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Sbrana F, Chellini F, Tani A, Parigi M, Garella R, Palmieri F, Zecchi-Orlandini S, Squecco R, Sassoli C. Label-free three-dimensional imaging and quantitative analysis of living fibroblasts and myofibroblasts by holotomographic microscopy. Microsc Res Tech 2024; 87:2757-2773. [PMID: 38984377 DOI: 10.1002/jemt.24648] [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: 05/20/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/11/2024]
Abstract
Holotomography (HT) is a cutting-edge fast live-cell quantitative label-free imaging technique. Based on the principle of quantitative phase imaging, it combines holography and tomography to record a three-dimensional map of the refractive index, used as intrinsic optical and quantitative imaging contrast parameter of biological samples, at a sub-micrometer spatial resolution. In this study HT has been employed for the first time to analyze the changes of fibroblasts differentiating towards myofibroblasts - recognized as the main cell player of fibrosis - when cultured in vitro with the pro-fibrotic factor, namely transforming growth factor-β1. In parallel, F-actin, vinculin, α-smooth muscle actin, phospho-myosin light chain 2, type-1 collagen, peroxisome proliferator-activated receptor-gamma coactivator-1α expression and mitochondria were evaluated by confocal laser scanning microscopy. Plasmamembrane passive properties and transient receptor potential canonical channels' currents were also recorded by whole-cell patch-clamp. The fluorescence images and electrophysiological results have been compared to the data obtained by HT and their congruence has been discussed. HT turned out to be a valid approach to morphologically distinguish fibroblasts from well differentiated myofibroblasts while obtaining objective measures concerning volume, surface area, projection area, surface index and dry mass (i.e., the mass of the non-aqueous content inside the cell including proteins and subcellular organelles) of the entire cell, nuclei and nucleoli with the major advantage to monitor outer and inner features in living cells in a non-invasive, rapid and label-free approach. HT might open up new research opportunities in the field of fibrotic diseases. RESEARCH HIGHLIGHTS: Holotomography (HT) is a label-free laser interferometric imaging technology exploiting the intrinsic optical property of cells namely refractive index (RI) to enable a direct imaging and analysis of whole cells or intracellular organelles. HT turned out a valid approach to distinguish morphological features of living unlabeled fibroblasts from differentiated myofibroblasts. HT provided quantitative information concerning volume, surface area, projection area, surface index and dry mass of the entire fibroblasts/myofibroblasts, nuclei and nucleoli.
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Affiliation(s)
| | - Flaminia Chellini
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Alessia Tani
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Martina Parigi
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Rachele Garella
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Francesco Palmieri
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Sandra Zecchi-Orlandini
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
| | - Roberta Squecco
- Department of Experimental and Clinical Medicine, Section of Physiological Sciences, University of Florence, Florence, Italy
| | - Chiara Sassoli
- Department of Experimental and Clinical Medicine, Section of Anatomy and Histology, Imaging Platform, University of Florence, Florence, Italy
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2
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Chen R, Zhao Y, Li M, Wang Y, Zhang L, Fei P. Efficient super-resolution volumetric imaging by radial fluctuation Bayesian analysis light-sheet microscopy. JOURNAL OF BIOPHOTONICS 2020; 13:e201960242. [PMID: 32314491 DOI: 10.1002/jbio.201960242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 04/04/2020] [Accepted: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Various computational super-resolution methods are available based on the analysis of fluorescence fluctuation behind acquired frames. However, dilemmas often exist in the balance of fluorophore characteristics, computation cost, and achievable resolution. Here we present an approach that uses a super-resolution radial fluctuations (SRRF) image to guide the Bayesian analysis of fluorophore blinking and bleaching (3B) events, allowing greatly accelerated localization of overlapping fluorophores with high accuracy. This radial fluctuation Bayesian analysis (RFBA) approach is also extended to three dimensions for the first time and combined with light-sheet fluorescence microscopy, to achieve super-resolution volumetric imaging of thick samples densely labeled with common fluorophores. For example, a 700-nm thin Bessel plane illumination is developed to optically section the Drosophila brain, providing a high-contrast 3D image of rhythmic neurons. RFBA analyzes 30 serial volumes to reconstruct a super-resolved 3D image at 4-times higher resolutions (~70 and 170 nm), and precisely resolve the axon terminals. The computation is over 2-orders faster than conventional 3B analysis microscopy. The capability of RFBA is also verified through dual-color imaging of cell nucleus in live Drosophila brain. The spatial co-localization patterns of the nuclear envelope and DNA in a neuron deep inside the brain can be precisely extracted by our approach.
