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Ito K, Takizawa T. Nuclear Architecture in the Nervous System. Results Probl Cell Differ 2022; 70:419-442. [PMID: 36348117 DOI: 10.1007/978-3-031-06573-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Neurons and glial cells in the nervous system exhibit different gene expression programs for neural development and function. These programs are controlled by the epigenetic regulatory layers in the nucleus. The nucleus is a well-organized subcellular organelle that includes chromatin, the nuclear lamina, and nuclear bodies. These subnuclear components operate together as epigenetic regulators of neural development and function and are collectively called the nuclear architecture. In the nervous system, dynamic rearrangement of the nuclear architecture has been observed in each cell type, especially in neurons, allowing for their specialized functions, including learning and memory formation. Although the importance of nuclear architecture has been debated for decades, the paradigm has been changing rapidly, owing to the development of new technologies. Here, we reviewed the latest studies on nuclear geometry, nuclear bodies, and heterochromatin compartments, as well as summarized recent novel insights regarding radial positioning, chromatin condensation, and chromatin interaction between genes and cis-regulatory elements.
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Affiliation(s)
- Kenji Ito
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, Pennsylvania, USA
| | - Takumi Takizawa
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan.
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Ito K, Takizawa T. Nuclear Architecture in the Nervous System: Development, Function, and Neurodevelopmental Diseases. Front Genet 2018; 9:308. [PMID: 30127803 PMCID: PMC6087739 DOI: 10.3389/fgene.2018.00308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/19/2018] [Indexed: 12/22/2022] Open
Abstract
Decades of study have shown that epigenetic regulation plays an important role in neural development and function. Several layers of epigenetic mechanisms control functions of the eukaryotic cell nucleus, a well-organized subcellular organelle with distinct compartments: chromatin, its related architectural proteins, and nuclear bodies. As these components function together in the epigenetic regulation of cellular development and functions, they are collectively termed nuclear architecture. In the nervous system, dynamic rearrangement of nuclear architecture correlates with alteration of transcription programs. During maturation and upon depolarization, neurons undergo a reorganization of nuclear architecture that alters gene expression programs. As such changes allow for specialized functions, including learning and memory, nuclear architecture is distinct among cell types. Studying nuclear architecture of neurons may uncover cell-division-independent mechanisms of global and local changes to nuclear architecture. We herein review recent research concerning nuclear architecture in the nervous system and will discuss its importance to the development, maturation, function, and diseases of the nervous system.
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Affiliation(s)
- Kenji Ito
- Department of Pediatrics, Graduate School of Medicine, Gunma University, Maebashi, Japan.,Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Takumi Takizawa
- Department of Pediatrics, Graduate School of Medicine, Gunma University, Maebashi, Japan
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Manoli DS, Tollkuhn J. Gene regulatory mechanisms underlying sex differences in brain development and psychiatric disease. Ann N Y Acad Sci 2018; 1420:26-45. [PMID: 29363776 PMCID: PMC5991992 DOI: 10.1111/nyas.13564] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/26/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
Abstract
The sexual differentiation of the mammalian nervous system requires the precise coordination of the temporal and spatial regulation of gene expression in diverse cell types. Sex hormones act at multiple developmental time points to specify sex-typical differentiation during embryonic and early development and to coordinate subsequent responses to gonadal hormones later in life by establishing sex-typical patterns of epigenetic modifications across the genome. Thus, mutations associated with neuropsychiatric conditions may result in sexually dimorphic symptoms by acting on different neural substrates or chromatin landscapes in males and females. Finally, as stress hormone signaling may directly alter the molecular machinery that interacts with sex hormone receptors to regulate gene expression, the contribution of chronic stress to the pathogenesis or presentation of mental illness may be additionally different between the sexes. Here, we review the mechanisms that contribute to sexual differentiation in the mammalian nervous system and consider some of the implications of these processes for sex differences in neuropsychiatric conditions.
