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Sarić A, Rajić J, Tolić A, Dučić T, Vidaković M. Synchrotron-based FTIR microspectroscopy reveals DNA methylation profile in DNA-HALO structure. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 302:123090. [PMID: 37413921 DOI: 10.1016/j.saa.2023.123090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy is a rapid, non-destructive and label-free technique for identifying subtle changes in all bio-macromolecules, and has been used as a method of choice for studying DNA conformation, secondary DNA structure transition and DNA damage. In addition, the specific level of chromatin complexity is introduced via epigenetic modifications forcing the technological upgrade in the analysis of such an intricacy. As the most studied epigenetic mechanism, DNA methylation is a major regulator of transcriptional activity, involved in the suppression of a broad spectrum of genes and its deregulation is involved in all non-communicable diseases. The present study was designed to explore the use of synchrotron-based FTIR analysis to monitor the subtle changes in molecule bases regarding the DNA methylation status of cytosine in the whole genome. In order to reveal the conformation-related best sample for FTIR-based DNA methylation analysis in situ, we used methodology for nuclear HALO preparations and slightly modified it to isolated DNA in HALO formations. Nuclear DNA-HALOs represent samples with preserved higher-order chromatin structure liberated of any protein residues that are closer to native DNA conformation than genomic DNA (gDNA) isolated by the standard batch procedure. Using FTIR spectroscopy we analyzed the DNA methylation profile of isolated gDNA and compared it with the DNA-HALOs. This study demonstrated the potential of FTIR microspectroscopy to detect DNA methylation marks in analyzed DNA-HALO specimens more precisely in comparison with classical DNA extraction procedures that yield unstructured whole genomic DNA. In addition, we used different cell types to assess their global DNA methylation profile, as well as defined specific infrared peaks that can be used for screening DNA methylation.
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Affiliation(s)
- Ana Sarić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Jovana Rajić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Anja Tolić
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
| | - Tanja Dučić
- ALBA CELLS Synchrotron, Carrer de la Llum 2-26, Cerdanyola del Valles, 08290 Barcelona, Spain.
| | - Melita Vidaković
- Department of Molecular Biology, Institute for Biological Research "Siniša Stanković" - National Institute of the Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, Serbia.
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Dynamics of nuclear matrix attachment regions during 5 th instar posterior silk gland development in Bombyx mori. BMC Genomics 2022; 23:247. [PMID: 35361117 PMCID: PMC8973518 DOI: 10.1186/s12864-022-08446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/06/2022] [Indexed: 12/02/2022] Open
Abstract
Background Chromatin architecture is critical for gene expression during development. Matrix attachment regions (MARs) control and regulate chromatin dynamics. The position of MARs in the genome determines the expression of genes in the organism. In this study, we set out to elucidate how MARs temporally regulate the expression of the fibroin heavy chain (FIBH) gene during development. We addressed this by identifying MARs and studying their distribution and differentiation, in the posterior silk glands of Bombyx mori during 5th instar development. Results Of the MARs identified on three different days, 7.15% MARs were common to all 3 days, whereas, 1.41, 19.27 and 52.47% MARs were unique to day 1, day 5, and day 7, respectively highlighting the dynamic nature of the matrix associated DNA. The average chromatin loop length based on the chromosome wise distribution of MARs and the distances between these MAR regions decreased from day 1 (253.91 kb) to day 5 (73.54 kb) to day 7 (39.19 kb). Further significant changes in the MARs in the vicinity of the FIBH gene were found during different days of 5th instar development which implied their role in the regulation and expression of the FIBH gene. Conclusions The presence of MARs in the flanking regions of genes found to exhibit differential expression during 5th instar development indicates their possible role in the regulation of their expression. This reiterates the importance of MARs in the genomic functioning as regulators of the molecular mechanisms in the nucleus. This is the first study that takes into account the tissue specific genome-wide MAR association and the potential role of these MARs in developmentally regulated gene expression. The current study lays a foundation to understand the genome wide regulation of chromatin during development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08446-3.
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Choksi A, Parulekar A, Pant R, Shah VK, Nimma R, Firmal P, Singh S, Kundu GC, Shukla S, Chattopadhyay S. Tumor suppressor SMAR1 regulates PKM alternative splicing by HDAC6-mediated deacetylation of PTBP1. Cancer Metab 2021; 9:16. [PMID: 33863392 PMCID: PMC8052847 DOI: 10.1186/s40170-021-00252-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/30/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Highly proliferating cancer cells exhibit the Warburg effect by regulation of PKM alternative splicing and promoting the expression of PKM2. Majority of the alternative splicing events are known to occur in the nuclear matrix where various MARBPs actively participate in the alternative splicing events. SMAR1, being a MARBP and an important tumor suppressor, is known to regulate the splicing of various cancer-associated genes. This study focuses on the regulation of PKM alternative splicing and inhibition of the Warburg effect by SMAR1. METHODS Immunohistochemistry was performed in breast cancer patient samples to establish the correlation between SMAR1 and PKM isoform expression. Further, expression of PKM isoforms upon modulation in SMAR1 expression in breast cancer cell lines was quantified by qRT-PCR and western blot. The acetylation status of PTBP1 was estimated by immunoprecipitation along with its enrichment on PKM pre-mRNA by CLIP in SMAR1 knockdown conditions. The role of SMAR1 in tumor metabolism and tumorigenesis was explored by in vitro enzymatic assays and functional assays upon SMAR1 knockdown. Besides, in vivo tumor formation by injecting adeno-SMAR1-transduced MDA-MB-231 cells in NOD/SCID mice was performed. RESULTS The expression profile of SMAR1 and PKM isoforms in breast cancer patients revealed that SMAR1 has an inverse correlation with PKM2 and a positive correlation with PKM1. Further quantitative PKM isoform expression upon modulation in SMAR1 expression also reflects that SMAR1 promotes the expression of PKM1 over tumorigenic isoform PKM2. SMAR1 deacetylates PTBP1 via recruitment of HDAC6 resulting in reduced enrichment of PTBP1 on PKM pre-mRNA. SMAR1 inhibits the Warburg effect, tumorigenic potential of cancer cells, and in vivo tumor generation in a PKM2-dependent manner. CONCLUSIONS SMAR1 regulates PKM alternative splicing by causing HDAC6-dependent deacetylation of PTBP1, resulting in reduced enrichment of PTBP1 on PKM pre-mRNA. Additionally, SMAR1 suppresses glucose utilization and lactate production via repression of PKM2 expression. This suggests that tumor suppressor SMAR1 inhibits tumor cell metabolism and tumorigenic properties of cancer cells via regulation of PKM alternative splicing.
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Affiliation(s)
| | | | - Richa Pant
- National Centre for Cell Science, Pune, 411007, India
| | | | | | | | - Smriti Singh
- Indian Institute of Science Education and Research, Bhopal, 462066, India
| | - Gopal C Kundu
- National Centre for Cell Science, Pune, 411007, India.,Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, 751024, India
| | - Sanjeev Shukla
- Indian Institute of Science Education and Research, Bhopal, 462066, India
| | - Samit Chattopadhyay
- National Centre for Cell Science, Pune, 411007, India. .,Birla Institute of Technology and Science, Pilani - K K Birla Goa Campus, Goa, 403726, India.
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4
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Yu X, Buck MJ. Pioneer factors and their in vitro identification methods. Mol Genet Genomics 2020; 295:825-835. [PMID: 32296927 DOI: 10.1007/s00438-020-01675-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/02/2020] [Indexed: 11/27/2022]
Abstract
Pioneer transcription factors are a special group of transcription factors that can interact with nucleosomal DNA and initiate regulatory events. Their binding to regulatory regions is the first event in gene activation and can occur in silent or heterochromatin regions. Several research groups have endeavored to define pioneer factors and study their binding characteristics using various techniques. In this review, we describe the in vitro methods used to define and characterize pioneer factors, paying particular attention to differences in methodologies and how these differences can affect results.
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Affiliation(s)
- Xinyang Yu
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, 519000, Guangdong, P.R. China.
| | - Michael J Buck
- Department of Biochemistry, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
- Department of Biomedical Informatics, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
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Fritz AJ, Sehgal N, Pliss A, Xu J, Berezney R. Chromosome territories and the global regulation of the genome. Genes Chromosomes Cancer 2019; 58:407-426. [PMID: 30664301 DOI: 10.1002/gcc.22732] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 12/29/2022] Open
Abstract
Spatial positioning is a fundamental principle governing nuclear processes. Chromatin is organized as a hierarchy from nucleosomes to Mbp chromatin domains (CD) or topologically associating domains (TADs) to higher level compartments culminating in chromosome territories (CT). Microscopic and sequencing techniques have substantiated chromatin organization as a critical factor regulating gene expression. For example, enhancers loop back to interact with their target genes almost exclusively within TADs, distally located coregulated genes reposition into common transcription factories upon activation, and Mbp CDs exhibit dynamic motion and configurational changes in vivo. A longstanding question in the nucleus field is whether an interactive nuclear matrix provides a direct link between structure and function. The findings of nonrandom radial positioning of CT within the nucleus suggest the possibility of preferential interaction patterns among populations of CT. Sequential labeling up to 10 CT followed by application of computer imaging and geometric graph mining algorithms revealed cell-type specific interchromosomal networks (ICN) of CT that are altered during the cell cycle, differentiation, and cancer progression. It is proposed that the ICN correlate with the global level of genome regulation. These approaches also demonstrated that the large scale 3-D topology of CT is specific for each CT. The cell-type specific proximity of certain chromosomal regions in normal cells may explain the propensity of distinct translocations in cancer subtypes. Understanding how genes are dysregulated upon disruption of the normal "wiring" of the nucleus by translocations, deletions, and amplifications that are hallmarks of cancer, should enable more targeted therapeutic strategies.