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Affiliation(s)
- Rong Chen
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Yuxuan Zhao
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Mengna Li
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yarong Wang
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Luoying Zhang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Peng Fei
- School of Optical and Electronic Information- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
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3
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Fischer EG. Nuclear Morphology and the Biology of Cancer Cells. Acta Cytol 2020; 64:511-519. [PMID: 32570234 DOI: 10.1159/000508780] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND For more than a century, diagnostic pathologists have used morphologic abnormalities of the nucleus as essential diagnostic features to distinguish benign from malignant cells. These features include nuclear enlargement and increased nuclear-to-cytoplasmic ratio, nuclear membrane irregularities, hyperchromasia, and abnormal chromatin distribution. As our knowledge about the genetic and epigenetic abnormalities of cancer cells has increased in recent decades, the pathophysiologic mechanisms that underlie these morphologic abnormalities remain incompletely understood. SUMMARY This review attempts to summarize biologic abnormalities in malignant cells related to these morphologic changes. The molecular anatomy of the nuclear envelope in normal and malignant cells is discussed as well as regulation of nuclear size and shape, regulation of signal transduction pathways by molecules of the nuclear envelope, chromatin distribution, and the effects of HPV infection on dysplastic cells in the uterine cervix. Key Message: Causes of morphologic nuclear abnormalities in malignant cells are likely multifactorial. They probably include mutations, dysregulation of signal transduction pathways, abnormal gene expression patterns, alterations of nuclear envelope proteins and chromatin, and aneuploidy.
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Affiliation(s)
- Edgar G Fischer
- Division of Surgical Pathology and Cytopathology, Department of Pathology, University of New Mexico, Albuquerque, New Mexico, USA,
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4
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Dunlevy KL, Medvedeva V, Wilson JE, Hoque M, Pellegrin T, Maynard A, Kremp MM, Wasserman JS, Poleshko A, Katz RA. The PRR14 heterochromatin tether encodes modular domains that mediate and regulate nuclear lamina targeting. J Cell Sci 2020; 133:jcs240416. [PMID: 32317397 PMCID: PMC7272351 DOI: 10.1242/jcs.240416] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 04/01/2020] [Indexed: 01/01/2023] Open
Abstract
A large fraction of epigenetically silent heterochromatin is anchored to the nuclear periphery via 'tethering proteins' that function to bridge heterochromatin and the nuclear membrane or nuclear lamina. We previously identified a human tethering protein, PRR14, that binds heterochromatin through an N-terminal domain, but the mechanism and regulation of nuclear lamina association remained to be investigated. Here we identify an evolutionarily conserved PRR14 nuclear lamina binding domain (LBD) that is both necessary and sufficient for positioning of PRR14 at the nuclear lamina. We show that PRR14 associates dynamically with the nuclear lamina, and provide evidence that such dynamics are regulated through phosphorylation and dephosphorylation of the LBD. Furthermore, we identify a PP2A phosphatase recognition motif within the evolutionarily conserved C-terminal Tantalus domain of PRR14. Disruption of this motif affects PRR14 localization to the nuclear lamina. The overall findings demonstrate a heterochromatin anchoring mechanism whereby the PRR14 tether simultaneously binds heterochromatin and the nuclear lamina through two separable modular domains. Our findings also describe an optimal PRR14 LBD fragment that could be used for efficient targeting of fusion proteins to the nuclear lamina.
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Affiliation(s)
- Kelly L Dunlevy
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Valentina Medvedeva
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Jade E Wilson
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Mohammed Hoque
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Trinity Pellegrin
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Adam Maynard
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Madison M Kremp
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Jason S Wasserman
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
| | - Andrey Poleshko
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Richard A Katz
- Cancer Epigenetics Program, Fox Chase Cancer Center, Temple University Health System, Philadelphia, PA 19111, USA
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5
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The role of transposable elements activity in aging and their possible involvement in laminopathic diseases. Ageing Res Rev 2020; 57:100995. [PMID: 31786372 DOI: 10.1016/j.arr.2019.100995] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/17/2019] [Accepted: 11/25/2019] [Indexed: 01/17/2023]
Abstract
Eukaryotic genomes contain a large number of transposable elements, part of which are still active and able to transpose in the host genome. Mobile element activation is repressed to avoid deleterious effects, such as gene mutations or chromosome rearrangements. Control of transposable elements includes a variety of mechanisms comprising silencing pathways, which are based on the production of small non-coding RNAs. Silencing can occur either through transposable element RNA degradation or through the targeting of DNA sequences by heterochromatin formation and consequent transcriptional inhibition. Since the important role of the heterochromatin silencing, the gradual loss of heterochromatin marks in constitutive heterochromatin regions during the aging process promotes derepression of transposable elements, which is considered a cause of the progressive increase in genomic instability and of the activation of inflammatory responses. This review provides an overview of the effects of heterochromatin loss on the activity of transposable elements during the aging process and the possible impact on genome function. In this context, we discuss the possible role of the nuclear lamina, a major player in heterochromatin dynamics, in the regulation of transposable element activity and potential implications in laminopathic diseases.