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Affiliation(s)
- Devanand S. Manoli
- Department of Psychiatry and Weill Institute for Neuroscience, University of California, San Francisco, San Francisco, California
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Xin Y, Chanrion B, Liu MM, Galfalvy H, Costa R, Ilievski B, Rosoklija G, Arango V, Dwork AJ, Mann JJ, Tycko B, Haghighi F. Genome-wide divergence of DNA methylation marks in cerebral and cerebellar cortices. PLoS One 2010; 5:e11357. [PMID: 20596539 PMCID: PMC2893206 DOI: 10.1371/journal.pone.0011357] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 06/09/2010] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Emerging evidence suggests that DNA methylation plays an expansive role in the central nervous system (CNS). Large-scale whole genome DNA methylation profiling of the normal human brain offers tremendous potential in understanding the role of DNA methylation in brain development and function. METHODOLOGY/SIGNIFICANT FINDINGS Using methylation-sensitive SNP chip analysis (MSNP), we performed whole genome DNA methylation profiling of the prefrontal, occipital, and temporal regions of cerebral cortex, as well as cerebellum. These data provide an unbiased representation of CpG sites comprising 377,509 CpG dinucleotides within both the genic and intergenic euchromatic region of the genome. Our large-scale genome DNA methylation profiling reveals that the prefrontal, occipital, and temporal regions of the cerebral cortex compared to cerebellum have markedly different DNA methylation signatures, with the cerebral cortex being hypermethylated and cerebellum being hypomethylated. Such differences were observed in distinct genomic regions, including genes involved in CNS function. The MSNP data were validated for a subset of these genes, by performing bisulfite cloning and sequencing and confirming that prefrontal, occipital, and temporal cortices are significantly more methylated as compared to the cerebellum. CONCLUSIONS These findings are consistent with known developmental differences in nucleosome repeat lengths in cerebral and cerebellar cortices, with cerebrum exhibiting shorter repeat lengths than cerebellum. Our observed differences in DNA methylation profiles in these regions underscores the potential role of DNA methylation in chromatin structure and organization in CNS, reflecting functional specialization within cortical regions.
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Affiliation(s)
- Yurong Xin
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
| | - Benjamin Chanrion
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
| | - Meng-Min Liu
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
- Taub Institute for Research on the Aging Brain, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Hanga Galfalvy
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
| | - Ramiro Costa
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
| | - Boro Ilievski
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
- School Of Medicine, University Ss. Cyril and Methodius, Skopje, Macedonia
| | - Gorazd Rosoklija
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
- School Of Medicine, University Ss. Cyril and Methodius, Skopje, Macedonia
- Macedonian Academy of Sciences and Arts, University Ss. Cyril and Methodius, Skopje, Macedonia
| | - Victoria Arango
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
| | - Andrew J. Dwork
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
- School Of Medicine, University Ss. Cyril and Methodius, Skopje, Macedonia
| | - J. John Mann
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
- School Of Medicine, University Ss. Cyril and Methodius, Skopje, Macedonia
| | - Benjamin Tycko
- Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
- Taub Institute for Research on the Aging Brain, Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Fatemeh Haghighi
- Department of Psychiatry, Columbia University and The New York State Psychiatric Institute, New York, New York, United States of America
- * E-mail:
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Takizawa T, Meshorer E. Chromatin and nuclear architecture in the nervous system. Trends Neurosci 2008; 31:343-52. [PMID: 18538423 DOI: 10.1016/j.tins.2008.03.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 03/28/2008] [Accepted: 03/28/2008] [Indexed: 01/24/2023]
Abstract
Neurons are arguably the most varied cell type both morphologically and functionally. Their fate during differentiation and development and the activity of mature neurons are significantly determined and regulated by chromatin. The nucleus is compartmentalized and the arrangement of these compartments, termed the nuclear architecture, distinguishes one cell type from another and dictates many nuclear processes. Nuclear architecture determines the arrangement of chromosomes, the positioning of genes within chromosomes, the distribution of nuclear bodies and the interplay between these different factors. Importantly, chromatin regulation has been shown to be the basis for a variety of central nervous system processes including grooming and nursing, depression and stress, and drug abuse, among others. Here we review the regulation and function of nuclear architecture and chromatin structure in the context of the nervous system and discuss the potential use of histone deacetylase inhibitors as chromatin-directed therapy for nervous system disorders.