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Affiliation(s)
- Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, The University of Vermont Larner College of Medicine, Burlington, Vermont
| | - Nitasha Sehgal
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics and the Department of Chemistry, University at Buffalo, Buffalo, New York
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, Buffalo, New York
| | - Ronald Berezney
- Department of Biological Sciences, University at Buffalo, Buffalo, New York
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Tan SN, Sim SP, Khoo ASB. Matrix association region/scaffold attachment region (MAR/SAR) sequence: its vital role in mediating chromosome breakages in nasopharyngeal epithelial cells via oxidative stress-induced apoptosis. BMC Mol Biol 2018; 19:15. [PMID: 30514321 PMCID: PMC6278157 DOI: 10.1186/s12867-018-0116-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 11/26/2018] [Indexed: 12/15/2022] Open
Abstract
Background Oxidative stress is known to be involved in most of the aetiological factors of nasopharyngeal carcinoma (NPC). Cells that are under oxidative stress may undergo apoptosis. We have previously demonstrated that oxidative stress-induced apoptosis could be a potential mechanism mediating chromosome breakages in nasopharyngeal epithelial cells. Additionally, caspase-activated DNase (CAD) may be the vital player in mediating the chromosomal breakages during oxidative stress-induced apoptosis. Chromosomal breakage occurs during apoptosis and chromosome rearrangement. Chromosomal breakages tend to cluster in certain regions, such as matrix association region/scaffold attachment region (MAR/SAR). We hypothesised that oxidative stress-induced apoptosis may result in chromosome breaks preferentially at the MAR/SAR sites. The AF9 gene at 9p22 was targeted in this study because 9p22 is a deletion site commonly found in NPC. Results By using MAR/SAR recognition signature (MRS), potential MAR/SAR sites were predicted in the AF9 gene. The predicted MAR/SAR sites precisely match to the experimentally determined MAR/SARs. Hydrogen peroxide (H2O2) was used to induce apoptosis in normal nasopharyngeal epithelial cells (NP69) and NPC cells (HK1). Nested inverse polymerase chain reaction was employed to identify the AF9 gene cleavages. In the SAR region, the gene cleavage frequency of H2O2-treated cells was significantly higher than that of the non-treated cells. A few chromosomal breakages were detected within the AF9 region which was previously found to be involved in the mixed lineage leukaemia (MLL)-AF9 translocation in an acute lymphoblastic leukaemia patient. As for the non-SAR region, no significant difference in the gene cleavage frequency was found between the untreated control and H2O2-treated cells. Furthermore, H2O2-induced cleavages within the SAR region were reduced by caspase-3 inhibitor, which indirectly inhibits CAD. Conclusions These results reaffirm our previous findings that oxidative stress-induced apoptosis could be one of the potential mechanisms underlying chromosome breakages in nasopharyngeal epithelial cells. MAR/SAR may play a vital role in defining the location of chromosomal breakages mediated by oxidative stress-induced apoptosis, where CAD is the major nuclease. Electronic supplementary material The online version of this article (10.1186/s12867-018-0116-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sang-Nee Tan
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Sai-Peng Sim
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia.
| | - Alan S B Khoo
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Kuala Lumpur, Malaysia
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Papadopoulos N, Lennartsson J, Heldin CH. PDGFRβ translocates to the nucleus and regulates chromatin remodeling via TATA element-modifying factor 1. J Cell Biol 2018; 217:1701-1717. [PMID: 29545370 PMCID: PMC5940298 DOI: 10.1083/jcb.201706118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 01/05/2018] [Accepted: 02/01/2018] [Indexed: 12/24/2022] Open
Abstract
PDGFRβ translocates to the nucleus in a ligand-dependent manner tethered by TATA element–modifying factor 1 (TMF-1). Papadopoulos et al. show that PDGFRβ interacts with TMF-1 and Fer kinase in the nucleus, regulating chromatin remodeling by the SWI–SNF complex and controlling proliferation via a p21-dependent mechanism. Translocation of full-length or fragments of receptors to the nucleus has been reported for several tyrosine kinase receptors. In this paper, we show that a fraction of full-length cell surface platelet-derived growth factor (PDGF) receptor β (PDGFRβ) accumulates in the nucleus at the chromatin and the nuclear matrix after ligand stimulation. Nuclear translocation of PDGFRβ was dependent on PDGF-BB–induced receptor dimerization, clathrin-mediated endocytosis, β-importin, and intact Golgi, occurring in both normal and cancer cells. In the nucleus, PDGFRβ formed ligand-inducible complexes with the tyrosine kinase Fer and its substrate, TATA element–modifying factor 1 (TMF-1). PDGF-BB stimulation decreased TMF-1 binding to the transcriptional regulator Brahma-related gene 1 (Brg-1) and released Brg-1 from the SWI–SNF chromatin remodeling complex. Moreover, knockdown of TMF-1 by small interfering RNA decreased nuclear translocation of PDGFRβ and caused significant up-regulation of the Brg-1/p53-regulated cell cycle inhibitor CDKN1A (encoding p21) without affecting PDGFRβ-inducible immediate-early genes. In conclusion, nuclear interactions of PDGFRβ control proliferation by chromatin remodeling and regulation of p21 levels.
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Affiliation(s)
- Natalia Papadopoulos
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Ludwig Institute for Cancer Research, Uppsala University, Uppsala, Sweden
| | - Johan Lennartsson
- Science for Life Laboratory, Ludwig Institute for Cancer Research, Uppsala University, Uppsala, Sweden.,Department of Pharmaceutical Biomedicine, Uppsala University, Uppsala, Sweden
| | - Carl-Henrik Heldin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden .,Science for Life Laboratory, Ludwig Institute for Cancer Research, Uppsala University, Uppsala, Sweden
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Charó NL, Rodríguez Ceschan MI, Galigniana NM, Toneatto J, Piwien-Pilipuk G. Organization of nuclear architecture during adipocyte differentiation. Nucleus 2017; 7:249-69. [PMID: 27416359 DOI: 10.1080/19491034.2016.1197442] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Obesity is a serious health problem worldwide since it is a major risk factor for chronic diseases such as type II diabetes. Obesity is the result of hyperplasia (associated with increased adipogenesis) and hypertrophy (associated with decreased adipogenesis) of the adipose tissue. Therefore, understanding the molecular mechanisms underlying the process of adipocyte differentiation is relevant to delineate new therapeutic strategies for treatment of obesity. As in all differentiation processes, temporal patterns of transcription are exquisitely controlled, allowing the acquisition and maintenance of the adipocyte phenotype. The genome is spatially organized; therefore decoding local features of the chromatin language alone does not suffice to understand how cell type-specific gene expression patterns are generated. Elucidating how nuclear architecture is built during the process of adipogenesis is thus an indispensable step to gain insight in how gene expression is regulated to achieve the adipocyte phenotype. Here we will summarize the recent advances in our understanding of the organization of nuclear architecture as progenitor cells differentiate in adipocytes, and the questions that still remained to be answered.
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Affiliation(s)
- Nancy L Charó
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
| | - María I Rodríguez Ceschan
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
| | - Natalia M Galigniana
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
| | - Judith Toneatto
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
| | - Graciela Piwien-Pilipuk
- a Laboratory of Nuclear Architecture, Instituto de Biología y Medicina Experimental (IByME) - CONICET , Buenos Aires , Argentina
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Pochukalina GN, Ilicheva NV, Podgornaya OI, Voronin AP. Nucleolus-like body of mouse oocytes contains lamin A and B and TRF2 but not actin and topo II. Mol Cytogenet 2016; 9:50. [PMID: 27347007 PMCID: PMC4921027 DOI: 10.1186/s13039-016-0259-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 06/18/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND During the final stages of oocyte development, all chromosomes join in a limited nuclear volume for the final formation of a single complex chromatin structure - the karyosphere. In the majority of mammalian species, the chromosomes surround a round protein/fibrillar body known as the central body, or nucleolus-like body (NLB). Nothing seems to unite the inner portion of the karyosphere with the nucleolus except position at its remnants. Nevertheless, in this study we will use term NLB as the conventional one for karyosphere with the central body. At the morphological level, NLBs consist of tightly-packed fibres of 6-10 nm. The biochemical structure of this dense, compact NLB fibre centre remains uncertain. RESULTS The aim of this study was to determine which proteins represent the NLB components at final stages of karyosphere formation in mouse oogenesis. To determine this, three antibodies (ABs) have been examined against different actin epitopes. Examination of both ABs against the actin N-end provided similar results: spots inside the nucleus. Double staining with AB against SC35 and actin revealed the colocalization of these proteins in IGCs (interchromatin granule clusters/nuclear speckles/SC35 domains). In contrast, examination of polyclonal AB against peptide at the C-end reveals a different result: actin is localized exclusively in connection with the chromatin. Surprisingly, no forms of actin or topoisomerase II are present as components of the NLB. It was discovered that: (1) lamin B is an NLB component from the beginning of NLB formation, and a major portion of it resides in the NLB at the end of oocyte development; (2) lamin A undergoes rapid movement into the NLB, and a majority of it remains in the NLB; (3) the telomere-binding protein TRF2 resides in the IGCs/nuclear speckles until the end of oocyte development, when significant part of it transfers to the NLB. CONCLUSIONS NLBs do not contain actin or topo II. Lamin B is involved from the beginning of NLB formation. Both Lamin A and TRF2 exhibit rapid movement to the NLB at the end of oogenesis. This dynamic distribution of proteins may reflect the NLB's role in future chromatin organization post-fertilisation.
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Affiliation(s)
| | - Nadya V. Ilicheva
- />Institute of Cytology, Russian Academy of Sciences, St Petersburg, 194064 Russia
| | - Olga I. Podgornaya
- />Institute of Cytology, Russian Academy of Sciences, St Petersburg, 194064 Russia
- />Saint Petersburg State University, St Petersburg, 199034 Russia
- />Far Eastern Federal University, Vladivostok, 690950 Russia
| | - Alexey P. Voronin
- />Institute of Cytology, Russian Academy of Sciences, St Petersburg, 194064 Russia
- />Saint Petersburg State University, St Petersburg, 199034 Russia
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Tan SN, Sim SP, Khoo ASB. Potential role of oxidative stress-induced apoptosis in mediating chromosomal rearrangements in nasopharyngeal carcinoma. Cell Biosci 2016; 6:35. [PMID: 27231526 PMCID: PMC4880972 DOI: 10.1186/s13578-016-0103-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 05/10/2016] [Indexed: 12/27/2022] Open
Abstract
Background Genetic aberrations have been identified in nasopharyngeal carcinoma (NPC), however, the underlying mechanism remains elusive. There are increasing evidences that the apoptotic nuclease caspase-activated deoxyribonuclease (CAD) is one of the players leading to translocation in leukemia. Oxidative stress, which has been strongly implicated in carcinogenesis, is a potent apoptotic inducer. Most of the NPC etiological factors are known to induce oxidative stress. Although apoptosis is a cell death process, cells possess the potential to survive apoptosis upon DNA repair. Eventually, the surviving cells may carry rearranged chromosomes. We hypothesized that oxidative stress-induced apoptosis may cause chromosomal breaks mediated by CAD. Upon erroneous DNA repair, cells that survive apoptosis may harbor chromosomal rearrangements contributing to NPC pathogenesis. This study focused on the AF9 gene at 9p22, a common deletion region in NPC. We aimed to propose a possible model for molecular mechanism underlying the chromosomal rearrangements in NPC. Results In the present study, we showed that hydrogen peroxide (H2O2) induced apoptosis in NPC (HK1) and normal nasopharyngeal epithelial (NP69) cells, as evaluated by flow cytometric analyses. Activity of caspases 3/7 was detected in H2O2-treated cells. This activity was inhibited by caspase inhibitor (CI). By nested inverse polymerase chain reaction (IPCR), we demonstrated that oxidative stress-induced apoptosis in HK1 and NP69 cells resulted in cleavages within the breakpoint cluster region (BCR) of the AF9 gene. The gene cleavage frequency detected in the H2O2-treated cells was found to be significantly higher than untreated control. We further found that treatment with CI, which indirectly inhibits CAD, significantly reduced the chromosomal breaks in H2O2-cotreated cells. Intriguingly, a few breakpoints were mapped within the AF9 region that was previously reported to translocate with the mixed lineage leukemia (MLL) gene in acute lymphoblastic leukemia (ALL) patient. Conclusions In conclusion, our findings suggested that oxidative stress-induced apoptosis could be one of the mechanisms underlying the chromosomal rearrangements in NPC. CAD may play an important role in chromosomal cleavages mediated by oxidative stress-induced apoptosis. A potential model for oxidative stress-induced apoptosis mediating chromosomal rearrangements in NPC is proposed.