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6
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Bu B, He W, Song L, Zhang L. Nuclear Envelope Protein MAN1 Regulates the Drosophila Circadian Clock via Period. Neurosci Bull 2019; 35:969-978. [PMID: 31230212 DOI: 10.1007/s12264-019-00404-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 01/13/2019] [Indexed: 01/28/2023] Open
Abstract
Almost all organisms exhibit ~24-h rhythms, or circadian rhythms, in a plentitude of biological processes. These rhythms are driven by endogenous molecular clocks consisting of a series of transcriptional and translational feedback loops. Previously, we have shown that the inner nuclear membrane protein MAN1 regulates this clock and thus the locomotor rhythm in flies, but the mechanism remains unclear. Here, we further confirmed the previous findings and found that knocking down MAN1 in the pacemaker neurons of adult flies is sufficient to lengthen the period of the locomotor rhythm. Molecular analysis revealed that knocking down MAN1 led to reduced mRNA and protein levels of the core clock gene period (per), likely by reducing its transcription. Over-expressing per rescued the long period phenotype caused by MAN1 deficiency whereas per mutation had an epistatic effect on MAN1, indicating that MAN1 sets the pace of the clock by targeting per.
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Affiliation(s)
- Bei Bu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Weiwei He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Li Song
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Luoying Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China. .,Institute of Brain Research, Huazhong University of Science and Technology, Wuhan, 430074, China.
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7
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Pereira CD, Serrano JB, Martins F, da Cruz E Silva OAB, Rebelo S. Nuclear envelope dynamics during mammalian spermatogenesis: new insights on male fertility. Biol Rev Camb Philos Soc 2019; 94:1195-1219. [PMID: 30701647 DOI: 10.1111/brv.12498] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 02/06/2023]
Abstract
The production of highly specialized spermatozoa from undifferentiated spermatogonia is a strictly organized and programmed process requiring extensive restructuring of the entire cell. One of the most remarkable cellular transformations accompanying the various phases of spermatogenesis is the profound remodelling of the nuclear architecture, in which the nuclear envelope (NE) seems to be crucially involved. In recent years, several proteins from the distinct layers forming the NE (i.e. the inner and outer nuclear membranes as well as the nuclear lamina) have been associated with meiosis and/or spermiogenesis in different mammalian species. Among these are A- and B-type lamins, Dpy-19-like protein 2 (DPY19L2), lamin B receptor (LBR), lamina-associated polypeptide 1 (LAP1), LAP2/emerin/MAN1 (LEM) domain-containing proteins, spermatogenesis-associated 46 (SPATA46) and diverse elements of the linker of nucleoskeleton and cytoskeleton (LINC) complex, namely Sad-1/UNC-84 homology (SUN) and Klarsicht/ANC-1/Syne-1 homology (KASH) domain-containing proteins. Herein, we summarize the current state of the art on the cellular and subcellular distribution of NE proteins expressed during mammalian spermatogenesis, and discuss the latest research developments regarding their testis-specific functions. This review provides a comprehensive and innovative overview of the NE network as a regulatory platform and as an essential determinant of efficient meiotic chromosome recombination as well as spermiogenesis-associated nuclear remodelling and differentiation in mammalian male germline cells. Thus, this review provides important novel insights on the biological relevance of NE proteins for male fertility.
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Affiliation(s)
- Cátia D Pereira
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute for Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Joana B Serrano
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute for Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Filipa Martins
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute for Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal
| | - Odete A B da Cruz E Silva
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute for Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal.,The Discovery CTR, University of Aveiro Campus, 3810-193 Aveiro, Portugal
| | - Sandra Rebelo
- Department of Medical Sciences, Neuroscience and Signalling Laboratory, Institute for Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal
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8
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de Bruyn Kops A, Burke JE, Guthrie C. Brr6 plays a role in gene recruitment and transcriptional regulation at the nuclear envelope. Mol Biol Cell 2018; 29:2578-2590. [PMID: 30133335 PMCID: PMC6254580 DOI: 10.1091/mbc.e18-04-0258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Correlation between transcriptional regulation and positioning of genes at the nuclear envelope is well established in eukaryotes, but the mechanisms involved are not well understood. We show that brr6-1, a mutant of the essential yeast envelope transmembrane protein Brr6p, impairs normal positioning and expression of the PAB1 and FUR4-GAL1,10,7 loci. Similarly, expression of a dominant negative nucleoplasmic Brr6 fragment in wild-type cells reproduced many of the brr6-1 effects. Histone chromatin immunoprecipitation (ChIP) experiments showed decreased acetylation at the key histone H4K16 residue in the FUR4-GAL1,10,7 region in brr6-1. Importantly, blocking deacetylation significantly suppressed selected brr6-1 phenotypes. ChIPseq with FLAG-tagged Brr6 fragments showed enrichment at FUR4 and several other genes that showed striking changes in brr6-1 RNAseq data. These associations depended on a Brr6 putative zinc finger domain. Importantly, artificially tethering the GAL1 locus to the envelope suppressed the brr6-1 effects on GAL1 and FUR4 expression and increased H4K16 acetylation between GAL1 and FUR4 in the mutant. Together these results argue that Brr6 interacts with chromatin, helping to maintain normal chromatin architecture and transcriptional regulation of certain loci at the nuclear envelope.