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Affiliation(s)
- Takumi Takizawa
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Ivanov TR, Brown IR. Genes expressed in cortical neurons--chromatin conformation and DNase I hypersensitive sites. Neurochem Res 1989; 14:129-37. [PMID: 2498750 DOI: 10.1007/bf00969627] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNase I sensitivity experiments were performed utilizing DNA probes to genes which are either transcribed in rat cortical neurons (the 68 kDa neurofilament gene and the neuron-specific enolase gene) or are transcriptionally silent (albumin). Results suggest that unlike liver, in which a hierarchy in chromatin conformation exists between transcribed and nontranscribed genes, the majority of protein coding sequences in cortical neurons may be relatively sensitive to nuclease digestion. This supports our previous observation of an increased DNase I sensitivity of total chromatin in cortical neurons. Nuclease sensitivity experiments also revealed the presence of brain-specific DNase I hypersensitive sites associated with the two neuron-specific genes.
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Affiliation(s)
- T R Ivanov
- Department of Zoology, University of Toronto, Scarborough Campus, Ontario, Canada
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8
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Vidali G, Ferrari N, Pfeffer U. Histone acetylation: a step in gene activation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1988; 231:583-96. [PMID: 3046254 DOI: 10.1007/978-1-4684-9042-8_49] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cellular ageing appears to consist mainly in a loss of adaptability and a progressive decrease in the capacity of the cell to maintain homeostasis. Such age related phenomenon can be the result of stochastic or of programmed events, and may occur through changes in the base pairs or coding of the DNA, through increasing levels of error in transcription and finally through alterations at the translation step of proteins synthesis. The purpose of this chapter is to present histone acetylation as a key event in the control of chromatin structure and transcription.
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Affiliation(s)
- G Vidali
- Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
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Brown IR, Sutcliffe JG. Atypical nucleosome spacing of rat neuronal identifier elements in non-neuronal chromatin. Nucleic Acids Res 1987; 15:3563-71. [PMID: 3575101 PMCID: PMC340749 DOI: 10.1093/nar/15.8.3563] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Rat neuronal identifier (ID) elements are located in chromatin regions that are organized in nucleosomal structures in both neuronal and non-neuronal cells. A subpopulation of ID sequences in chromatin of liver and kidney cells are relatively resistant to micrococcal nuclease digestion and are organized in nucleosomes exhibiting an atypically short repeat length. Other repetitive elements do not show this organization.
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Brown IR, Danielson P, Rush S, Godbout M, Sutcliffe JG. Rat and mouse identifier sequences are preferentially but not exclusively located in cortical neuronal genes expressed postnatally. J Neurosci Res 1987; 18:267-73. [PMID: 2447285 DOI: 10.1002/jnr.490180202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A genetic element called the identifier (ID) sequence, highly repeated in the rat genome, has previously been reported to be located in the introns of some genes transcribed in the adult rat brain by RNA polymerase II (Pol II). We show that nuclear RNA isolated from neurons of cerebral hemispheres (cortex) of 14-day old rats is enriched more than 10-fold in ID sequences compared to nuclear RNA from liver, kidney, cerebellum, or cortical glia. The developmental onset of the difference is during the first 2 weeks after birth. Mouse cortical neuronal nuclear RNA is similarly enriched in an element related but not identical to the rat ID element, and the enrichment also has postnatal onset. The enriched appearance of ID sequences in transcripts whose expression is increased postnatally in cortical neurons correlates developmentally and spatially with the transcription of ID elements by RNA polymerase III (Pol III) and with a change in chromatin structure.
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Affiliation(s)
- I R Brown
- Department of Molecular Biology, Research Institute of Scripps Clinic, La Jolla, California 92037
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Dell'Orco RT, Whittle WL, Macieira-Coelho A. Changes in the higher order organization of DNA during aging of human fibroblast-like cells. Mech Ageing Dev 1986; 35:199-208. [PMID: 3736139 DOI: 10.1016/0047-6374(86)90010-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nucleosome spacing (DNA repeat length) was determined in human diploid fibroblast-like cells (HDF) of different in vitro ages following the electrophoretic separation of micrococcal nuclease digestion products. The results indicate that a heterogeneity of DNA repeat lengths is present in HDF of all in vitro ages. In older cells the organization of part of the DNA is conserved, but a greater proportion of shorter repeats is evident. The shorter repeat lengths are not due to nucleosome sliding, but result from the presence of shorter linker regions which are reduced by as much as 25% in part of the chromatin of high PDL cells.