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Affiliation(s)
- Sang-Nee Tan
- Faculty of Medicine and Health Sciences, Department of Paraclinical Sciences, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Sai-Peng Sim
- Faculty of Medicine and Health Sciences, Department of Paraclinical Sciences, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Alan S B Khoo
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Kuala Lumpur, Malaysia
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Nuclear matrix protein SMAR1 control regulatory T-cell fate during inflammatory bowel disease (IBD). Mucosal Immunol 2015; 8:1184-200. [PMID: 25993445 PMCID: PMC4762908 DOI: 10.1038/mi.2015.42] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/31/2015] [Indexed: 02/04/2023]
Abstract
Regulatory T (Treg) cells are essential for self-tolerance and immune homeostasis. Transcription factor Foxp3, a positive regulator of Treg cell differentiation, has been studied to some extent. Signal transducer and activator of transcription factor 3 (STAT3) is known to negatively regulate Foxp3. It is not clear how STAT3 is regulated during Treg differentiation. We show that SMAR1, a known transcription factor and tumor suppressor, is directly involved in maintaining Treg cell fate decision. T-cell-specific conditional knockdown of SMAR1 exhibits increased susceptibility towards inflammatory disorders, such as colitis. The suppressive function of Treg cells is compromised in the absence of SMAR1 leading to increased T helper type 17 (Th17) differentiation and inflammation. Compared with wild-type, the SMAR1(-/-) Treg cells showed increased susceptibility of inflammatory bowel disease in Rag1(-/ -) mice, indicating the role of SMAR1 in compromising Treg cell differentiation resulting in severe colitis. We show that SMAR1 negatively regulate STAT3 expression favoring Foxp3 expression and Treg cell differentiation. SMAR1 binds to the MAR element of STAT3 promoter, present adjacent to interleukin-6 response elements. Thus Foxp3, a major driver of Treg cell differentiation, is regulated by SMAR1 via STAT3 and a fine-tune balance between Treg and Th17 phenotype is maintained.
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Pliss A, Fritz AJ, Stojkovic B, Ding H, Mukherjee L, Bhattacharya S, Xu J, Berezney R. Non-Random Patterns in the Distribution of NOR-Bearing Chromosome Territories in Human Fibroblasts: A Network Model of Interactions. J Cell Physiol 2015; 230:427-39. [PMID: 25077974 DOI: 10.1002/jcp.24726] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 07/25/2014] [Indexed: 12/24/2022]
Abstract
We present a 3-D mapping in WI38 human diploid fibroblast cells of chromosome territories (CT) 13,14,15,21, and 22, which contain the nucleolar organizing regions (NOR) and participate in the formation of nucleoli. The nuclear radial positioning of NOR-CT correlated with the size of chromosomes with smaller CT more interior. A high frequency of pairwise associations between NOR-CT ranging from 52% (CT13-21) to 82% (CT15-21) was detected as well as a triplet arrangement of CT15-21-22 (72%). The associations of homologous CT were significantly lower (24-36%). Moreover, singular contacts between CT13-14 or CT13-22 were found in the majority of cells, while CT13-15 or CT13-21 predominantly exhibited multiple interactions. In cells with multiple nucleoli, one of the nucleoli (termed "dominant") always associated with a higher number of CT. Moreover, certain CT pairs more frequently contributed to the same nucleolus than to others. This nonrandom pattern suggests that a large number of the NOR-chromosomes are poised in close proximity during the postmitotic nucleolar recovery and through their NORs may contribute to the formation of the same nucleolus. A global data mining program termed the chromatic median determined the most probable interchromosomal arrangement of the entire NOR-CT population. This interactive network model was significantly above randomized simulation and was composed of 13 connections among the NOR-CT. We conclude that the NOR-CT form a global interactive network in the cell nucleus that may be a fundamental feature for the regulation of nucleolar and other genomic functions.
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Affiliation(s)
- Artem Pliss
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York
| | - Andrew J Fritz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York
| | - Branislav Stojkovic
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, New York
| | - Hu Ding
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, New York
| | - Lopamudra Mukherjee
- Department of Computer Sciences, University at Wisconsin Whitewater, Whitewater, Wisconsin
| | - Sambit Bhattacharya
- Department of Computer Sciences, Fayetteville State University, Fayetteville, North Carolina
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, New York
| | - Ronald Berezney
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York
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13
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Nuclear matrix-associated protein SMAR1 regulates alternative splicing via HDAC6-mediated deacetylation of Sam68. Proc Natl Acad Sci U S A 2015; 112:E3374-83. [PMID: 26080397 DOI: 10.1073/pnas.1418603112] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Pre-mRNA splicing is a complex regulatory nexus modulated by various trans-factors and their posttranslational modifications to create a dynamic transcriptome through alternative splicing. Signal-induced phosphorylation and dephosphorylation of trans-factors are known to regulate alternative splicing. However, the role of other posttranslational modifications, such as deacetylation/acetylation, methylation, and ubiquitination, that could modulate alternative splicing in either a signal-dependent or -independent manner remain enigmatic. Here, we demonstrate that Scaffold/matrix-associated region-binding protein 1 (SMAR1) negatively regulates alternative splicing through histone deacetylase 6 (HDAC6)-mediated deacetylation of RNA-binding protein Sam68 (Src-associated substrate during mitosis of 68 kDa). SMAR1 is enriched in nuclear splicing speckles and associates with the snRNAs that are involved in splice site recognition. ERK-MAPK pathway that regulates alternative splicing facilitates ERK-1/2-mediated phosphorylation of SMAR1 at threonines 345 and 360 and localizes SMAR1 to the cytoplasm, preventing its interaction with Sam68. We showed that endogenously, SMAR1 through HDAC6 maintains Sam68 in a deacetylated state. However, knockdown or ERK-mediated phosphorylation of SMAR1 releases the inhibitory SMAR1-HDAC6-Sam68 complex, facilitating Sam68 acetylation and alternative splicing. Furthermore, loss of heterozygosity at the Chr.16q24.3 locus in breast cancer cells, wherein the human homolog of SMAR1 (BANP) has been mapped, enhances Sam68 acetylation and CD44 variant exon inclusion. In addition, tail-vein injections in mice with human breast cancer MCF-7 cells depleted for SMAR1 showed increased CD44 variant exon inclusion and concomitant metastatic propensity, confirming the functional role of SMAR1 in regulation of alternative splicing. Thus, our results reveal the complex molecular mechanism underlying SMAR1-mediated signal-dependent and -independent regulation of alternative splicing via Sam68 deacetylation.
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14
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Yang S, Quaresma AJC, Nickerson JA, Green KM, Shaffer SA, Imbalzano AN, Martin-Buley LA, Lian JB, Stein JL, van Wijnen AJ, Stein GS. Subnuclear domain proteins in cancer cells support the functions of RUNX2 in the DNA damage response. J Cell Sci 2015; 128:728-40. [PMID: 25609707 DOI: 10.1242/jcs.160051] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cancer cells exhibit modifications in nuclear architecture and transcriptional control. Tumor growth and metastasis are supported by RUNX family transcriptional scaffolding proteins, which mediate the assembly of nuclear-matrix-associated gene-regulatory hubs. We used proteomic analysis to identify RUNX2-dependent protein-protein interactions associated with the nuclear matrix in bone, breast and prostate tumor cell types and found that RUNX2 interacts with three distinct proteins that respond to DNA damage - RUVBL2, INTS3 and BAZ1B. Subnuclear foci containing these proteins change in intensity or number following UV irradiation. Furthermore, RUNX2, INTS3 and BAZ1B form UV-responsive complexes with the serine-139-phosphorylated isoform of H2AX (γH2AX). UV irradiation increases the interaction of BAZ1B with γH2AX and decreases histone H3 lysine 9 acetylation levels, which mark accessible chromatin. RUNX2 depletion prevents the BAZ1B-γH2AX interaction and attenuates loss of H3K9 and H3K56 acetylation. Our data are consistent with a model in which RUNX2 forms functional complexes with BAZ1B, RUVBL2 and INTS3 to mount an integrated response to DNA damage. This proposed cytoprotective function for RUNX2 in cancer cells might clarify its expression in chemotherapy-resistant and/or metastatic tumors.
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Affiliation(s)
- Seungchan Yang
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Alexandre J C Quaresma
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA Institute of Biomedicine, Department of Biochemistry and Developmental Biology, FI-00014 University of Helsinki, Finland
| | - Jeffrey A Nickerson
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Karin M Green
- Department of Biochemistry and Molecular Pharmacology and Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Scott A Shaffer
- Department of Biochemistry and Molecular Pharmacology and Proteomics and Mass Spectrometry Facility, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Anthony N Imbalzano
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Lori A Martin-Buley
- Department of Biochemistry & Vermont Cancer Center, University of Vermont Medical School, Burlington, VT 05405, USA
| | - Jane B Lian
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA Department of Biochemistry & Vermont Cancer Center, University of Vermont Medical School, Burlington, VT 05405, USA
| | - Janet L Stein
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA Department of Biochemistry & Vermont Cancer Center, University of Vermont Medical School, Burlington, VT 05405, USA
| | - Andre J van Wijnen
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA Departments of Orthopedic Surgery & Biochemistry and Molecular Biology, Mayo Clinic, 200 First Street S.W., MSB 3-69, Rochester, MN 55905, USA
| | - Gary S Stein
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA Department of Biochemistry & Vermont Cancer Center, University of Vermont Medical School, Burlington, VT 05405, USA
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15
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Tai PWL, Zaidi SK, Wu H, Grandy RA, Montecino MM, van Wijnen AJ, Lian JB, Stein GS, Stein JL. The dynamic architectural and epigenetic nuclear landscape: developing the genomic almanac of biology and disease. J Cell Physiol 2014; 229:711-27. [PMID: 24242872 PMCID: PMC3996806 DOI: 10.1002/jcp.24508] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/11/2013] [Indexed: 12/31/2022]
Abstract
Compaction of the eukaryotic genome into the confined space of the cell nucleus must occur faithfully throughout each cell cycle to retain gene expression fidelity. For decades, experimental limitations to study the structural organization of the interphase nucleus restricted our understanding of its contributions towards gene regulation and disease. However, within the past few years, our capability to visualize chromosomes in vivo with sophisticated fluorescence microscopy, and to characterize chromosomal regulatory environments via massively parallel sequencing methodologies have drastically changed how we currently understand epigenetic gene control within the context of three-dimensional nuclear structure. The rapid rate at which information on nuclear structure is unfolding brings challenges to compare and contrast recent observations with historic findings. In this review, we discuss experimental breakthroughs that have influenced how we understand and explore the dynamic structure and function of the nucleus, and how we can incorporate historical perspectives with insights acquired from the ever-evolving advances in molecular biology and pathology.
