as a precursor for many additional messengers. Here, recent advances in the understanding of nuclear phosphoinositide signaling and its functions are reviewed with an emphasis on PI4,5P(2) and its role in gene expression. The compartmentalization of nuclear phosphoinositide phosphates (PIP(n)) remains a mystery, but emerging evidence suggests that phosphoinositides occupy several functionally distinct compartments.
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Affiliation(s)
- Christy A Barlow
- University of Wisconsin-Madison, Department of Pharmacology, 1300 University Ave. University of Wisconsin Medical School, Madison, WI 53706, USA
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38
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Dimauro T, David G. Chromatin modifications: the driving force of senescence and aging? Aging (Albany NY) 2009; 1:182-90. [PMID: 20157508 PMCID: PMC2806002 DOI: 10.18632/aging.100023] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 02/11/2009] [Indexed: 12/23/2022]
Abstract
An emerging field of
investigation in the search for treatment of human disease is the
modulation of chromatin modifications. Chromatin modifications impart
virtually all processes occurring in the mammalian nucleus, from regulation
of transcription to genomic stability and nuclear high order organization.
It has been well recognized that, as the mammalian cell ages, its chromatin
structure evolves, both at a global level and at specific loci. While these
observations are mostly correlative, recent technical developments allowing
loss-of-function experiments and genome-wide approaches have permitted the
identification of a causal relationship between specific changes in
chromatin structure and the aging phenotype. Here we review the evidence
pointing to the modulation of chromatin structure as a potential driving
force of cellular aging in mammals.
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Affiliation(s)
- Teresa Dimauro
- Department of Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA
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