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Choi BH, Simpkins H. Changes in the molecular structure of mouse fetal astrocyte nucleosomes produced in vitro by methylmercuric chloride. ENVIRONMENTAL RESEARCH 1986; 39:321-330. [PMID: 3956461 DOI: 10.1016/s0013-9351(86)80058-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The fluorescent probe N-(3-pyrene)maleimide, which specifically labels the cysteine residues of histone H3 within the nucleosome, was used to monitor changes in the nucleosomal structure of mouse fetal astrocytes exposed to varying concentrations of methylmercuric chloride. Methylmercuric chloride treatment (10 microM) for 6 hr produced a significant decrease in the degree of fluorescence of the probe. The decrease was much smaller following a 4-hr incubation period. These results correlate with recent observations showing that significant changes in the thymidine labeling index occur following 4-6 hr of exposure to methylmercury (MeHg). It is hypothesized that MeHg enters the cells during the growth phase and attaches to the protein moiety of the nucleosome in or near the cysteine groups of histone H3, thus diminishing the binding capacity of the fluorescent probe. Addition of a detergent (sodium dodecyl sulfate) resulted in only a small increase in the degree of fluorescence of the treated nucleosomes as compared to controls, showing that the interaction of MeHg with the nuclear proteins was not dissociated by detergent. In view of the strong interaction between DNA and the histone dimer H3-H4 and the potential importance of the latter in gene regulation, these results suggest an additional means by which MeHg may exert its toxic effects.
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Ivanov VA, Melnikov AA, Terpilovska ON. DNA topoisomerase I from rat brain neurons. BIOCHIMICA ET BIOPHYSICA ACTA 1986; 866:154-60. [PMID: 3006775 DOI: 10.1016/0167-4781(86)90112-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The DNA topoisomerase I has been isolated from neurons of rat cerebral cortex. The most homogeneous fraction purified contains only one polypeptide of Mr approx. 100 000. The enzyme relaxes supercoiled DNA in the absence of ATP or Mg2+. The optimum monovalent cation concentration for the relaxation of superhelical DNA under conditions of DNA excess is found to be 175-200 mM. The neuron enzyme is similar to other mammalian type I DNA topoisomerases in that it links to the 3' ends of the broken DNA strands. Like calf thymus DNA topoisomerase I, the neuron topoisomerase can be selectively inhibited by poly(dG) but not by other homopolymerical deoxyribonucleotides.
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Czupryn M, Fronk J, Toczko K. Chromatin reorganization during early differentiation of Physarum polycephalum. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/0167-4781(85)90113-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Due to rapid advancement in biochemical and biophysical techniques during the last decade, extensive studies have been undertaken to understand the structure and function of chromatin. Several interesting results have been reported regarding the changes in basic organization and function of chromatin during the life time of a eukaryotic cell. The data accumulated so far have been obtained with different organs and organisms and widely differing methods, and the conclusions drawn from them are sometimes contradictory. In this paper, therefore, the available data on the age-associated alterations in the composition, structure and function of chromatin have been discussed, and an attempt has been made to correlate the structural changes in chromatin with alteration in gene expression during aging.
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Abstract
Poly[d(A-T)].poly[d(A-T)], when reconstituted with chicken erythrocyte core histones and subsequently incubated with sufficient histone H5 in a solution containing polyglutamic acid, forms structures resembling chromatin. H5 induces nucleosome alignment in about two hours at physiological ionic strength and 37 degrees C. The nucleosome spacing and apparent linker heterogeneity in the assembled nucleoprotein are very similar to those in chicken erythrocyte chromatin. Also, condensed chromatin-like fibers on the polynucleotide can be visualized. The binding of one mole of H5 per mole of core octamer is necessary to generate the physiological nucleosome spacing, which remains constant with the addition of more H5. The nucleosome repeat length is not a function of the core histone to poly[d(A-T)] ratio for values lower than the physiological ratio. With increasing ratios, in excess of the physiological value, nucleosome spacing first becomes non-uniform, and then takes on the close packing limit of approximately 165 base-pairs. In addition to eliminating possible base sequence effects on nucleosome positioning, poly[d(A-T)] allows nucleosomes to slide more readily than does DNA, thereby facilitating alignment. Evidence is presented that polyglutamic acid facilitates the nucleosome spacing activity of histone H5, primarily by keeping the nucleoprotein soluble. This model system should be useful for understanding how different repeat lengths arise in chromatin.