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Affiliation(s)
- Phillip W. L. Tai
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Sayyed K. Zaidi
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Hai Wu
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Rodrigo A. Grandy
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Martin M. Montecino
- Center for Biomedical Research and FONDAP Center for Genome Regulation, Universidad Andres Bello, Santiago, Chile
| | - André J. van Wijnen
- Departments of Orthopedic Surgery and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT
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Mitchell TRH, Zhu XD. Methylated TRF2 associates with the nuclear matrix and serves as a potential biomarker for cellular senescence. Aging (Albany NY) 2014; 6:248-63. [PMID: 24721747 PMCID: PMC4032793 DOI: 10.18632/aging.100650] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 04/03/2014] [Indexed: 11/25/2022]
Abstract
Methylation of N-terminal arginines of the shelterin component TRF2 is important for cellular proliferation. While TRF2 is found at telomeres, where it plays an essential role in maintaining telomere integrity, little is known about the cellular localization of methylated TRF2. Here we report that the majority of methylated TRF2 is resistant to extraction by high salt buffer and DNase I treatment, indicating that methylated TRF2 is tightly associated with the nuclear matrix. We show that methylated TRF2 drastically alters its nuclear staining as normal human primary fibroblast cells approach and enter replicative senescence. This altered nuclear staining, which is found to be overwhelmingly associated with misshapen nuclei and abnormal nuclear matrix folds, can be suppressed by hTERT and it is barely detectable in transformed and cancer cell lines. We find that dysfunctional telomeres and DNA damage, both of which are potent inducers of cellular senescence, promote the altered nuclear staining of methylated TRF2, which is dependent upon the ATM-mediated DNA damage response. Collectively, these results suggest that the altered nuclear staining of methylated TRF2 may represent ATM-mediated nuclear structural alteration associated with cellular senescence. Our data further imply that methylated TRF2 can serve as a potential biomarker for cellular senescence.
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Affiliation(s)
- Taylor R H Mitchell
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
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17
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Razin SV, Iarovaia OV, Vassetzky YS. A requiem to the nuclear matrix: from a controversial concept to 3D organization of the nucleus. Chromosoma 2014; 123:217-24. [PMID: 24664318 DOI: 10.1007/s00412-014-0459-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 03/10/2014] [Accepted: 03/14/2014] [Indexed: 12/13/2022]
Abstract
The first papers coining the term "nuclear matrix" were published 40 years ago. Here, we review the data obtained during the nuclear matrix studies and discuss the contribution of this controversial concept to our current understanding of nuclear architecture and three-dimensional organization of genome.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334, Moscow, Russia
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18
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Yasui DH, Gonzales ML, Aflatooni JO, Crary FK, Hu DJ, Gavino BJ, Golub MS, Vincent JB, Carolyn Schanen N, Olson CO, Rastegar M, Lasalle JM. Mice with an isoform-ablating Mecp2 exon 1 mutation recapitulate the neurologic deficits of Rett syndrome. Hum Mol Genet 2013; 23:2447-58. [PMID: 24352790 DOI: 10.1093/hmg/ddt640] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mutations in MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT OMIM 312750). Alternative inclusion of MECP2/Mecp2 exon 1 with exons 3 and 4 encodes MeCP2-e1 or MeCP2-e2 protein isoforms with unique amino termini. While most MECP2 mutations are located in exons 3 and 4 thus affecting both isoforms, MECP2 exon 1 mutations but not exon 2 mutations have been identified in RTT patients, suggesting that MeCP2-e1 deficiency is sufficient to cause RTT. As expected, genetic deletion of Mecp2 exons 3 and/or 4 recapitulates RTT-like neurologic defects in mice. However, Mecp2 exon 2 knockout mice have normal neurologic function. Here, a naturally occurring MECP2 exon 1 mutation is recapitulated in a mouse model by genetic engineering. A point mutation in the translational start codon of Mecp2 exon 1, transmitted through the germline, ablates MeCP2-e1 translation while preserving MeCP2-e2 production in mouse brain. The resulting MeCP2-e1 deficient mice developed forelimb stereotypy, hindlimb clasping, excessive grooming and hypo-activity prior to death between 7 and 31 weeks. MeCP2-e1 deficient mice also exhibited abnormal anxiety, sociability and ambulation. Despite MeCP2-e1 and MeCP2-e2 sharing, 96% amino acid identity, differences were identified. A fraction of phosphorylated MeCP2-e1 differed from the bulk of MeCP2 in subnuclear localization and co-factor interaction. Furthermore, MeCP2-e1 exhibited enhanced stability compared with MeCP2-e2 in neurons. Therefore, MeCP2-e1 deficient mice implicate MeCP2-e1 as the sole contributor to RTT with non-redundant functions.
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Affiliation(s)
- Dag H Yasui
- Department of Medical Microbiology and Immunology, UC Davis, Davis, CA, USA
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19
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Sherstyuk VV, Shevchenko AI, Zakian SM. Epigenetic landscape for initiation of DNA replication. Chromosoma 2013; 123:183-99. [PMID: 24337246 DOI: 10.1007/s00412-013-0448-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 11/27/2013] [Accepted: 12/02/2013] [Indexed: 02/07/2023]
Abstract
The key genetic process of DNA replication is initiated at specific sites referred to as replication origins. In eukaryotes, origins of DNA replication are not specified by a defined nucleotide sequence. Recent studies have shown that the structural context and topology of DNA sequence, chromatin features, and its transcriptional activity play an important role in origin choice. During differentiation and development, significant changes in chromatin organization and transcription occur, influencing origin activity and choice. In the last few years, a number of different genome-wide studies have broadened the understanding of replication origin regulation. In this review, we discuss the epigenetic factors and mechanisms that modulate origin choice and firing.
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Affiliation(s)
- Vladimir V Sherstyuk
- Russian Academy of Sciences, Siberian Branch, Institute of Cytology and Genetics, pr. Akad. Lavrentieva 10, Novosibirsk, 630090, Russia
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20
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Ohsaki E, Ueda K. Kaposi's Sarcoma-Associated Herpesvirus Genome Replication, Partitioning, and Maintenance in Latency. Front Microbiol 2012; 3:7. [PMID: 22291692 PMCID: PMC3264903 DOI: 10.3389/fmicb.2012.00007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 01/05/2012] [Indexed: 02/03/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is thought to be an oncogenic member of the γ-herpesvirus subfamily. The virus usually establishes latency upon infection as a default infection pattern. The viral genome replicates according to the host cell cycle by recruiting the host cellular replication machinery. Among the latently expressing viral factors, LANA plays pivotal roles in viral genome replication, partitioning, and maintenance. LANA binds with two LANA-binding sites (LBS1/2) within a terminal repeat (TR) sequence and is indispensable for viral genome replication in latency. The nuclear matrix region seems to be important as a replication site, since LANA as well as cellular replication factors accumulate there and recruit the viral replication origin in latency (ori-P) by its binding activity to LBS. KSHV ori-P consists of LBS followed by a 32-bp GC-rich segment (32GC). Although it has been reported that LANA recruits cellular pre-replication complexes (pre-RC) such as origin recognition complexes (ORCs) to the ori-P through its interaction with ORCs, this mechanism does not account completely for the requirement of the 32GC. On the other hand, there are few reports about the partitioning and maintenance of the viral genome. LANA interacts with many kinds of chromosomal proteins, including Brd2/RING3, core histones, such as H2A/H2B and histone H1, and so on. The detailed molecular mechanisms by which LANA enables KSHV genome partitioning and maintenance still remain obscure. By integrating the findings reported thus far on KSHV genome replication, partitioning, and maintenance in latency, we will summarize what we know now, discuss what questions remain to be answered, and determine what needs to be done next to understand the mechanisms underlying viral replication, partitioning, and maintenance strategy.
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Affiliation(s)
- Eriko Ohsaki
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine Suita, Osaka, Japan
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21
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Razin SV, Gavrilov AA, Pichugin A, Lipinski M, Iarovaia OV, Vassetzky YS. Transcription factories in the context of the nuclear and genome organization. Nucleic Acids Res 2011; 39:9085-92. [PMID: 21880598 PMCID: PMC3241665 DOI: 10.1093/nar/gkr683] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In the eukaryotic nucleus, genes are transcribed in transcription factories. In the present review, we re-evaluate the models of transcription factories in the light of recent and older data. Based on this analysis, we propose that transcription factories result from the aggregation of RNA polymerase II-containing pre-initiation complexes assembled next to each other in the nuclear space. Such an aggregation can be triggered by the phosphorylation of the C-terminal domain of RNA polymerase II molecules and their interaction with various transcription factors. Individual transcription factories would thus incorporate tissue-specific, co-regulated as well as housekeeping genes based only on their initial proximity to each other in the nuclear space. Targeting genes to be transcribed to protein-dense factories that contain all factors necessary for transcription initiation and elongation through chromatin templates clearly favors a more economical utilization and better recycling of the transcription machinery.
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Affiliation(s)
- S V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.
