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Mukherjee A, Epperly MW, Shields D, Hou W, Fisher R, Hamade D, Wang H, Saiful Huq M, Bao R, Tabib T, Monier D, Watkins S, Calderon M, Greenberger JS. Ionizing irradiation-induced Fgr in senescent cells mediates fibrosis. Cell Death Discov 2021; 7:349. [PMID: 34772919 PMCID: PMC8585734 DOI: 10.1038/s41420-021-00741-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/15/2021] [Accepted: 10/21/2021] [Indexed: 11/09/2022] Open
Abstract
The role of cellular senescence in radiation-induced pulmonary fibrosis (RIPF) and the underlying mechanisms are unknown. We isolated radiation-induced senescent tdTOMp16 positive mesenchymal stem cells, established their absence of cell division, then measured levels of irradiation-induced expression of biomarkers of senescence by RNA-seq analysis. We identified a Log2 6.17-fold upregulation of tyrosine kinase Fgr, which was a potent inducer of biomarkers of fibrosis in target cells in non-contact co-cultures. Inhibition of Fgr by shRNA knockdown did not block radiation-induced senescence in vitro; however, both shRNA knockdown, or addition of a specific small-molecule inhibitor of Fgr, TL02-59, abrogated senescent cell induction of profibrotic genes in transwell-separated target cells. Single-cell RNA-seq (scRNAseq) analysis of mouse lungs at day 150 after 20 Gy thoracic irradiation revealed upregulation of Fgr in senescent neutrophils, and macrophages before detection of lung fibrosis. Thus, upregulated Fgr in radiation-induced senescent cells mediates RIPF and is a potential therapeutic target for the prevention of this radiation late effect.
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Affiliation(s)
- Amitava Mukherjee
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Michael W Epperly
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Donna Shields
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Wen Hou
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Renee Fisher
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Diala Hamade
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Hong Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Saiful Huq
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Riyue Bao
- Department of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Tracy Tabib
- Department of Rheumatology & Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daisy Monier
- Department of Rheumatology & Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Simon Watkins
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Calderon
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joel S Greenberger
- Department of Radiation Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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Rivera-Mulia JC, Schwerer H, Besnard E, Desprat R, Trevilla-Garcia C, Sima J, Bensadoun P, Zouaoui A, Gilbert DM, Lemaitre JM. Cellular senescence induces replication stress with almost no affect on DNA replication timing. Cell Cycle 2018; 17:1667-1681. [PMID: 29963964 DOI: 10.1080/15384101.2018.1491235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Organismal aging entails a gradual decline of normal physiological functions and a major contributor to this decline is withdrawal of the cell cycle, known as senescence. Senescence can result from telomere diminution leading to a finite number of population doublings, known as replicative senescence (RS), or from oncogene overexpression, as a protective mechanism against cancer. Senescence is associated with large-scale chromatin re-organization and changes in gene expression. Replication stress is a complex phenomenon, defined as the slowing or stalling of replication fork progression and/or DNA synthesis, which has serious implications for genome stability, and consequently in human diseases. Aberrant replication fork structures activate the replication stress response leading to the activation of dormant origins, which is thought to be a safeguard mechanism to complete DNA replication on time. However, the relationship between replicative stress and the changes in the spatiotemporal program of DNA replication in senescence progression remains unclear. Here, we studied the DNA replication program during senescence progression in proliferative and pre-senescent cells from donors of various ages by single DNA fiber combing of replicated DNA, origin mapping by sequencing short nascent strands and genome-wide profiling of replication timing (TRT). We demonstrate that, progression into RS leads to reduced replication fork rates and activation of dormant origins, which are the hallmarks of replication stress. However, with the exception of a delay in RT of the CREB5 gene in all pre-senescent cells, RT was globally unaffected by replication stress during entry into either oncogene-induced or RS. Consequently, we conclude that RT alterations associated with physiological and accelerated aging, do not result from senescence progression. Our results clarify the interplay between senescence, aging and replication programs and demonstrate that RT is largely resistant to replication stress.