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Ivanov TR, Brown IR. Developmental changes in the synthesis of nonhistone nuclear proteins relative to the appearance of a short nucleosomal DNA repeat length in cerebral hemisphere neurons. Neurochem Res 1984; 9:1323-37. [PMID: 6504239 DOI: 10.1007/bf00973043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Fluctuations in the pattern of synthesis of nonhistone nuclear proteins were noted in cerebral hemisphere neurons during early postnatal development of the rat. Noteworthy changes included the synthesis of an acidic nuclear protein of relative molecular weight 41,000 (41K), two chromatin-associated basic proteins (37K and 38K) and several high molecular weight chromatin acidic proteins. These changes in the synthesis of nonhistone nuclear proteins occur at a developmental stage when a short nucleosomal DNA repeat length has appeared in cerebral hemisphere neurons.
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Abstract
Polynucleosomes from calf brain cortical neurone nuclei have an average repeat length of less than 168 base pairs. The ability of this material to adopt higher order structure has been assessed by various physical techniques. Although containing on average less DNA per nucleosome than is required to form a chromatosome, this short repeat length chromatin folded in an H1 dependent manner to a structure with properties similar to those observed for longer repeat length chromatins such as that of chicken erythrocyte (McGhee, J.D., D.C. Rau, E. Charney, and G. Felsenfeld, 1980, Cell, 22:87-96). These observations are discussed in the context of H1 location in the higher order chromatin fiber.
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Ralph-Edwards A, Silver JC. Nucleosome DNA repeat length and histone complement in a fungus exhibiting condensed chromatin. Exp Cell Res 1983; 148:363-76. [PMID: 6685049 DOI: 10.1016/0014-4827(83)90159-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungal chromatins are reported to exhibit unusually short nucleosomal DNA repeat lengths. To test whether this is a phylogenetic feature of fungi or rather is correlated with an apparent absence of condensed chromatin in the organisms studied, we have examined the chromatin organization and the complement of basic nuclear proteins in the fungus Entomophthora, an organism which exhibits marked chromatin condensation. Micrococcal nuclease digestion of Entomophthora chromatin revealed a nucleosomal DNA repeat length of 197 +/- 1.2 base pairs (bp). This repeat length is 20-40 bp longer than that reported for any fungus. Entomophthora nucleosomes exhibited an HI-like protein which was much less basic than the HI histones reported for higher eukaryotes but which was similar in basicity to the HI histone reported for the fungus Neurospora. However, the nucleosomal DNA repeat length of Neurospora chromatin is reported to be unusually short, whereas that of Entomophthora was found to be typical of the repeat lengths observed for chromatins of higher eukaryotes. Thus, repeat length, at least in fungi, would not appear to be directly determined by the basicity of the fungal cognate of histone HI.
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Berkowitz EM, Sanborn AC, Vaughan DW. Chromatin structure in neuronal and neuroglial cell nuclei as a function of age. J Neurochem 1983; 41:516-23. [PMID: 6875550 DOI: 10.1111/j.1471-4159.1983.tb04769.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Nuclei from the cerebral cortices of animals of different ages were separated into neuronal and neuroglial populations. Nuclei from cerebellar neurons were also studied. Using the enzyme micrococcal nuclease as a probe for chromatin structure, we found that the DNA from both neuronal preparations showed a decreased susceptibility to digestion during aging, although the onset of this alteration varies. In addition, both neuronal populations showed dramatic increases in the nucleosome spacing of the chromatin. Cerebral neuronal chromatin has a repeat length (nucleosome core and linker region) of 164 base pairs at 22 days and 11 months, 186 base pairs at 24 months, and 199 base pairs at 30 months. Cerebellar neuronal chromatin has a repeat of 188 base pairs at both 22 days and 11 months, 208 base pairs at 24 months, and 243 base pairs at 30 months. Neuroglial chromatin, on the other hand, showed no change in either accessibility to nuclease or repeat length.