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22
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Nikolaev LG, Akopov SB, Didych DA, Sverdlov ED. Vertebrate Protein CTCF and its Multiple Roles in a Large-Scale Regulation of Genome Activity. Curr Genomics 2011; 10:294-302. [PMID: 20119526 PMCID: PMC2729993 DOI: 10.2174/138920209788921038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 06/15/2009] [Accepted: 06/18/2009] [Indexed: 11/24/2022] Open
Abstract
The CTCF transcription factor is an 11 zinc fingers multifunctional protein that uses different zinc finger combinations to recognize and bind different sites within DNA. CTCF is thought to participate in various gene regulatory networks including transcription activation and repression, formation of independently functioning chromatin domains and regulation of imprinting. Sequencing of human and other genomes opened up a possibility to ascertain the genomic distribution of CTCF binding sites and to identify CTCF-dependent cis-regulatory elements, including insulators. In the review, we summarized recent data on genomic distribution of CTCF binding sites in the human and other genomes within a framework of the loop domain hypothesis of large-scale regulation of the genome activity. We also tried to formulate possible lines of studies on a variety of CTCF functions which probably depend on its ability to specifically bind DNA, interact with other proteins and form di- and multimers. These three fundamental properties allow CTCF to serve as a transcription factor, an insulator and a constitutive dispersed genome-wide demarcation tool able to recruit various factors that emerge in response to diverse external and internal signals, and thus to exert its signal-specific function(s).
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Affiliation(s)
- L G Nikolaev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya, 117997, Moscow, Russia
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23
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Chavali PL, Funa K, Chavali S. Cis-regulation of microRNA expression by scaffold/matrix-attachment regions. Nucleic Acids Res 2011; 39:6908-18. [PMID: 21586588 PMCID: PMC3167628 DOI: 10.1093/nar/gkr303] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
microRNAs (miRNAs) spatio-temporally modulate gene expression; however, very little is known about the regulation of their expression. Here, we hypothesized that the well-known cis-regulatory elements of gene expression, scaffold/matrix-attachment regions (MARs) could modulate miRNA expression. Accordingly, we found MARs to be enriched in the upstream regions of miRNA genes. To determine their role in cell type-specific expression of miRNAs, we examined four individual miRNAs (let-7b, miR-17, miR-93 and miR-221) and the miR-17-92 cluster, known to be overexpressed in neuroblastoma. Our results show that MARs indeed define the cell-specific expression of these miRNAs by tethering the chromatin to nuclear matrix. This is brought about by cell type-specific binding of HMG I/Y protein to MARs that then promotes the local acetylation of histones, serving as boundary elements for gene activation. The binding, chromatin tethering and gene activation by HMG I/Y was not observed in fibroblast control cells but were restricted to neuroblastoma cells. This study implies that the association of MAR binding proteins to MARs could dictate the tissue/context specific regulation of miRNA genes by serving as a boundary element signaling the transcriptional activation.
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24
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Gong F, Sun L, Wang Z, Shi J, Li W, Wang S, Han X, Sun Y. The BCL2 gene is regulated by a special AT-rich sequence binding protein 1-mediated long range chromosomal interaction between the promoter and the distal element located within the 3'-UTR. Nucleic Acids Res 2011; 39:4640-52. [PMID: 21310710 PMCID: PMC3113567 DOI: 10.1093/nar/gkr023] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The 279-bp major breakpoint region (mbr) within the 3′-untranslated region (3′-UTR) of the BCL2 gene is a binding site of special AT-rich sequence binding protein 1 (SATB1) that is well known to participate in the long-range regulation of gene transcription. Our previous studies have revealed that the mbr could regulate BCL2 transcription over a 200-kb distance and this regulatory function was closely related to SATB1. This study is to explore the underlying mechanism and its relevance to cellular apoptosis. With chromosome conformation capture (3C) and chromatin immunoprecipitation (ChIP) assays we demonstrated that the mbr could physically interact with BCL2 promoter through SATB1-mediated chromatin looping, which was required for epigenetic modifications of the promoter, CREB accessibility and high expression of the BCL2 gene. During early apoptosis, SATB1 was a key regulator of BCL2 expression. Inhibition of SATB1 cleavage by treatment of cells with a caspase-6 inhibitor or overexpression of mutant SATB1 that was resistant to caspase-6, inhibited disassembly of the SATB1-mediated chromatin loop and restored the BCL2 mRNA level in Jurkat cells. These data revealed a novel mechanism of BCL2 regulation and mechanistically link SATB1-mediated long-range interaction with the regulation of a gene controlling apoptosis pathway for the first time.
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Affiliation(s)
- Feiran Gong
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Cell Biology and Jiangsu Key Lab of Cancer Biomarkers, Prevention & Treatment, Cancer Center, Nanjing Medical University, Nanjing 210029, PR China
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25
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26
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Nakka KK, Chattopadhyay S. Modulation of chromatin by MARs and MAR binding oncogenic transcription factor SMAR1. Mol Cell Biochem 2009; 336:75-84. [PMID: 19802523 DOI: 10.1007/s11010-009-0262-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 09/15/2009] [Indexed: 11/29/2022]
Abstract
The orchestration of the events in the cell during the progression of the cell cycle is modulated by various phenomenon which are regulated by structural modules of the cell. The nucleus is a major hub for all these regulatory units which harbour the nuclear matrix, matrix proteins and chromatin. The histone modifications etch a complex code on the chromatin and the matrix proteins in consort with the histone code regulate the gene expression. SMAR1 is a matrix attachment region binding protein that interacts with chromatin modulators like HDAC1, Sin3A and causes chromatin condensation. SMAR1 modulates the chromatin at the Vbeta locus and plays a prominent role in V(D)J recombination. Such indispensable function of SMAR1 by the modulation of chromatin in the context of malignancy and V(D)J recombination emphasizes that MAR binding proteins regulate the complex events of the cell and perturbed expression causes disease conditions.
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Affiliation(s)
- Kiran K Nakka
- National Centre for Cell Science, Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India
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27
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Zeng Y, Kulkarni P, Inoue T, Getzenberg RH. Down-regulating cold shock protein genes impairs cancer cell survival and enhances chemosensitivity. J Cell Biochem 2009; 107:179-88. [PMID: 19277990 DOI: 10.1002/jcb.22114] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The microenvironment of the cancer cell is pivotal to its phenotypic regulation. One of the central components of the microenvironment is temperature. An elevation in environmental temperature has been shown to increase the cancer cell's susceptibility to chemo- and radiation therapy. The goal of the studies described here was to identify some of the pathways that are modified by a mild increase in temperature in cancer cells. Using prostate cancer cells as a model system we found that in addition to the well described and anticipated up-regulation of the heat shock family of proteins, there is a significant down-regulation of certain members of the "cold shock" family of proteins such as, RNA binding motif protein 3 (RBM3) and cold inducible RNA binding protein (CIRBP). siRNA-mediated down-regulation of the cold shock protein (CSP) encoding mRNAs dramatically attenuates cell survival in the absence of any heat application. Furthermore, we also demonstrate that knocking down the CSPs can enhance the therapeutic response of prostate cancer cells to chemotherapy. Our findings suggest that down-regulating CSPs in cancer cells may "mimic" the stress response the cells experience when exposed to heat treatment rendering them more susceptible to therapy. Thus, the pharmacological modulation of RBM3 and CIRBP may represent novel therapeutic approaches for prostate cancer.
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Affiliation(s)
- Yu Zeng
- Department of Urology, James Buchanan Brady Urological Institute, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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28
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Senderek J, Garvey SM, Krieger M, Guergueltcheva V, Urtizberea A, Roos A, Elbracht M, Stendel C, Tournev I, Mihailova V, Feit H, Tramonte J, Hedera P, Crooks K, Bergmann C, Rudnik-Schöneborn S, Zerres K, Lochmüller H, Seboun E, Weis J, Beckmann JS, Hauser MA, Jackson CE. Autosomal-dominant distal myopathy associated with a recurrent missense mutation in the gene encoding the nuclear matrix protein, matrin 3. Am J Hum Genet 2009; 84:511-8. [PMID: 19344878 DOI: 10.1016/j.ajhg.2009.03.006] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Revised: 02/19/2009] [Accepted: 03/10/2009] [Indexed: 11/17/2022] Open
Abstract
Distal myopathies represent a heterogeneous group of inherited skeletal muscle disorders. One type of adult-onset, progressive autosomal-dominant distal myopathy, frequently associated with dysphagia and dysphonia (vocal cord and pharyngeal weakness with distal myopathy [VCPDM]), has been mapped to chromosome 5q31 in a North American pedigree. Here, we report the identification of a second large VCPDM family of Bulgarian descent and fine mapping of the critical interval. Sequencing of positional candidate genes revealed precisely the same nonconservative S85C missense mutation affecting an interspecies conserved residue in the MATR3 gene in both families. MATR3 is expressed in skeletal muscle and encodes matrin 3, a component of the nuclear matrix, which is a proteinaceous network that extends throughout the nucleus. Different disease related haplotype signatures in the two families provided evidence that two independent mutational events at the same position in MATR3 cause VCPDM. Our data establish proof of principle that the nuclear matrix is crucial for normal skeletal muscle structure and function and put VCPDM on the growing list of monogenic disorders associated with the nuclear proteome.
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Affiliation(s)
- Jan Senderek
- Institute of Cell Biology, ETH Zürich, 8093 Zürich, Switzerland.
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29
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Brázdová M, Quante T, Tögel L, Walter K, Loscher C, Tichý V, Cincárová L, Deppert W, Tolstonog GV. Modulation of gene expression in U251 glioblastoma cells by binding of mutant p53 R273H to intronic and intergenic sequences. Nucleic Acids Res 2009; 37:1486-500. [PMID: 19139068 PMCID: PMC2655687 DOI: 10.1093/nar/gkn1085] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Missense point mutations in the TP53 gene are frequent genetic alterations in human tumor tissue and cell lines derived thereof. Mutant p53 (mutp53) proteins have lost sequence-specific DNA binding, but have retained the ability to interact in a structure-selective manner with non-B DNA and to act as regulators of transcription. To identify functional binding sites of mutp53, we established a small library of genomic sequences bound by p53R273H in U251 human glioblastoma cells using chromatin immunoprecipitation (ChIP). Mutp53 binding to isolated DNA fragments confirmed the specificity of the ChIP. The mutp53 bound DNA sequences are rich in repetitive DNA elements, which are dispersed over non-coding DNA regions. Stable down-regulation of mutp53 expression strongly suggested that mutp53 binding to genomic DNA is functional. We identified the PPARGC1A and FRMD5 genes as p53R273H targets regulated by binding to intronic and intra-genic sequences. We propose a model that attributes the oncogenic functions of mutp53 to its ability to interact with intronic and intergenic non-B DNA sequences and modulate gene transcription via re-organization of chromatin.