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Affiliation(s)
- Anne de Bruyn Kops
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
| | - Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143
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9
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Lapetina DL, Ptak C, Roesner UK, Wozniak RW. Yeast silencing factor Sir4 and a subset of nucleoporins form a complex distinct from nuclear pore complexes. J Cell Biol 2017; 216:3145-3159. [PMID: 28883038 PMCID: PMC5626528 DOI: 10.1083/jcb.201609049] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 05/26/2017] [Accepted: 07/31/2017] [Indexed: 11/22/2022] Open
Abstract
Lapetina et al. identify a protein interaction network involved in the association of chromatin with the nuclear envelope. This network includes a telomere tether, a silencing factor, a SUMO E3 ligase, and an array of nucleoporins that together form a complex distinct from nuclear pore complexes. Interactions occurring at the nuclear envelope (NE)–chromatin interface influence both NE structure and chromatin organization. Insights into the functions of NE–chromatin interactions have come from the study of yeast subtelomeric chromatin and its association with the NE, including the identification of various proteins necessary for tethering subtelomeric chromatin to the NE and the silencing of resident genes. Here we show that four of these proteins—the silencing factor Sir4, NE-associated Esc1, the SUMO E3 ligase Siz2, and the nuclear pore complex (NPC) protein Nup170—physically and functionally interact with one another and a subset of NPC components (nucleoporins or Nups). Importantly, this group of Nups is largely restricted to members of the inner and outer NPC rings, but it lacks numerous others including cytoplasmically and nucleoplasmically positioned Nups. We propose that this Sir4-associated Nup complex is distinct from holo-NPCs and that it plays a role in subtelomeric chromatin organization and NE tethering.
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Affiliation(s)
- Diego L Lapetina
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Ulyss K Roesner
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
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10
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Chaix A, Zarrinpar A, Panda S. The circadian coordination of cell biology. J Cell Biol 2017; 215:15-25. [PMID: 27738003 PMCID: PMC5057284 DOI: 10.1083/jcb.201603076] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 09/21/2016] [Indexed: 02/07/2023] Open
Abstract
Chaix et al. review how cells generate circadian oscillations and how circadian clocks control cell biology. Circadian clocks are cell-autonomous timing mechanisms that organize cell functions in a 24-h periodicity. In mammals, the main circadian oscillator consists of transcription–translation feedback loops composed of transcriptional regulators, enzymes, and scaffolds that generate and sustain daily oscillations of their own transcript and protein levels. The clock components and their targets impart rhythmic functions to many gene products through transcriptional, posttranscriptional, translational, and posttranslational mechanisms. This, in turn, temporally coordinates many signaling pathways, metabolic activity, organelles’ structure and functions, as well as the cell cycle and the tissue-specific functions of differentiated cells. When the functions of these circadian oscillators are disrupted by age, environment, or genetic mutation, the temporal coordination of cellular functions is lost, reducing organismal health and fitness.
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Affiliation(s)
- Amandine Chaix
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
| | - Amir Zarrinpar
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037 Division of Gastroenterology, University of California, San Diego, La Jolla, CA 92093
| | - Satchidananda Panda
- Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037
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Tariq Z, Zhang H, Chia-Liu A, Shen Y, Gete Y, Xiong ZM, Tocheny C, Campanello L, Wu D, Losert W, Cao K. Lamin A and microtubules collaborate to maintain nuclear morphology. Nucleus 2017; 8:433-446. [PMID: 28557611 DOI: 10.1080/19491034.2017.1320460] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Lamin A (LA) is a critical structural component of the nuclear lamina. Mutations within the LA gene (LMNA) lead to several human disorders, most striking of which is Hutchinson-Gilford Progeria Syndrome (HGPS), a premature aging disorder. HGPS cells are best characterized by an abnormal nuclear morphology known as nuclear blebbing, which arises due to the accumulation of progerin, a dominant mutant form of LA. The microtubule (MT) network is known to mediate changes in nuclear morphology in the context of specific events such as mitosis, cell polarization, nucleus positioning and cellular migration. What is less understood is the role of the microtubule network in determining nuclear morphology during interphase. In this study, we elucidate the role of the cytoskeleton in regulation and misregulation of nuclear morphology through perturbations of both the lamina and the microtubule network. We found that LA knockout cells exhibit a crescent shape morphology associated with the microtubule-organizing center. Furthermore, this crescent shape ameliorates upon treatment with MT drugs, Nocodazole or Taxol. Expression of progerin, in LA knockout cells also rescues the crescent shape, although the response to Nocodazole or Taxol treatment is altered in comparison to cells expressing LA. Together these results describe a collaborative effort between LA and the MT network to maintain nuclear morphology.