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21
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Levy L, Moav B. Developmental Patterns in Histones and Histone Synthesis During Early Embryogenesis of the Sea Urchin Paracentrotus lividus. Differentiation 1982. [DOI: 10.1111/j.1432-0436.1982.tb01262.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Brown IR. Prenatal appearance of a short nucleosomal DNA repeat length in neurons of the guinea pig cerebral cortex. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 698:307-9. [PMID: 7138872 DOI: 10.1016/0167-4781(82)90162-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The organization of chromatin in neurons of the cerebral cortex of the guinea pig brain was analyzed by digesting isolated nuclei with micrococcal nuclease. During development, cortical neurons were observed to undergo an alteration in chromatin structure which results in an atypically short nucleosomal DNA repeat length of 164 bp. This change in chromatin organization occurs postnatally in certain mammals but in the guinea pig it takes place prior to birth between days 32 and 44 of fetal development. This suggests that the appearance of the short nucleosomal DNA repeat length in cortical neurons correlates to a particular stage of differentiation of cortical neurons rather than to the event of birth.
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Greenwood PD, Brown IR. Developmental changes in DNAse I digestibility and RNA template activity of neuronal nuclei relative to the postnatal appearance of a short DNA repeat length. Neurochem Res 1982; 7:965-76. [PMID: 6183600 DOI: 10.1007/bf00965136] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Neurons of the rat cerebral hemispheres are known to undergo a postnatal shift to a short DNA repeat length. In the present study we report that rat neuronal nuclei are more sensitive to digestion with DNAse I when isolated at a developmental stage after the shift in neuronal DNA repeated length compared to nuclei isolated before the shift. This observation may suggest that a decondensation of neuronal chromatin accompanies the postnatal shift in DNA repeat length. We have also found that neuronal nuclei isolated after the shift to a short DNA repeat length demonstrate an increased ability to synthesize RNA in vitro.
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Greenwood PD, Heikkila JJ, Brown IR. Developmental changes in chromatin organization in rat cerebral hemisphere neurons and analysis of DNA reassociation kinetics. Neurochem Res 1982; 7:525-39. [PMID: 7121711 DOI: 10.1007/bf00965120] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Previous reports have demonstrated that neuronal nuclei of rabbit, mouse and rat cerebral hemispheres exhibit a short DNA repeat length of 160 bp compared to the more typical repeat size of 200 bp found in glial nuclei and other cell types of higher eukaryotes. In this study we report that the conversion of chromatin to a short DNA repeat length in rat cerebral hemisphere neurons is a gradual process which begins between the first and second day after birth and is complete by 8 days. In these neurons, histone H1 appears to be less accessible to degradation by trypsin in the newborn rat brain compared to the 8 day old rat. This suggests that the developmental shift to a short DNA repeat length may be accompanied by a dispersal or decondensation of neuronal chromatin which results in an increased accessibility of neuronal histone H1 to degradation by trypsin. The increase in nuclear DNA content to 3.5C which has been reported in rat cortical neurons during early postnatal development does not appear to be associated with a selective amplification of a subset of DNA sequences as determined by DNA reassociation kinetics.
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Rossi R, Viola-Magni MP. Changes in endonuclease activity and in chromatin structure of rat hepatocytes during fetal and neonatal life. CELL DIFFERENTIATION 1982; 11:91-8. [PMID: 6279317 DOI: 10.1016/0045-6039(82)90023-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A developmental study of rat hepatic endonuclease has been performed. Nuclei, from different stages of hepatocyte maturation, were analyzed for endogenous endonuclease activity. The chromatin extracted from these nuclei does not show any fragmentation during the first 17 days of fetal development. On the 18th day of fetal life there is a massive increase in specific endonuclease activity. At birth this activity reaches a maximum level (3.5 units/mg DNA); thereafter it undergoes a gradual decrease. The size of the basic DNA repeats produced by the endonuclease action is 218.9 +/- 1.6 in 18-day-old fetuses and decreases to 204.9 +/- 2.5 in 19-day-old fetuses, a value which remains constant in the following fetal and postnatal life. This difference in monomer size is due to changes in the chromatin structure. Micrococcal nuclease digests show that the "nucleosome core" does not change during hepatocyte development. Therefore, the difference in size of the endonuclease DNA fragments must be due to the linker regions.