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Affiliation(s)
| | - Hélène Schwerer
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Emilie Besnard
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Romain Desprat
- c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| | | | - Jiao Sima
- a Department of Biological Science , Florida State University , Tallahassee , FL , USA
| | - Paul Bensadoun
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France
| | - Anissa Zouaoui
- c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
| | - David M Gilbert
- a Department of Biological Science , Florida State University , Tallahassee , FL , USA.,d Center for Genomics and Personalized Medicine , Florida State University , Tallahassee , FL , USA
| | - Jean-Marc Lemaitre
- b Laboratory of Genome and Stem Cell Plasticity in Development and Aging , Institute of Regenerative Medicine, U1183, Université de Montpellier , Montpellier Cedex , France.,c Stem cell Core Facility SAFE-iPS INGESTEM , CHU Montpellier, Saint Eloi Hospital , Montpellier Cedex , France
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3
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Aranda-Anzaldo A, Dent MAR. Why Cortical Neurons Cannot Divide, and Why Do They Usually Die in the Attempt? J Neurosci Res 2016; 95:921-929. [PMID: 27402311 DOI: 10.1002/jnr.23765] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/25/2016] [Accepted: 04/25/2016] [Indexed: 12/19/2022]
Abstract
Cortical neurons are prime examples of terminally differentiated, postmitotic cells. However, under experimental or pathological conditions, they can re-enter the cell cycle and replicate DNA but are unable to divide, dying by apoptosis or becoming either polyploid or aneuploid. Any cellular state that depends on the action of genes and their products can be reverted or bypassed by spontaneous or induced mutations, yet there are currently no reports of dividing cortical neurons. Thus, it seems unlikely that the remarkably stable postmitotic condition of cortical neurons depends on specific gene functions. This Review summarizes evidence that the postmitotic state of cortical neurons depends on the high stability of its underlying nuclear structure that results from an entropy-driven process aimed at dissipating the intrinsic structural stress present in chromosomal DNA in such a way that the structural stability of the neuronal nucleus becomes an insurmountable energy barrier for karyokinesis and mitosis. From this perspective, the integral properties of the nuclear higher order structure in neurons provide an explanation not only for why cortical neurons cannot divide but also for why they usually die if they happen to replicate their DNA. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado México, México
| | - Myrna A R Dent
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado México, México
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4
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Aranda-Anzaldo A. The interphase mammalian chromosome as a structural system based on tensegrity. J Theor Biol 2016; 393:51-9. [PMID: 26780650 DOI: 10.1016/j.jtbi.2016.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 12/11/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022]
Abstract
Each mammalian chromosome is constituted by a DNA fiber of macroscopic length that needs to be fitted in a microscopic nucleus. The DNA fiber is subjected at physiological temperature to random thermal bending and looping that must be constrained so as achieve structural stability thus avoiding spontaneous rupturing of the fiber. Standard textbooks assume that chromatin proteins are primarily responsible for the packaging of DNA and so of its protection against spontaneous breakage. Yet the dynamic nature of the interactions between chromatin proteins and DNA is unlikely to provide the necessary long-term structural stability for the chromosomal DNA. On the other hand, longstanding evidence indicates that stable interactions between DNA and constituents of a nuclear compartment commonly known as the nuclear matrix organize the chromosomal DNA as a series of topologically constrained, supercoiled loops during interphase. This results in a primary level of DNA condensation and packaging within the nucleus, as well as in protection against spontaneous DNA breakage, independently of chromatin proteins which nevertheless increase and dynamically modulate the degree of DNA packaging and its role in the regulation of DNA function. Thus current evidence, presented hereunder, supports a model for the organization of the interphase chromosome as resilient system that satisfies the principles of structural tensegrity.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, 50180 Edo. Méx., México.