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Affiliation(s)
- Zeshan Tariq
- a Department of Cell Biology and Molecular Genetics , University of Maryland , College Park , MD , USA
| | - Haoyue Zhang
- a Department of Cell Biology and Molecular Genetics , University of Maryland , College Park , MD , USA
| | - Alexander Chia-Liu
- b Department of Physics , University of Maryland , College Park , MD , USA
| | - Yang Shen
- b Department of Physics , University of Maryland , College Park , MD , USA
| | - Yantenew Gete
- a Department of Cell Biology and Molecular Genetics , University of Maryland , College Park , MD , USA
| | - Zheng-Mei Xiong
- a Department of Cell Biology and Molecular Genetics , University of Maryland , College Park , MD , USA
| | - Claire Tocheny
- c Department of Biology , The College of William and Mary , Williamsburg , VA , USA
| | - Leonard Campanello
- b Department of Physics , University of Maryland , College Park , MD , USA
| | - Di Wu
- a Department of Cell Biology and Molecular Genetics , University of Maryland , College Park , MD , USA
| | - Wolfgang Losert
- b Department of Physics , University of Maryland , College Park , MD , USA
| | - Kan Cao
- a Department of Cell Biology and Molecular Genetics , University of Maryland , College Park , MD , USA
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Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes. Sci Rep 2017; 7:100. [PMID: 28273906 PMCID: PMC5427898 DOI: 10.1038/s41598-017-00176-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 02/13/2017] [Indexed: 01/10/2023] Open
Abstract
Because a large portion of the mammalian genome is associated with the nuclear lamina (NL), it is interesting to study how native genes resided there are transcribed and regulated. In this study, we report unique transcriptional and epigenetic features of nearly 3,500 NL-associated genes (NL genes). Promoter regions of active NL genes are often excluded from NL-association, suggesting that NL-promoter interactions may repress transcription. Active NL genes with higher RNA polymerase II (Pol II) recruitment levels tend to display Pol II promoter-proximal pausing, while Pol II recruitment and Pol II pausing are not correlated among non-NL genes. At the genome-wide scale, NL-association and H3K27me3 distinguishes two large gene classes with low transcriptional activities. Notably, NL-association is anti-correlated with both transcription and active histone mark levels among genes not significantly enriched with H3K9me3 or H3K27me3, suggesting that NL-association may represent a novel gene repression pathway. Interestingly, an NL gene subgroup is not significantly enriched with H3K9me3 or H3K27me3 and is transcribed at higher levels than the rest of NL genes. Furthermore, we identified distal enhancers associated with active NL genes and reported their epigenetic features.
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Abstract
SUMMARYThe nucleoskeleton is an important structural feature of the metazoan nucleus and is involved in the regulation of genome expression and maintenance. The nuclear lamins are intermediate filament proteins that form a peripheral nucleoskeleton in concert with other lamin-associated proteins. Several other proteins normally found in the cytoskeleton have also been identified in the nucleus, but, as will be discussed here, their roles in forming a nucleoskeleton have not been elucidated. Nevertheless, mutations in lamins and lamin-associated proteins cause a spectrum of diseases, making them interesting targets for future research.
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Affiliation(s)
- Stephen A Adam
- Department of Cell and Molecular Biology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611
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14
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Heinrich S, Derrer CP, Lari A, Weis K, Montpetit B. Temporal and spatial regulation of mRNA export: Single particle RNA-imaging provides new tools and insights. Bioessays 2017; 39. [PMID: 28052353 DOI: 10.1002/bies.201600124] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The transport of messenger RNAs (mRNAs) from the nucleus to cytoplasm is an essential step in the gene expression program of all eukaryotes. Recent technological advances in the areas of RNA-labeling, microscopy, and sequencing are leading to novel insights about mRNA biogenesis and export. This includes quantitative single molecule imaging (SMI) of RNA molecules in live cells, which is providing knowledge of the spatial and temporal dynamics of the export process. As this information becomes available, it leads to new questions, the reinterpretation of previous findings, and revised models of mRNA export. In this review, we will briefly highlight some of these recent findings and discuss how live cell SMI approaches may be used to further our current understanding of mRNA export and gene expression.