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Greenwood PD, Silver JC, Brown IR. Analysis of histones associated with neuronal and glial nuclei exhibiting divergent DNA repeat lengths. J Neurochem 1981; 37:498-505. [PMID: 6790674 DOI: 10.1111/j.1471-4159.1981.tb00483.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Total cerebral hemisphere nuclei purified from adult rabbit brain were subfractionated into neuronal and glial populations. Previous studies have shown that chromatin in neuronal nuclei is organized in an unusual nucleosome conformation compared with glial or kidney nuclei, i.e., a short DNA repeat length is present. We now analyze whether this difference in chromatin organization is associated with an alteration in the histone component of nucleosomes. Total histone isolated by acid/urea-protamine extraction of purified neuronal, glial, and kidney nuclei was analyzed by electrophoresis on SDS-polyacrylamide slab gels. Histone H1 that was selectively extracted from nuclei was also examined. Differences were not observed on SDS gels in the electrophoretic mobilities of histones associated with either the nucleosome core particle (histones (H2A, H2B, H3, H4) or the nucleosome linker region (histone H1). Total histone and selectively extracted histone H1 were also analyzed on acid/urea slab gels that resolve histones on the basis of both molecular weight and charge differences. When analyzed in this system, differences with respect to electrophoretic mobility were not detected when comparing either selectively extracted histone H1 or total histone from neuronal and glial nuclei. Quantitative analyses were also performed and neuronal nuclei were found to contain less histone H1 per milligram DNA compared with glial or kidney nuclei. Neuronal nuceli also demonstrated a lower ratio of histone H1/core histone. These results suggest that the pronounced difference in chromatin organization in neuronal compared with glial nuclei, which is reflected by a short DNA repeat length in neurons, appears to be associated with quantitative differences in neuronal histone H1.
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Greenwood P, Silver JC, Brown IR. Analysis of putative high-mobility-group (HMG) proteins in neuronal and glial nuclei from rabbit brain. Neurochem Res 1981; 6:673-9. [PMID: 6456426 DOI: 10.1007/bf00963883] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Putative high-mobility-group (HMG) proteins 1, 2, and 17 were detected in neuronal and glial nuclei isolated from the cerebral hemisphere of rabbit brain. Although divergent chromatin structures are present in these two populations of brain nuclei (i.e., neuronal nuclei exhibit a short DNA repeat length), no differences were apparent in the electrophoretic mobilities of putative HMG proteins 1, 2, and 17 on SDS gels.
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Whatley SA, Hall C, Lim L. Chromatin organization in the rat hypothalamus during early development. Biochem J 1981; 196:115-9. [PMID: 7306065 PMCID: PMC1162974 DOI: 10.1042/bj1960115] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The organization of chromatin in neuronal and glial nuclei isolated from different brain regions of rats during development was studied by digestion of nuclei with micrococcal nuclease. A short chromatin repeat length (approx. 176 base-pairs compared with that of glial nuclei from foetal cerebral cortex (approx. 200 base-pairs) was present in hypothalamic neurons throughout the ages studied, which was similar to the repeat length of cortical neurons from 7- and 25-day-old animals (approx. 174 base-pairs). Whereas in cortical neurons the chromatin repeat length shortened from approx. 200 base-pairs in the foetus to approx. 174 base-pairs in the first postnatal week, the short chromatin repeat length of hypothalamic neurons was already present 2 days before birth, indicating that hypothalamic neurons differentiate earlier than cortical neurons during brain development.
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Levy A, Noll M. Multiple phases of nucleosomes in the hsp 70 genes of Drosophila melanogaster. Nucleic Acids Res 1980; 8:6059-68. [PMID: 6258161 PMCID: PMC328072 DOI: 10.1093/nar/8.24.6059] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The arrangement of the nucleosomes with respect to the DNA sequence has been examined in the genes coding for the major heat shock protein (hsp 70) in Drosophila. In the repressed state of the genes, the nucleosomes are precisely phased in at least three frames.