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5
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Barboro P, Ferrari N, Capaia M, Petretto A, Salvi S, Boccardo S, Balbi C. Expression of nuclear matrix proteins binding matrix attachment regions in prostate cancer. PARP-1: New player in tumor progression. Int J Cancer 2015; 137:1574-86. [DOI: 10.1002/ijc.29531] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/11/2015] [Accepted: 03/17/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Paola Barboro
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
| | - Nicoletta Ferrari
- IRCCs AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Terapie Oncologiche Integrate; Genoa Italy
| | - Matteo Capaia
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
| | - Andrea Petretto
- Laboratorio di Spettrometria di Massa, Core Facility, Istituto Giannina Gaslini; Genoa Italy
| | - Sandra Salvi
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
| | - Simona Boccardo
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
| | - Cecilia Balbi
- IRCCS AOU San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Dipartimento Diagnostica della Patologia e delle Cure ad Alta Complessità Tecnologica; Genoa Italy
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6
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The higher-order structure in the cells nucleus as the structural basis of the post-mitotic state. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:137-45. [DOI: 10.1016/j.pbiomolbio.2014.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/09/2014] [Indexed: 11/19/2022]
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7
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Castillo-Mora RC, Aranda-Anzaldo A. Reorganization of the DNA-nuclear matrix interactions in a 210 kb genomic region centered on c-myc after DNA replication in vivo. J Cell Biochem 2012; 113:2451-63. [PMID: 22396210 DOI: 10.1002/jcb.24123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). DNA loops are operationally classified in structural and facultative. Varied evidence indicates that DNA replication occurs in replication foci organized upon the NM and that structural DNA loops may correspond to the replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration. Using this model we have previously determined that the DNA loops corresponding to a gene-rich genomic region move in a sequential fashion towards the NM during replication and then return to their original configuration in newly quiescent cells, once liver regeneration has been achieved. In the present work we determined the organization into structural DNA loops of a gene-poor region centered on c-myc and tracked-down its movement at the peak of S phase and after the return to cellular quiescence during and after liver regeneration. The results confirmed that looped DNA moves towards the NM during replication but in this case the configuration of the gene-poor region into DNA loops becomes reorganized and after replication only the loop containing c-myc resembles the original in the control G0 hepatocytes. Our results suggest that the local chromatin configuration around potentially active genes constraints the formation of specific structural DNA loops after DNA replication, while in non-coding regions the structural DNA loops are only loosely determined after DNA replication by structural constraints that modulate the DNA-NM interactions.
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Affiliation(s)
- Rebeca C Castillo-Mora
- Facultad de Medicina, Universidad Autónoma del Estado de México, Paseo Tollocan y Jesús Carranza s/n, Toluca, Edo. México, Mexico
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Gwon MR, Cho JH, Kim JR. Mitotic centromere-associated kinase (MCAK/Kif2C) regulates cellular senescence in human primary cells through a p53-dependent pathway. FEBS Lett 2012; 586:4148-56. [PMID: 23098759 DOI: 10.1016/j.febslet.2012.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 09/18/2012] [Accepted: 10/09/2012] [Indexed: 01/21/2023]
Abstract
Mitotic centromere-associated kinase (MCAK/Kif2C) plays a critical role in chromosome movement and segregation with ATP-dependent microtubule depolymerase activity. However, its role in cellular senescence remains unclear. MCAK/Kif2C expression decreased in human primary cells under replicative and premature senescence. MCAK/Kif2C down-regulation in young cells induced premature senescence. MCAK/Kif2C overexpression in old cells partially reversed cell senescence. Senescence phenotypes by MCAK/Kif2C knockdown were observed in p16-knockdown cells, but not in p53-knockdown cells. These results suggest that MCAK/Kif2C plays an important role in the regulation of cellular senescence through a p53-dependent pathway and might contribute to tissue/organism aging and protection of cellular transformation.
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Affiliation(s)
- Mi-Ri Gwon
- Department of Biochemistry and Molecular Biology, Aging-associated Vascular Disease Research Center, College of Medicine, Yeungnam University, Daegu 705-717, Republic of Korea
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Barboro P, Repaci E, D’Arrigo C, Balbi C. The role of nuclear matrix proteins binding to matrix attachment regions (Mars) in prostate cancer cell differentiation. PLoS One 2012; 7:e40617. [PMID: 22808207 PMCID: PMC3394767 DOI: 10.1371/journal.pone.0040617] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 06/11/2012] [Indexed: 11/19/2022] Open
Abstract
In tumor progression definite alterations in nuclear matrix (NM) protein composition as well as in chromatin structure occur. The NM interacts with chromatin via specialized DNA sequences called matrix attachment regions (MARs). In the present study, using a proteomic approach along with a two-dimensional Southwestern assay and confocal laser microscopy, we show that the differentiation of stabilized human prostate carcinoma cells is marked out by modifications both NM protein composition and bond between NM proteins and MARs. Well-differentiated androgen-responsive and slowly growing LNCaP cells are characterized by a less complex pattern and by a major number of proteins binding MAR sequences in comparison to 22Rv1 cells expressing androgen receptor but androgen-independent. Finally, in the poorly differentiated and strongly aggressive androgen-independent PC3 cells the complexity of NM pattern further increases and a minor number of proteins bind the MARs. Furthermore, in this cell line with respect to LNCaP cells, these changes are synchronous with modifications in both the nuclear distribution of the MAR sequences and in the average loop dimensions that significantly increase. Although the expression of many NM proteins changes during dedifferentiation, only a very limited group of MAR-binding proteins seem to play a key role in this process. Variations in the expression of poly (ADP-ribose) polymerase (PARP) and special AT-rich sequence-binding protein-1 (SATB1) along with an increase in the phosphorylation of lamin B represent changes that might trigger passage towards a more aggressive phenotype. These results suggest that elucidating the MAR-binding proteins that are involved in the differentiation of prostate cancer cells could be an important tool to improve our understanding of this carcinogenesis process, and they could also be novel targets for prostate cancer therapy.