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Affiliation(s)
| | | | - Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Karsten Weis
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Department of Viticulture and Enology, University of California, Davis, CA, USA
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15
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Padiath QS. Lamin B1 mediated demyelination: Linking Lamins, Lipids and Leukodystrophies. Nucleus 2016; 7:547-553. [PMID: 27854160 PMCID: PMC5214339 DOI: 10.1080/19491034.2016.1260799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/01/2016] [Accepted: 11/10/2016] [Indexed: 01/08/2023] Open
Abstract
Autosomal Dominant Leukodystrophy (ADLD), a fatal adult onset demyelinating disorder, is the only human disease that has been linked to mutations of the nuclear lamina protein, lamin B1, and is primarily caused by duplications of the LMNB1 gene. Why CNS myelin is specifically targeted and the mechanisms underlying ADLD are unclear. Recent work from our group has demonstrated that over expression of lamin B1 in oligodendrocytes, the myelin producing cells in the CNS, resulted in age dependent epigenetic modifications, transcriptional down-regulation of lipogenic gene expression and significant reductions of myelin-enriched lipids. Given the high lipid content of meylin, we hypothesize that lipid loss is one of the primary drivers of the demyelination phenotype. These results can, at least partially, explain the age dependence and cell type specificity in ADLD and are discussed in the context of the existing literature, in an attempt to delineate potential pathways underlying the disease phenotype.
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Affiliation(s)
- Quasar S. Padiath
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
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16
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Abstract
ATR (Ataxia Telangiectasia and Rad3-related) is a member of the Phosphatidylinositol 3-kinase-related kinases (PIKKs) family, amongst six other vertebrate proteins known so far. ATR is indispensable for cell survival and its essential role is in sensing DNA damage and initiating appropriate repair responses. In this review we highlight emerging and recent observations connecting ATR to alternative roles in controlling the nuclear envelope, nucleolus, centrosome and other organelles in response to both internal and external stress conditions. We propose that ATR functions control cell plasticity by sensing structural deformations of different cellular components, including DNA and initiating appropriate repair responses, most of which are yet to be understood completely.
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Affiliation(s)
- Gururaj Rao Kidiyoor
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy
| | - Amit Kumar
- Developmental Toxicology Laboratory, Systems Toxicology and Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), India
| | - Marco Foiani
- Istituto FIRC di Oncologia Molecolare, Milan, Italy; University of Milan, Milan, Italy.
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17
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Ptak C, Wozniak RW. Nucleoporins and chromatin metabolism. Curr Opin Cell Biol 2016; 40:153-160. [PMID: 27085162 DOI: 10.1016/j.ceb.2016.03.024] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/26/2016] [Accepted: 03/31/2016] [Indexed: 01/04/2023]
Abstract
Mounting evidence has implicated a group of proteins termed nucleoporins, or Nups, in various processes that regulate chromatin structure and function. Nups were first recognized as building blocks for nuclear pore complexes, but several members of this group of proteins also reside in the cytoplasm and within the nucleus. Moreover, many are dynamic and move between these various locations. Both at the nuclear envelope, as part of nuclear pore complexes, and within the nucleoplasm, Nups interact with protein complexes that function in gene transcription, chromatin remodeling, DNA repair, and DNA replication. Here, we review recent studies that provide further insight into the molecular details of these interactions and their role in regulating the activity of chromatin modifying factors.
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Affiliation(s)
- Christopher Ptak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Richard W Wozniak
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.
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18
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Xiong Z, Choi JY, Wang K, Zhang H, Tariq Z, Wu D, Ko E, LaDana C, Sesaki H, Cao K. Methylene blue alleviates nuclear and mitochondrial abnormalities in progeria. Aging Cell 2016; 15:279-90. [PMID: 26663466 PMCID: PMC4783354 DOI: 10.1111/acel.12434] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2015] [Indexed: 12/17/2022] Open
Abstract
Hutchinson–Gilford progeria syndrome (HGPS), a fatal premature aging disease, is caused by a single‐nucleotide mutation in the LMNA gene. Previous reports have focused on nuclear phenotypes in HGPS cells, yet the potential contribution of the mitochondria, a key player in normal aging, remains unclear. Using high‐resolution microscopy analysis, we demonstrated a significantly increased fraction of swollen and fragmented mitochondria and a marked reduction in mitochondrial mobility in HGPS fibroblast cells. Notably, the expression of PGC‐1α, a central regulator of mitochondrial biogenesis, was inhibited by progerin. To rescue mitochondrial defects, we treated HGPS cells with a mitochondrial‐targeting antioxidant methylene blue (MB). Our analysis indicated that MB treatment not only alleviated the mitochondrial defects but also rescued the hallmark nuclear abnormalities in HGPS cells. Additional analysis suggested that MB treatment released progerin from the nuclear membrane, rescued perinuclear heterochromatin loss and corrected misregulated gene expression in HGPS cells. Together, these results demonstrate a role of mitochondrial dysfunction in developing the premature aging phenotypes in HGPS cells and suggest MB as a promising therapeutic approach for HGPS.