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Affiliation(s)
- Marie Brázdová
- Department of Tumor Virology, Heinrich-Pette-Institute for Experimental Virology and Immunology, D-20251 Hamburg, Germany
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30
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Malyavantham KS, Bhattacharya S, Barbeitos M, Mukherjee L, Xu J, Fackelmayer FO, Berezney R. Identifying functional neighborhoods within the cell nucleus: proximity analysis of early S-phase replicating chromatin domains to sites of transcription, RNA polymerase II, HP1gamma, matrin 3 and SAF-A. J Cell Biochem 2009; 105:391-403. [PMID: 18618731 DOI: 10.1002/jcb.21834] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Higher order chromatin organization in concert with epigenetic regulation is a key process that determines gene expression at the global level. The organization of dynamic chromatin domains and their associated protein factors is intertwined with nuclear function to create higher levels of functional zones within the cell nucleus. As a step towards elucidating the organization and dynamics of these functional zones, we have investigated the spatial proximities among a constellation of functionally related sites that are found within euchromatic regions of the cell nucleus including: HP1gamma, nascent transcript sites (TS), active DNA replicating sites in early S-phase (PCNA) and RNA polymerase II sites. We report close associations among these different sites with proximity values specific for each combination. Analysis of matrin 3 and SAF-A sites demonstrates that these nuclear matrix proteins are highly proximal with the functionally related sites as well as to each other and display closely aligned and overlapping regions following application of the minimal spanning tree (MST) algorithm to visualize higher order network-like patterns. Our findings suggest that multiple factors within the nuclear microenvironment collectively form higher order combinatorial arrays of function. We propose a model for the organization of these functional neighborhoods which takes into account the proximity values of the individual sites and their spatial organization within the nuclear architecture.
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31
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Using cells encapsulated in agarose microbeads to analyse nuclear structure and functions. Methods Mol Biol 2008. [PMID: 18951184 DOI: 10.1007/978-1-60327-461-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
It is now generally agreed that the nuclei of higher eukaryotes, and particularly of mammalian cells, are highly structured and that different aspects of this structure contribute to the regulation of function (1, 2). Despite the general consensus, the key mechanisms that link nuclear structure and function have proved elusive. A major reason for this is a lack of techniques that allow nuclei to be manipulated in a way that preserves the complex architectural features that are present in vivo. Historically, significant progress in understanding the makeup of nuclei from mammalian cells has been made using cells that are permeabilised in a physiological buffer after being encapsulated in agarose microbeads. By using such beads, cells are protected from shear forces that otherwise can degrade crucial elements of the architecture that it is essential to preserve.
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32
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Ottaviani D, Lever E, Mitter R, Jones T, Forshew T, Christova R, Tomazou EM, Rakyan VK, Krawetz SA, Platts AE, Segarane B, Beck S, Sheer D. Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex. Genome Res 2008; 18:1778-86. [PMID: 18849521 PMCID: PMC2577859 DOI: 10.1101/gr.082313.108] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The folding of chromatin into topologically constrained loop domains is essential for genomic function. We have identified genomic anchors that define the organization of chromatin loop domains across the human major histocompatibility complex (MHC). This locus contains critical genes for immunity and is associated with more diseases than any other region of the genome. Classical MHC genes are expressed in a cell type-specific pattern and can be induced by cytokines such as interferon-gamma (IFNG). Transcriptional activation of the MHC was associated with a reconfiguration of chromatin architecture resulting from the formation of additional genomic anchors. These findings suggest that the dynamic arrangement of genomic anchors and loops plays a role in transcriptional regulation.
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Affiliation(s)
- Diego Ottaviani
- Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, United Kingdom
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33
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Abstract
Summary It has been postulated that bacterial DNA replication occurs via a factory mechanism in which unreplicated DNA is spooled into a centrally located replisome and newly synthesized DNA is discharged towards opposite cell poles. Although there is considerable support for this view, it does not fit with many key observations. I review new findings, and provide alternative interpretations for old findings, which challenge this model. As a whole, current data suggest that the replisome, at least in slowly growing Escherichia coli cells, tracks along a stationary chromosome. These replisomes are not stationary, tethered or restricted in their movement, but rather travel throughout the nucleoid. One possibility is that the replisome navigates along a chromosome made up of looped domains as has been previously envisioned.
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Affiliation(s)
- David Bates
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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34
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Spatio-temporal dynamics of replication and transcription sites in the mammalian cell nucleus. Chromosoma 2008; 117:553-67. [PMID: 18600338 DOI: 10.1007/s00412-008-0172-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 05/22/2008] [Accepted: 05/23/2008] [Indexed: 12/16/2022]
Abstract
To study when and where active genes replicated in early S phase are transcribed, a series of pulse-chase experiments are performed to label replicating chromatin domains (RS) in early S phase and subsequently transcription sites (TS) after chase periods of 0 to 24 h. Surprisingly, transcription activity throughout these chase periods did not show significant colocalization with early RS chromatin domains. Application of novel image segmentation and proximity algorithms, however, revealed close proximity of TS with the labeled chromatin domains independent of chase time. In addition, RNA polymerase II was highly proximal and showed significant colocalization with both TS and the chromatin domains. Based on these findings, we propose that chromatin activated for transcription dynamically unfolds or "loops out" of early RS chromatin domains where it can interact with RNA polymerase II and other components of the transcriptional machinery. Our results further suggest that the early RS chromatin domains are transcribing genes throughout the cell cycle and that multiple chromatin domains are organized around the same transcription factory.
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35
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Tang CW, Maya-Mendoza A, Martin C, Zeng K, Chen S, Feret D, Wilson SA, Jackson DA. The integrity of a lamin-B1-dependent nucleoskeleton is a fundamental determinant of RNA synthesis in human cells. J Cell Sci 2008; 121:1014-24. [PMID: 18334554 DOI: 10.1242/jcs.020982] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Spatial organisation of nuclear compartments is an important regulator of chromatin function, yet the molecular principles that maintain nuclear architecture remain ill-defined. We have used RNA interference to deplete key structural nuclear proteins, the nuclear lamins. In HeLa cells, we show that reduced expression of lamin B1, but not lamin A/C, severely inhibits RNA synthesis--first by RNA polymerase II and later by RNA polymerase I. Declining levels of transcription correlate with different morphological changes in major nuclear compartments, nucleoli and nuclear speckles. Ultimately, nuclear changes linked to the loss of synthetic activity result in expansion of the inter-chromatin domain and corresponding changes in the structure and spatial organisation of chromosome territories, which relocate towards the nuclear periphery. These results show that a lamin B1-containing nucleoskeleton is required to maintain RNA synthesis and that ongoing synthesis is a fundamental determinant of global nuclear architecture in mammalian cells.
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Affiliation(s)
- Chi W Tang
- Faculty of Life Sciences, University of Manchester, MIB, 131 Princess Street, Manchester, M1 7DN, UK
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36
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Abstract
Although the principles governing chromosomal architecture are largely unresolved, there is evidence that higher-order chromatin folding is mediated by the anchoring of specific DNA sequences to the nuclear matrix. These genome anchors are also crucial regulators of gene expression and DNA replication, and play a role in pathogenesis.
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Affiliation(s)
- Diego Ottaviani
- Cancer Research UK London Research Institute, Lincoln's Inn Fields, London WC2A 3PX, UK
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37
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Seng S, Avraham HK, Jiang S, Yang S, Sekine M, Kimelman N, Li H, Avraham S. The Nuclear Matrix Protein, NRP/B, Enhances Nrf2-Mediated Oxidative Stress Responses in Breast Cancer Cells. Cancer Res 2007; 67:8596-604. [PMID: 17875699 DOI: 10.1158/0008-5472.can-06-3785] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The transcription factor NF-E2-related factor 2 (Nrf2) translocates into the nucleus and activates phase II genes encoding detoxification enzymes and antioxidant proteins, resulting in the protection of cells from oxidative insults. However, the involvement of Nrf2-mediated oxidative stress responses in breast cancer cells is largely unknown. Notably, during our study of the Nrf2 pathway in breast cancer cells, we observed that the nuclear matrix protein NRP/B was expressed and colocalized with Nrf2 in these cells, suggesting that NRP/B is involved in Nrf2-mediated oxidative stress responses. The expression level of NRP/B was variable in different breast cancer cells and breast cancer tissues, and was found to be localized in the nucleus. NRP/B expression was increased after exposure to the oxidative stress agent, hydrogen peroxide (H(2)O(2)), particularly in the highly aggressive MDA-MB-231 breast cancer cells. Association of NRP/B with Nrf2 in vitro and in vivo was observed in MDA-MB-231 breast cancer cells, and this association was up-regulated upon exposure to H(2)O(2), but not to sodium nitroprusside, SIN-1, and DETA-NO. NRP/B also enhanced Nrf2-mediated NAD(P)H:quinine oxidoreductase 1 promoter activity. Thus, this study reveals that NRP/B enhances oxidative stress responses in breast cancer cells via the Nrf2 pathway, identifying a novel role of nuclear matrix protein(s) in oxidative stress responses.
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Affiliation(s)
- Seyha Seng
- Division of Experimental Medicine, Beth Israel Deaconess Medical Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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38
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Rao VA, Conti C, Guirouilh-Barbat J, Nakamura A, Miao ZH, Davies SL, Saccá B, Hickson ID, Bensimon A, Pommier Y. Endogenous γ-H2AX-ATM-Chk2 Checkpoint Activation in Bloom's Syndrome Helicase–Deficient Cells Is Related to DNA Replication Arrested Forks. Mol Cancer Res 2007; 5:713-24. [PMID: 17634426 DOI: 10.1158/1541-7786.mcr-07-0028] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Bloom syndrome helicase (BLM) is critical for genomic stability. A defect in BLM activity results in the cancer-predisposing Bloom syndrome (BS). Here, we report that BLM-deficient cell lines and primary fibroblasts display an endogenously activated DNA double-strand break checkpoint response with prominent levels of phosphorylated histone H2AX (gamma-H2AX), Chk2 (p(T68)Chk2), and ATM (p(S1981)ATM) colocalizing in nuclear foci. Interestingly, the mitotic fraction of gamma-H2AX foci did not seem to be higher in BLM-deficient cells, indicating that these lesions form transiently during interphase. Pulse labeling with iododeoxyuridine and immunofluorescence microscopy showed the colocalization of gamma-H2AX, ATM, and Chk2 together with replication foci. Those foci costained for Rad51, indicating homologous recombination at these replication sites. We therefore analyzed replication in BS cells using a single molecule approach on combed DNA fibers. In addition to a higher frequency of replication fork barriers, BS cells displayed a reduced average fork velocity and global reduction of interorigin distances indicative of an elevated frequency of origin firing. Because BS is one of the most penetrant cancer-predisposing hereditary diseases, it is likely that the lack of BLM engages the cells in a situation similar to precancerous tissues with replication stress. To our knowledge, this is the first report of high ATM-Chk2 kinase activation and its linkage to replication defects in a BS model.