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Affiliation(s)
- Paola Barboro
- IRCCS Azienda Ospedaliera Universitaria San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Department of Diagnostic Technologies, Genoa, Italy
| | - Erica Repaci
- IRCCS Azienda Ospedaliera Universitaria San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Department of Diagnostic Technologies, Genoa, Italy
| | - Cristina D’Arrigo
- C.N.R., Istituto per lo Studio delle Macromolecole, ISMAC, Sezione di Genova, Genoa, Italy
| | - Cecilia Balbi
- IRCCS Azienda Ospedaliera Universitaria San Martino IST-Istituto Nazionale per la Ricerca sul Cancro, Department of Diagnostic Technologies, Genoa, Italy
- * E-mail:
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Aranda-Anzaldo A. The post-mitotic state in neurons correlates with a stable nuclear higher-order structure. Commun Integr Biol 2012; 5:134-9. [PMID: 22808316 PMCID: PMC3376047 DOI: 10.4161/cib.18761] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Neurons become terminally differentiated (TD) post-mitotic cells very early during development yet they may remain alive and functional for decades. TD neurons preserve the molecular machinery necessary for DNA synthesis that may be reactivated by different stimuli but they never complete a successful mitosis. The non-reversible nature of the post-mitotic state in neurons suggests a non-genetic basis for it since no set of mutations has been able to revert it. Comparative studies of the nuclear higher-order structure in neurons and cells with proliferating potential suggest that the non-reversible nature of the post-mitotic state in neurons has a structural basis in the stability of the nuclear higher-order structure.
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Affiliation(s)
- Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular; Facultad de Medicina; Universidad Autónoma del Estado de México; Toluca, México
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11
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The organization of a large transcriptional unit (Fyn) into structural DNA loops is cell-type specific and independent of transcription. Gene 2012; 493:1-8. [DOI: 10.1016/j.gene.2011.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 10/21/2011] [Accepted: 11/14/2011] [Indexed: 11/19/2022]
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Alva-Medina J, Maya-Mendoza A, Dent MAR, Aranda-Anzaldo A. Continued stabilization of the nuclear higher-order structure of post-mitotic neurons in vivo. PLoS One 2011; 6:e21360. [PMID: 21731716 PMCID: PMC3121788 DOI: 10.1371/journal.pone.0021360] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 05/26/2011] [Indexed: 11/19/2022] Open
Abstract
Background Cellular terminal differentiation (TD) correlates with a permanent exit from the cell cycle and so TD cells become stably post-mitotic. However, TD cells express the molecular machinery necessary for cell proliferation that can be reactivated by experimental manipulation, yet it has not been reported the stable proliferation of any type of reactivated TD cells. Neurons become post-mitotic after leaving the ventricular zone. When neurons are forced to reenter the cell cycle they invariably undergo cell death. Wider evidence indicates that the post-mitotic state cannot solely depend on gene products acting in trans, otherwise mutations in the corresponding genes may lead to reentry and completion of the cell cycle in TD cells, but this has not been observed. In the interphase, nuclear DNA of metazoan cells is organized in supercoiled loops anchored to a nuclear nuclear matrix (NM). The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS). We have previously compared the NHOS of aged rat hepatocytes with that of early post-mitotic rat neurons and our results indicated that a very stable NHOS is a common feature of both senescent and post-mitotic cells in vivo. Principal Findings In the present work we compared the NHOS in rat neurons from different post-natal ages. Our results show that the trend towards further stabilization of the NHOS in neurons continues throughout post-natal life. This phenomenon occurs in absence of overt changes in the post-mitotic state and transcriptional activity of neurons, suggesting that it is independent of functional constraints. Conclusions Apparently the continued stabilization of the NHOS as a function of time is basically determined by thermodynamic and structural constraints. We discuss how the resulting highly stable NHOS of neurons may be the structural, non-genetic basis of their permanent and irreversible post-mitotic state.