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Affiliation(s)
- Zheng‐Mei Xiong
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
| | - Ji Young Choi
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
| | - Kun Wang
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
- Center for Bioinformatics and Computational Biology University of Maryland College Park MD 20742 USA
| | - Haoyue Zhang
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
| | - Zeshan Tariq
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
| | - Di Wu
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
| | - Eunae Ko
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
| | - Christina LaDana
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
| | - Hiromi Sesaki
- Department of Cell Biology Johns Hopkins University School of Medicine Baltimore MD 21205 USA
| | - Kan Cao
- Department of Cell Biology and Molecular Genetics University of Maryland College Park MD 20742 USA
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19
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Noncoding RNA as regulators of cardiac fibrosis: current insight and the road ahead. Pflugers Arch 2016; 468:1103-11. [PMID: 26786602 DOI: 10.1007/s00424-016-1792-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/11/2015] [Accepted: 01/07/2016] [Indexed: 12/19/2022]
Abstract
Cardiac fibrosis is an important pathological feature of cardiac remodeling in heart diseases. The molecular mechanisms of cardiac fibrosis are unknown. Genomic analyses estimated that many noncoding DNA regions generate noncoding RNAs (ncRNAs). ncRNAs have emerged as key molecular players in the regulation of gene expression in different biological processes. Recent studies have started to reveal the importance of ncRNAs in heart development and suggest also an involvement in cardiac fibrosis. These molecules are emerging as important regulators of cellular process. Here, we review particularly focuses on the involvement of two large families of ncRNAs, namely microRNAs (miRNAs) and long noncoding RNAs (LncRNAs) in the regulation of cardiac fibrosis. Furthermore, we review the functions and role of ncRNAs in cardiac biology and discuss these reports and the therapeutic potential of ncRNAs for cardiac fibrosis associated with fibroblast activation and proliferation.
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20
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Rolyan H, Tyurina YY, Hernandez M, Amoscato AA, Sparvero LJ, Nmezi BC, Lu Y, Estécio MRH, Lin K, Chen J, He RR, Gong P, Rigatti LH, Dupree J, Bayır H, Kagan VE, Casaccia P, Padiath QS. Defects of Lipid Synthesis Are Linked to the Age-Dependent Demyelination Caused by Lamin B1 Overexpression. J Neurosci 2015; 35:12002-17. [PMID: 26311780 PMCID: PMC4549407 DOI: 10.1523/jneurosci.1668-15.2015] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Revised: 06/24/2015] [Accepted: 07/23/2015] [Indexed: 11/21/2022] Open
Abstract
Lamin B1 is a component of the nuclear lamina and plays a critical role in maintaining nuclear architecture, regulating gene expression and modulating chromatin positioning. We have previously shown that LMNB1 gene duplications cause autosomal dominant leukodystrophy (ADLD), a fatal adult onset demyelinating disease. The mechanisms by which increased LMNB1 levels cause ADLD are unclear. To address this, we used a transgenic mouse model where Lamin B1 overexpression is targeted to oligodendrocytes. These mice showed severe vacuolar degeneration of the spinal cord white matter together with marked astrogliosis, microglial infiltration, and secondary axonal damage. Oligodendrocytes in the transgenic mice revealed alterations in histone modifications favoring a transcriptionally repressed state. Chromatin changes were accompanied by reduced expression of genes involved in lipid synthesis pathways, many of which are known to play important roles in myelin regulation and are preferentially expressed in oligodendrocytes. Decreased lipogenic gene expression resulted in a significant reduction in multiple classes of lipids involved in myelin formation. Many of these gene expression changes and lipid alterations were observed even before the onset of the phenotype, suggesting a causal role. Our findings establish, for the first time, a link between LMNB1 and lipid synthesis in oligodendrocytes, and provide a mechanistic framework to explain the age dependence and white matter involvement of the disease phenotype. These results have implications for disease pathogenesis and may also shed light on the regulation of lipid synthesis pathways in myelin maintenance and turnover. SIGNIFICANCE STATEMENT Autosomal dominant leukodystrophy (ADLD) is fatal neurological disorder caused by increased levels of the nuclear protein, Lamin B1. The disease is characterized by an age-dependent loss of myelin, the fatty sheath that covers nerve fibers. We have studied a mouse model where Lamin B1 level are increased in oligodendrocytes, the cell type that produces myelin in the CNS. We demonstrate that destruction of myelin in the spinal cord is responsible for the degenerative phenotype in our mouse model. We show that this degeneration is mediated by reduced expression of lipid synthesis genes and the subsequent reduction in myelin enriched lipids. These findings provide a mechanistic framework to explain the age dependence and tissue specificity of the ADLD disease phenotype.