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Affiliation(s)
- V Ashutosh Rao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, U.S. Department of Health and Human Services, Bethesda, Maryland, USA
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39
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Conti C, Saccà B, Herrick J, Lalou C, Pommier Y, Bensimon A. Replication fork velocities at adjacent replication origins are coordinately modified during DNA replication in human cells. Mol Biol Cell 2007; 18:3059-67. [PMID: 17522385 PMCID: PMC1949372 DOI: 10.1091/mbc.e06-08-0689] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The spatial organization of replicons into clusters is believed to be of critical importance for genome duplication in higher eukaryotes, but its functional organization still remains to be fully clarified. The coordinated activation of origins is insufficient on its own to account for a timely completion of genome duplication when interorigin distances vary significantly and fork velocities are constant. Mechanisms coordinating origin distribution with fork progression are still poorly elucidated, because of technical difficulties of visualizing the process. Taking advantage of a single molecule approach, we delineated and compared the DNA replication kinetics at the genome level in human normal primary and malignant cells. Our results show that replication forks moving from one origin, as well as from neighboring origins, tend to exhibit the same velocity, although the plasticity of the replication program allows for their adaptation to variable interorigin distances. We also found that forks that emanated from closely spaced origins tended to move slower than those associated with long replicons. Taken together, our results indicate a functional role for origin clustering in the dynamic regulation of genome duplication.
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Affiliation(s)
- Chiara Conti
- *Department of Genome Stability, Pasteur Institute, Paris F-75724, France
| | - Barbara Saccà
- *Department of Genome Stability, Pasteur Institute, Paris F-75724, France
| | - John Herrick
- *Department of Genome Stability, Pasteur Institute, Paris F-75724, France
| | - Claude Lalou
- Institut National de la Santé et de la Recherche Médicale U532, Hôpital Saint-Louis, Paris 75010, France; and
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817
| | - Aaron Bensimon
- *Department of Genome Stability, Pasteur Institute, Paris F-75724, France
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40
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Zhao CH, Li QF, Zhao Y, Niu JW, Li ZX, Chen JA. Changes of nuclear matrix proteins following the differentiation of human osteosarcoma MG-63 cells. GENOMICS PROTEOMICS & BIOINFORMATICS 2006; 4:10-7. [PMID: 16689697 PMCID: PMC5053975 DOI: 10.1016/s1672-0229(06)60011-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human osteosarcoma MG-63 cells were induced into differentiation by 5 mmol/L hexamethylene bisacetamide (HMBA). Their nuclear matrix proteins (NMPs) were selectively extracted and subjected to two-dimensional gel electrophoresis analysis. The results of protein patterns were analyzed by Melanie software. The spots of differentially expressed NMPs were excised and subjected to in situ digestion with trypsin. The maps of peptide mass fingerprinting were obtained by MALDI-TOF-MS analysis, and were submitted for NCBI database searches by Mascot tool. There were twelve spots changed remarkably during the differentiation induced by HMBA, nine of which were identified. The roles of the regulated proteins during the MG-63 differentiation were analyzed. This study suggests that the induced differentiation of cancer cells is accompanied by the changes of NMPs, and confirms the presence of some specific NMPs related to the cancer cell proliferation and differentiation. The changed NMPs are potential markers for cancer diagnosis or targets for cancer therapy.
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Affiliation(s)
- Chun-Hong Zhao
- Laboratory of Cell Biology, the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Qi-Fu Li
- Laboratory of Cell Biology, the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, China
- Corresponding author.
| | - Yan Zhao
- Laboratory of Cell Biology, the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Jing-Wen Niu
- Laboratory of Cell Biology, the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Zhi-Xing Li
- Laboratory of Cell Biology, the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Jin-An Chen
- Analysis and Testing Center, School of Life Sciences, Xiamen University, Xiamen 361005, China
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41
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Sayer JA, Manczak M, Akileswaran L, Reddy PH, Coghlan VM. Interaction of the nuclear matrix protein NAKAP with HypA and huntingtin: implications for nuclear toxicity in Huntington's disease pathogenesis. Neuromolecular Med 2006; 7:297-310. [PMID: 16391387 DOI: 10.1385/nmm:7:4:297] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2005] [Revised: 07/05/2005] [Accepted: 07/08/2005] [Indexed: 11/11/2022]
Abstract
Although expansion of a polyglutamine tract in the huntingtin protein is known to cause Huntington's disease (HD), there is considerable debate as to how this mutation leads to the selective neuronal loss that characterizes the disease. The observation that mutant huntingtin accumulates in neuronal nuclei has led to the hypothesis that the molecular mechanism may involve the disruption of specific nuclear activities. Recently, several nuclear interaction partners for huntingtin have been identified, including HypA, a splicing factor-like protein of unknown function. Using a yeast two-hybrid screen, we have identified the interaction of HypA with the nuclear scaffold protein NAKAP. Interaction of NAKAP with HypA is specific and occurs both in yeast and in vitro. Deletion-mapping studies indicate that binding occurs via a proline-rich domain in NAKAP with a WW domain of HypA. In cultured cells, NAKAP and HypA localize within the nucleus and copurify with the nuclear matrix. Furthermore, NAKAP associates with HypA from human brain and copurifies with huntingtin protein in brain tissue obtained from HD patients. In HD neurons, NAKAP and mutant huntingtin were colocalized to the nuclear matrix and were found to be components of nuclear aggregates. Hence, the NAKAP-HypA scaffold is a potential nuclear docking site for huntingtin protein and may contribute to the nuclear accumulation of huntingtin observed in HD.
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Affiliation(s)
- Jonathan A Sayer
- Neurological Sciences Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
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42
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Platts AE, Quayle AK, Krawetz SA. In-silico prediction and observations of nuclear matrix attachment. Cell Mol Biol Lett 2006; 11:191-213. [PMID: 16847565 PMCID: PMC6276010 DOI: 10.2478/s11658-006-0016-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2005] [Accepted: 02/26/2006] [Indexed: 11/30/2022] Open
Abstract
The nuclear matrix is a functionally adaptive structural framework interior to the nuclear envelope. The nature and function of this nuclear organizer remains the subject of widespread discussion in the epigenetic literature. To draw this discussion together with a view to suggest a way forward we summarize the biochemical evidence for the modalities of DNA-matrix binding alongside the in-silico predictions. Concordance is exhibited at various, but not all levels. On the one hand, both the reiteration and sequence similarity of some elements of Matrix Attachment Regions suggest conservation. On the other hand, in-silico predictions suggest additional unique components. In bringing together biological and sequence evidence we conclude that binding may be hierarchical in nature, reflective of a biological role in replicating, transcribing and potentiating chromatin. Nuclear matrix binding may well be more complex than the widely accepted simple loop model.
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Affiliation(s)
- Adrian E. Platts
- Department of Obstetrics and Gynecology, University School of Medicine, 253 C.S. Mott Center, 275 E Hancock, Detroit, MI 48201 USA
| | - Amelia K. Quayle
- The Center for Molecular Medicine and Genetics, University School of Medicine, 253 C.S. Mott Center, 275 E Hancock, Detroit, MI 48201 USA
| | - Stephen A. Krawetz
- Department of Obstetrics and Gynecology, University School of Medicine, 253 C.S. Mott Center, 275 E Hancock, Detroit, MI 48201 USA
- The Center for Molecular Medicine and Genetics, University School of Medicine, 253 C.S. Mott Center, 275 E Hancock, Detroit, MI 48201 USA
- Institute for Scientific Computing Wayne State, University School of Medicine, 253 C.S. Mott Center, 275 E Hancock, Detroit, MI 48201 USA
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43
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Benchimol M. New ultrastructural observations on the skeletal matrix of Tritrichomonas foetus. Parasitol Res 2005; 97:408-16. [PMID: 16151733 DOI: 10.1007/s00436-005-1480-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Accepted: 07/27/2005] [Indexed: 11/28/2022]
Abstract
Tritrichomonas foetus, a parasitic protozoon of the urogenital tract in cattle, presents a poorly known cytoskeleton, formed by rootlets and proteinaceous structures, many of which have not yet been characterized. Studies on its skeletal organization sheds light on the evolution of the matrix system, characteristic of higher eukaryotes. The skeletal matrix system of T. foetus in interphasic and dividing cells were studied using whole mount cell procedures observed either in field emission scanning electron microscopy (FESEM) or in transmission electron microscope (TEM) after the cell-sandwich technique, where the plasma membrane was mechanically removed. Three-dimensional-like images of the cell matrix were attained revealing a network of filaments that has not been described previously. Freeze-etching and cytochemistry using acridine orange for TEM, were also used. Membrane-skeleton interactions were examined in the hydrogenosomes, on the nuclear envelope at mitosis and interphase, and in the overall matrix filling of the cytoplasm and nucleoplasm. It was demonstrated that this eukaryote has a complex skeletal matrix other than just the rigid cytoskeletal structures. Our analysis indicated that the nucleus has a defined position, and fibrils perform an anchoring system for the nucleus. The possibility of a mechanism for nuclei fidelity migration during mitosis is discussed.
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Affiliation(s)
- Marlene Benchimol
- Laboratório de Ultraestrutura Celular, Universidade Santa Ursula, Botafogo, 222-31-010 Rio de Janeiro, Brazil.
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44
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Zhao CH, Li QF. Altered profiles of nuclear matrix proteins during the differentiation of human gastric mucous adenocarcinoma MGc80-3 cells. World J Gastroenterol 2005; 11:4628-33. [PMID: 16094700 PMCID: PMC4615401 DOI: 10.3748/wjg.v11.i30.4628] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To find and identify specific nuclear matrix proteins associated with proliferation and differentiation of carcinoma cells, which will be potential markers for cancer diagnosis and targets in cancer therapy.
METHODS: Nuclear matrix proteins were selectively extracted from MGc80-3 cells treated with or without hexamethylamine bisacetamide (HMBA), and subjected to 2-D gel electrophoresis. The resulted protein patterns were analyzed by Melanie software. Spots of nuclear matrix proteins differentially expressed were excised and subjected to in situ digestion with trypsin. Peptide masses were obtained by matrix-assisted laser-desorption/ ionization time of flight mass spectrometry (MALDI-TOF-MS) analysis and submitted for database searching using Mascot tool.
RESULTS: The MGc80-3 cells were induced into differentiation by HMBA. There were 22 protein spots which changed remarkably in the nuclear matrix, from differentiation of MGc80-3 cells compared to control. Eleven of which were identified. Seven proteins - actin, prohibitin, porin 31HL, heterogeneous nuclear ribonucleoprotein A2/B1, vimentin, ATP synthase, and heat shock protein 60 were downregulated, whereas three proteins - heat shock protein gp96, heat shock protein 90-beta, and valosin-containing protein were upregulated, and the oxygen-regulated protein was only found in the differentiated MGc80-3 cells.