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Affiliation(s)
- Janeth Alva-Medina
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Apolinar Maya-Mendoza
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Myrna A. R. Dent
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
| | - Armando Aranda-Anzaldo
- Laboratorio de Biología Molecular y Neurociencias, Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, Estado de México, México
- * E-mail:
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13
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Rivera-Mulia JC, Hernández-Muñoz R, Martínez F, Aranda-Anzaldo A. DNA moves sequentially towards the nuclear matrix during DNA replication in vivo. BMC Cell Biol 2011; 12:3. [PMID: 21244708 PMCID: PMC3037911 DOI: 10.1186/1471-2121-12-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 01/19/2011] [Indexed: 11/21/2022] Open
Abstract
Background In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). There is varied evidence indicating that DNA replication occurs in replication factories organized upon the NM and that DNA loops may correspond to the actual replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but they synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration in vivo. We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops. Results In the present work we tracked down the movement relative to the NM of DNA sequences located at different points within such five structural DNA loops during the S phase and after the return to cellular quiescence during liver regeneration. Our results indicate that looped DNA moves sequentially towards the NM during replication and then returns to its original position in newly quiescent cells, once the liver regeneration has been achieved. Conclusions Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated. These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, CP 50000 Toluca, Edo Méx, México
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Alva-Medina J, Dent MAR, Aranda-Anzaldo A. Aged and post-mitotic cells share a very stable higher-order structure in the cell nucleus in vivo. Biogerontology 2010; 11:703-16. [PMID: 20512413 DOI: 10.1007/s10522-010-9285-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 05/13/2010] [Indexed: 10/19/2022]
Abstract
In the mammalian liver the quiescent primary hepatocytes preserve a proliferating potential in vivo, yet natural aging correlates with loss of proliferating potential and progression towards terminal differentiation of the hepatocytes. Thus aged, terminally-differentiated hepatocytes may survive in a de facto post-mitotic state, similarly to early post-mitotic cells, like neurons, suggesting that there might be a common factor linking both cellular states. In the interphase of metazoan cells the nuclear DNA is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS). Natural aging of the rat liver correlates with a progressive strengthening of the NM framework and the stabilization of the DNA-NM interactions in the hepatocytes indicating that the NHOS becomes highly stable with age. We compared the NHOS of post-mitotic rat neurons with that of aged rat hepatocytes. Our results indicate that a very stable NHOS is a common feature of both aged and post-mitotic cells in vivo.
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Affiliation(s)
- Janeth Alva-Medina
- Universidad Autónoma del Estado de México, Toluca, Estado de Mexico, Mexico
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Rivera-Mulia JC, Aranda-Anzaldo A. Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach. DNA Res 2010; 17:23-35. [PMID: 20047947 PMCID: PMC2818189 DOI: 10.1093/dnares/dsp027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Nuclear DNA of metazoans is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). DNA is anchored to the NM by non-coding sequences known as matrix attachment regions (MARs). There are no consensus sequences for identification of MARs and not all potential MARs are actually bound to the NM constituting loop attachment regions (LARs). Fundamental processes of nuclear physiology occur at macromolecular complexes organized on the NM; thus, the topological organization of DNA loops must be important. Here, we describe a general method for determining the structural DNA loop organization in any large genomic region with a known sequence. The method exploits the topological properties of loop DNA attached to the NM and elementary topological principles such as that points in a deformable string (DNA) can be positionally mapped relative to a position-reference invariant (NM), and from such mapping, the configuration of the string in third dimension can be deduced. Therefore, it is possible to determine the specific DNA loop configuration without previous characterization of the LARs involved. We determined in hepatocytes and B-lymphocytes of the rat the DNA loop organization of a genomic region that contains four members of the albumin gene family.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, Toluca, Edo. Méx., México
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