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Affiliation(s)
- Harshvardhan Rolyan
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15216
| | - Yulia Y Tyurina
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Marylens Hernandez
- Friedman Brain Institute Center for Neural Repair, Department of Neuroscience, and Graduate School of Biological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Andrew A Amoscato
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Louis J Sparvero
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Bruce C Nmezi
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15216
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, and Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Marcos R H Estécio
- Department of Epigenetics and Molecular Carcinogenesis, and Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, and Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - Junda Chen
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15216
| | - Rong-Rong He
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Pin Gong
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Lora H Rigatti
- Division of Laboratory Animal Resources, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Jeffrey Dupree
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, Virginia 23298, and
| | - Hülya Bayır
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, Safar Center for Resuscitation Research and Departments of Critical Care Medicine
| | - Valerian E Kagan
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, Pharmacology and Chemical Biology, Chemistry, and Radiation Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Patrizia Casaccia
- Graduate School of Biological Sciences, The Icahn School of Medicine at Mount Sinai, New York, New York 10029
| | - Quasar S Padiath
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15216,
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21
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Trussart M, Serra F, Baù D, Junier I, Serrano L, Marti-Renom MA. Assessing the limits of restraint-based 3D modeling of genomes and genomic domains. Nucleic Acids Res 2015; 43:3465-77. [PMID: 25800747 PMCID: PMC4402535 DOI: 10.1093/nar/gkv221] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/22/2015] [Indexed: 12/24/2022] Open
Abstract
Restraint-based modeling of genomes has been recently explored with the advent of Chromosome Conformation Capture (3C-based) experiments. We previously developed a reconstruction method to resolve the 3D architecture of both prokaryotic and eukaryotic genomes using 3C-based data. These models were congruent with fluorescent imaging validation. However, the limits of such methods have not systematically been assessed. Here we propose the first evaluation of a mean-field restraint-based reconstruction of genomes by considering diverse chromosome architectures and different levels of data noise and structural variability. The results show that: first, current scoring functions for 3D reconstruction correlate with the accuracy of the models; second, reconstructed models are robust to noise but sensitive to structural variability; third, the local structure organization of genomes, such as Topologically Associating Domains, results in more accurate models; fourth, to a certain extent, the models capture the intrinsic structural variability in the input matrices and fifth, the accuracy of the models can be a priori predicted by analyzing the properties of the interaction matrices. In summary, our work provides a systematic analysis of the limitations of a mean-field restrain-based method, which could be taken into consideration in further development of methods as well as their applications.
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Affiliation(s)
- Marie Trussart
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François Serra
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Davide Baù
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Ivan Junier
- Universitat Pompeu Fabra (UPF), Barcelona, Spain Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Luís Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Marc A Marti-Renom
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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22
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Abstract
Daily rhythms of behavior and physiology arise from endogenous circadian clocks. At the molecular level, the circadian clock consists of intricate transcriptional and post-transcriptional feedback loops that drive 24h rhythms in a vast repertoire of basic cellular processes. The nuclear envelope, as a fundamental component of the cell, has been shown to function as a global transcriptional regulatory machinery. Recently we found that nuclear envelope proteins regulate the circadian clock both in the mammalian system and in fruit flies. One of these proteins, MAN1, impinges on the clock by binding to the promoter region of the core clock gene BMAL1 and enhances its transcription. Here we discuss about other potential mechanisms employed by nuclear envelope proteins to regulate the circadian clock and possible biological relevance of these modulations.
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Affiliation(s)
- Luoying Zhang
- a Department of Neurology ; University of California ; San Francisco , CA USA
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23
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Fedorchak GR, Kaminski A, Lammerding J. Cellular mechanosensing: getting to the nucleus of it all. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 115:76-92. [PMID: 25008017 PMCID: PMC4252489 DOI: 10.1016/j.pbiomolbio.2014.06.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 06/28/2014] [Indexed: 12/12/2022]
Abstract
Cells respond to mechanical forces by activating specific genes and signaling pathways that allow the cells to adapt to their physical environment. Examples include muscle growth in response to exercise, bone remodeling based on their mechanical load, or endothelial cells aligning under fluid shear stress. While the involved downstream signaling pathways and mechanoresponsive genes are generally well characterized, many of the molecular mechanisms of the initiating 'mechanosensing' remain still elusive. In this review, we discuss recent findings and accumulating evidence suggesting that the cell nucleus plays a crucial role in cellular mechanotransduction, including processing incoming mechanoresponsive signals and even directly responding to mechanical forces. Consequently, mutations in the involved proteins or changes in nuclear envelope composition can directly impact mechanotransduction signaling and contribute to the development and progression of a variety of human diseases, including muscular dystrophy, cancer, and the focus of this review, dilated cardiomyopathy. Improved insights into the molecular mechanisms underlying nuclear mechanotransduction, brought in part by the emergence of new technologies to study intracellular mechanics at high spatial and temporal resolution, will not only result in a better understanding of cellular mechanosensing in normal cells but may also lead to the development of novel therapies in the many diseases linked to defects in nuclear envelope proteins.
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Affiliation(s)
- Gregory R Fedorchak
- Department of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Ashley Kaminski
- Department of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jan Lammerding
- Department of Biomedical Engineering, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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