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Heizmann C, Arnold E, Kuenzle C. Fluctuations of non-histone chromosomal proteins in differentiating brain cortex and cerebellar neurons. J Biol Chem 1980. [DOI: 10.1016/s0021-9258(19)70320-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Leonardson KE, Levy SB. Organizational changes in chromatin at different malignant stages of Friend erythroleukemia. Nucleic Acids Res 1980; 8:5317-31. [PMID: 7465415 PMCID: PMC324304 DOI: 10.1093/nar/8.22.5317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The chromatin structure of morphologically-similar, but increasingly-malignant erythroleukemia cells was investigated using milk micrococcal nuclease digestion of isolated nuclei. The maximum solubilization of chromatin was unique for each of the three cell types: the least malignant (our Stage II) released 61% of its chromatin DNA, the most malignant (Stage IV), 46%, and the intermediate (Stage III) released 36%. An analysis of the nucleosome oligomers liberated by digestion also demonstrated differences. After 15 minutes of digestion when release was reaching its maximum, a greater proportion of large nucleosomal oligomers (sizes > trinucleosome) was released from Stage II nuclei than from Stage III or IV nuclei. The cell types also differed in the relative amount of H1-depleted mononucleosomes released. Analysis of the size of the double-stranded DNA associated with mononucleosomal particles showed that Stage III mononucleosomes were smaller (148 bp) than Stage IV (167 bp) or Stage II (190 bp). In addition, while the DNA of mononucleosomes depleted in H1 was smaller than that in the H1-containing species, relative size differences among the different cell types were retained. These data suggested that the difference in the mononuocleosome particle size resistant to nuclease digestion was independent of histone H1. Differences in nucleosome repeat length were also noted among the cell types. These studies have demonstrated dramatic differences in chromatin structure associated with malignant potential of an otherwise morphologically identical cell type. These findings may reflect changes in the relative amounts of H2a variants which we have previously described among the different malignant cell types.
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Brown IR. Histone synthesis in isolated neuronal perikaryon relative to the postnatal appearance of a short DNA repeat length. Dev Biol 1980; 80:248-52. [PMID: 6777218 DOI: 10.1016/0012-1606(80)90512-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Schlegel RA, Litwack AH, Phelps BM. Nucleosome repeat lengths do not change during in vitro differentiation of erythroleukemia cells. Mol Biol Rep 1980; 6:115-8. [PMID: 6931965 DOI: 10.1007/bf00778439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
It has been previously demonstrated that nucleosome repeat lengths change during avian erythroid development and that repeat lengths correlate with histone H5 levels. Chromatin condensation also occurs during this process. In order to further investigate the relationship between histone H5 and/or chromatin condensation and nucleosome structure, repeat lengths were examined during in vitro differentiation of mouse erythroleukemia cells in which chromatin condensation occurs but in which histone H5 is absent. Our finding that repeat lengths do not change during this process supports the hypothesis that H5 plays a role in the mechanism which determines nucleosome repeat lengths.
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Schlegel RA, Haye KR, Litwack AH, Phelps BM. Nucleosome repeat lengths in the definitive erythroid series of the adult chicken. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 606:316-30. [PMID: 7357006 DOI: 10.1016/0005-2787(80)90041-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Morris [1] has suggested that the difference in nucleosome repeat length between chicken liver (200 base pairs) and mature chicken erythrocytes (212 base pairs) may be due to the presence of histone H5 which is found in chicken erythroid cells but not in other tissues. Levels of H5 increase during erythroid maturation in the adult chicken. To determine what influence H5 might have on repeat length, erythroid populations at various stages of maturation were isolated, and repeat lengths and levels of H5 were determined. Bone marrow cells from anemic chickens were cultured in vitro to permit non-cycling erythroblasts to mature and thus increase in density. Less dense cycling basophilic erythroblasts were then isolated by buoyant density centrifugation. This erythroblasts were then isolated by buoyant density centrifugation. This population has a repeat length of 205 base pairs and an H5 content roughly two-thirds that of mature erythrocytes, which have a repeat length of 212 base pairs. A population intermediate in maturation, consisting of cells of the anemic pheripheral blood, has a repeat length of 218 base pairs, and the predominant cell type in this population has an H5 content greater than that of mature erythrocytes. Therefore, changes in histone H5 content are reflected by the nucleosome repeat length during erythroid maturation.
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