CONCLUSION: The induced differentiation of carcinoma cells is accompanied by the changes of nuclear matrix proteins. Further characterization of those proteins will show the mechanism of cellular proliferation and differentiation, as well as cancer differentiation.
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Affiliation(s)
- Chun-Hong Zhao
- Laboratory of Cell Biology, School of Life Sciences, Xiamen University, Fujian Province, China
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Ocampo J, Mondragón R, Roa-Espitia AL, Chiquete-Félix N, Salgado ZO, Mújica A. Actin, myosin, cytokeratins and spectrin are components of the guinea pig sperm nuclear matrix. Tissue Cell 2005; 37:293-308. [PMID: 15979658 DOI: 10.1016/j.tice.2005.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2004] [Revised: 03/17/2005] [Accepted: 03/23/2005] [Indexed: 01/10/2023]
Abstract
The nuclear matrix (NM) of somatic cells is an internal nuclear framework structure, with a structural function and participation in DNA replication and transcription. The NM has been described in mouse, hamster and human spermatozoa. In this study, an NM structural component of the guinea pig sperm nucleus was obtained by removing nuclear proteins and DNA from DTT-CTAB nuclei. Removal was achieved with high ionic strength salt and microccocal nuclease treatments including a heparin treatment to cause a slight swelling of the nucleus and facilitate material extraction. Actin, myosin, cytokeratins and spectrin were detected associated to NM by indirect immunofluorescence, immunogold staining and Western blotting analysis using specific antibodies. The presence of NM in guinea pig sperm nucleus is shown for the first time and some of its components are identified. This is also the first report on cytokeratins and myosin presence in guinea pig sperm. A retarding effect of nuclear decondensation caused by heparin is induced after phalloidin and/or diacetyl-monoxime (a myosin ATPase activity inhibitor) treatment, suggesting a role for F-actin and myosin in the maintenance of nuclear stability in sperm. The actin role was supported by the decondensing effect that citochalasin D and gelsolin had on sperm nuclei.
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Affiliation(s)
- Juan Ocampo
- Departamento de Biología Celular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional. Apdo. Postal 14740, 07000 México, D.F., México.
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McPhillips MG, Ozato K, McBride AA. Interaction of bovine papillomavirus E2 protein with Brd4 stabilizes its association with chromatin. J Virol 2005; 79:8920-32. [PMID: 15994786 PMCID: PMC1168793 DOI: 10.1128/jvi.79.14.8920-8932.2005] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bovine papillomavirus E2 protein maintains and segregates the viral extrachromosomal genomes by tethering them to cellular mitotic chromosomes. E2 interacts with a cellular bromodomain protein, Brd4, to mediate the segregation of viral genomes into daughter cells. Brd4 binds acetylated histones and has been observed to diffusely coat mitotic chromosomes in several cell types. In this study, we show that in mitotic C127 cells, Brd4 diffusely coated the condensed chromosomes. However, in the presence of the E2 protein, E2 and Brd4 colocalized in punctate dots that were randomly distributed over the chromosomes. A similar pattern of E2 and Brd4 colocalization on mitotic chromosomes was observed in CV-1 cells, whereas only a faint chromosomal coating of Brd4 was detected in the absence of the E2 protein. Therefore, the viral E2 protein relocalizes and/or stabilizes the association of Brd4 with chromosomes in mitotic cells. The colocalization of E2 and Brd4 was also observed in interphase cells, indicating that this protein-protein interaction persists throughout the cell cycle. The interaction of E2 with Brd4 greatly stabilized the association of Brd4 with interphase chromatin. In both mitotic and interphase cells, this stabilization required a transcriptionally competent transactivation domain, but not the DNA binding function of the E2 protein. Thus, the E2 protein modulates the chromatin association of Brd4 during both interphase and mitosis. This study demonstrates that the segregation of papillomavirus genomes is not simply due to the passive hitchhiking of the E2/genome complex with a convenient cellular chromosomal protein.
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Affiliation(s)
- Maria G McPhillips
- Laboratory of Viral Diseases, NIAID, NIH, Building 4, Room 137, 4 Center Dr., MSC 0455, Bethesda, MD 20892-0455, USA
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Miccoli L, Frouin I, Novac O, Di Paola D, Harper F, Zannis-Hadjopoulos M, Maga G, Biard DSF, Angulo JF. The human stress-activated protein kin17 belongs to the multiprotein DNA replication complex and associates in vivo with mammalian replication origins. Mol Cell Biol 2005; 25:3814-30. [PMID: 15831485 PMCID: PMC1084281 DOI: 10.1128/mcb.25.9.3814-3830.2005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human stress-activated protein kin17 accumulates in the nuclei of proliferating cells with predominant colocalization with sites of active DNA replication. The distribution of kin17 protein is in equilibrium between chromatin-DNA and the nuclear matrix. An increased association with nonchromatin nuclear structure is observed in S-phase cells. We demonstrated here that kin17 protein strongly associates in vivo with DNA fragments containing replication origins in both human HeLa and monkey CV-1 cells. This association was 10-fold higher than that observed with nonorigin control DNA fragments in exponentially growing cells. In addition, the association of kin17 protein to DNA fragments containing replication origins was also analyzed as a function of the cell cycle. High binding of kin17 protein was found at the G(1)/S border and throughout the S phase and was negligible in both G(0) and M phases. Specific monoclonal antibodies against kin17 protein induced a threefold inhibition of in vitro DNA replication of a plasmid containing a minimal replication origin that could be partially restored by the addition of recombinant kin17 protein. Immunoelectron microscopy confirmed the colocalization of kin17 protein with replication proteins like RPA, PCNA, and DNA polymerase alpha. A two-step chromatographic fractionation of nuclear extracts from HeLa cells revealed that kin17 protein localized in vivo in distinct protein complexes of high molecular weight. We found that kin17 protein purified within an approximately 600-kDa protein complex able to support in vitro DNA replication by means of two different biochemical methods designed to isolate replication complexes. In addition, the reduced in vitro DNA replication activity of the multiprotein replication complex after immunodepletion for kin17 protein highlighted for a direct role in DNA replication at the origins.
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Affiliation(s)
- Laurent Miccoli
- Commissariat à l'Energie Atomique, Centre de Fontenay-aux-Roses, LGR/DRR/DSV, BP6, 92265 Fontenay-aux-Roses Cedex, France.
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48
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Daikoku T, Kudoh A, Fujita M, Sugaya Y, Isomura H, Shirata N, Tsurumi T. Architecture of replication compartments formed during Epstein-Barr virus lytic replication. J Virol 2005; 79:3409-18. [PMID: 15731235 PMCID: PMC1075702 DOI: 10.1128/jvi.79.6.3409-3418.2005] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epstein-Barr virus (EBV) productive DNA replication occurs at discrete sites, called replication compartments, in nuclei. In this study we performed comprehensive analyses of the architecture of the replication compartments. The BZLF1 oriLyt binding proteins showed a fine, diffuse pattern of distribution throughout the nuclei at immediate-early stages of induction and then became associated with the replicating EBV genome in the replication compartments during lytic infection. The BMRF1 polymerase (Pol) processivity factor showed a homogenous, not dot-like, distribution in the replication compartments, which completely coincided with the newly synthesized viral DNA. Inhibition of viral DNA replication with phosphonoacetic acid, a viral DNA Pol inhibitor, eliminated the DNA-bound form of the BMRF1 protein, although the protein was sufficiently expressed in the cells. These observations together with the findings that almost all abundantly expressed BMRF1 proteins existed in the DNA-bound form suggest that the BMRF1 proteins not only act at viral replication forks as Pol processive factors but also widely distribute on newly replicated EBV genomic DNA. In contrast, the BALF5 Pol catalytic protein, the BALF2 single-stranded-DNA binding protein, and the BBLF2/3 protein, a component of the helicase-primase complex, were colocalized as distinct dots distributed within replication compartments, representing viral replication factories. Whereas cellular replication factories are constructed based on nonchromatin nuclear structures and nuclear matrix, viral replication factories were easily solubilized by DNase I treatment. Thus, compared with cellular DNA replication, EBV lytic DNA replication factories would be simpler so that construction of the replication domain would be more relaxed.
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Affiliation(s)
- Tohru Daikoku
- Division of Virology, Aichi Cancer Center Research Institute, 1-1, Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan
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Abstract
Based on the idea that chromatin domains provide physical barriers for large molecules and multi-enzyme complexes, including the components of the transcription machinery, it has been proposed that transcription should be confined to the surfaces of chromatin domains. As a consequence nascent RNA should accumulate in the interchromatin space, which is thought to provide a special nuclear compartment involved in transcription, as well as in the processing and export of RNA (Cremer et al. 1993, Cremer & Cremer 2001). To further address the relationships between chromatin organization and RNA synthesis, we investigated the localization of BrUTP-labelled nascent RNA in HeLa cells stably expressing green fluorescent protein (GFP)-tagged histone H2B, which highlights the chromatin structure. Our results showed that nascent RNA does not preferentially localize within the interchromatin space. The findings do not support the idea that the interchromatin space provides a nuclear compartment playing an essential role in nascent RNA synthesis. However, the results are in agreement with the emerging view that even condensed chromatin domains display a highly dynamic organization and are not a physical barrier for transcription factors.
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Affiliation(s)
- Nicolas Sadoni
- Universität München (LMU), Department Biologie II, Goethestr. 31, 80336 München, Germany
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50
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Sadoni N, Cardoso MC, Stelzer EHK, Leonhardt H, Zink D. Stable chromosomal units determine the spatial and temporal organization of DNA replication. J Cell Sci 2004; 117:5353-65. [PMID: 15466893 DOI: 10.1242/jcs.01412] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA replication occurs in mammalian cells at so-called replication foci occupying defined nuclear sites at specific times during S phase. It is an unresolved problem how this specific spatiotemporal organization of replication foci is determined. Another unresolved question remains as to what extent DNA is redistributed during S phase. To investigate these problems, we visualized the replicating DNA and the replication machinery simultaneously in living HeLa cells. Time-lapse analyses revealed that DNA was not redistributed to other nuclear sites during S phase. Furthermore, the results showed that DNA is organized into stable aggregates equivalent to replication foci. These aggregates, which we call sub-chromosomal foci, stably maintained their replication timing from S phase to S phase. During S-phase progression, the replication machinery sequentially proceeded through spatially adjacent sets of sub-chromosomal foci. These findings imply that the specific nuclear substructure of chromosomes and the order of their stable subunits determine the spatiotemporal organization of DNA replication.
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Affiliation(s)
- Nicolas Sadoni
- University of Munich (LMU), Department Biology II, Grosshaderner Str. 2, 82152 Planegg-Martinsried, Germany
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