1
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Solovei I, Mirny L. Spandrels of the cell nucleus. Curr Opin Cell Biol 2024; 90:102421. [PMID: 39180905 DOI: 10.1016/j.ceb.2024.102421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 07/18/2024] [Accepted: 08/02/2024] [Indexed: 08/27/2024]
Abstract
S.J. Gould and R. Lewontin in their famous "Spandrels paper" (1979) argued that many anatomical elements arise in evolution not due to their "current utility" but rather due to other "reasons for origin", such as other developmental processes, physical constraints and mechanical forces. Here, in the same spirit, we argue that a variety of molecular processes, physical constraints, and mechanical forces, alone or together, generate structures that are detectable in the cell nucleus, yet these structures themselves may not carry any specific function, being a mere reflection of processes that produced them.
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Affiliation(s)
- Irina Solovei
- Biocenter, Ludwig Maximilians University Munich, Planegg-Martinsried, Germany.
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Bartelt LC, Fakhri M, Adamek G, Trybus M, Samelak-Czajka A, Jackowiak P, Fiszer A, Lowe CB, La Spada AR, Switonski PM. Antibody-assisted selective isolation of Purkinje cell nuclei from mouse cerebellar tissue. CELL REPORTS METHODS 2024; 4:100816. [PMID: 38981474 PMCID: PMC11294835 DOI: 10.1016/j.crmeth.2024.100816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/08/2024] [Accepted: 06/17/2024] [Indexed: 07/11/2024]
Abstract
We developed a method that utilizes fluorescent labeling of nuclear envelopes alongside cytometry sorting for the selective isolation of Purkinje cell (PC) nuclei. Beginning with SUN1 reporter mice, we GFP-tagged envelopes to confirm that PC nuclei could be accurately separated from other cell types. We then developed an antibody-based protocol to make PC nuclear isolation more robust and adaptable to cerebellar tissues of any genotypic background. Immunofluorescent labeling of the nuclear membrane protein RanBP2 enabled the isolation of PC nuclei from C57BL/6 cerebellum. By analyzing the expression of PC markers, nuclear size, and nucleoli number, we confirmed that our method delivers a pure fraction of PC nuclei. To demonstrate its applicability, we isolated PC nuclei from spinocerebellar ataxia type 7 (SCA7) mice and identified transcriptional changes in known and new disease-associated genes. Access to pure PC nuclei offers insights into PC biology and pathology, including the nature of selective neuronal vulnerability.
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Affiliation(s)
- Luke C Bartelt
- University Program in Genetics & Genomics, Duke University Medical Center, Durham, NC 27710, USA; Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mouad Fakhri
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Grazyna Adamek
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Trybus
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Samelak-Czajka
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Paulina Jackowiak
- Laboratory of Single Cell Analyses, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Agnieszka Fiszer
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Albert R La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92697, USA; Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA; UCI Center for Neurotherapeutics, University of California, Irvine, Irvine, CA 92697, USA.
| | - Pawel M Switonski
- Department of Neuronal Cell Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.
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3
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Schmidt A, Zhang H, Schmitt S, Rausch C, Popp O, Chen J, Cmarko D, Butter F, Dittmar G, Lermyte F, Cardoso MC. The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues. Cells 2024; 13:139. [PMID: 38247831 PMCID: PMC10814525 DOI: 10.3390/cells13020139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions from these tissues, analyzed their protein compositions using quantitative mass spectrometry, and compared them to identify common and tissue-specific PCH proteins. In addition to heterochromatin-enriched proteins, the PCH proteome includes RNA/transcription and membrane-related proteins, which showed lower abundance than PCH-enriched proteins. Thus, we applied a cut-off of PCH-unspecific candidates based on their abundance and validated PCH-enriched proteins. Amongst the hits, MeCP2 was classified into brain PCH-enriched proteins, while linker histone H1 was not. We found that H1 and MeCP2 compete to bind to PCH and regulate PCH organization in opposite ways. Altogether, our workflow of unbiased PCH isolation, quantitative mass spectrometry, and validation-based analysis allowed the identification of proteins that are common and tissue-specifically enriched at PCH. Further investigation of selected hits revealed their opposing role in heterochromatin higher-order architecture in vivo.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Stephanie Schmitt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Oliver Popp
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Jiaxuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dusan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gunnar Dittmar
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Frederik Lermyte
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
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4
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Takei Y, Yang Y, White J, Yun J, Prasad M, Ombelets LJ, Schindler S, Cai L. High-resolution spatial multi-omics reveals cell-type specific nuclear compartments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539762. [PMID: 37214923 PMCID: PMC10197539 DOI: 10.1101/2023.05.07.539762] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The mammalian nucleus is compartmentalized by diverse subnuclear structures. These subnuclear structures, marked by nuclear bodies and histone modifications, are often cell-type specific and affect gene regulation and 3D genome organization1-3. Understanding nuclear organization requires identifying the molecular constituents of subnuclear structures and mapping their associations with specific genomic loci in individual cells, within complex tissues. Here, we introduce two-layer DNA seqFISH+, which allows simultaneous mapping of 100,049 genomic loci, together with nascent transcriptome for 17,856 genes and a diverse set of immunofluorescently labeled subnuclear structures all in single cells in cell lines and adult mouse cerebellum. Using these multi-omics datasets, we showed that repressive chromatin compartments are more variable by cell type than active compartments. We also discovered a single exception to this rule: an RNA polymerase II (RNAPII)-enriched compartment was associated with long, cell-type specific genes (> 200kb), in a manner distinct from nuclear speckles. Further, our analysis revealed that cell-type specific facultative and constitutive heterochromatin compartments marked by H3K27me3 and H4K20me3 are enriched at specific genes and gene clusters, respectively, and shape radial chromosomal positioning and inter-chromosomal interactions in neurons and glial cells. Together, our results provide a single-cell high-resolution multi-omics view of subnuclear compartments, associated genomic loci, and their impacts on gene regulation, directly within complex tissues.
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Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yujing Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonathan White
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Meera Prasad
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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5
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Martino S, Carollo PS, Barra V. A Glimpse into Chromatin Organization and Nuclear Lamina Contribution in Neuronal Differentiation. Genes (Basel) 2023; 14:genes14051046. [PMID: 37239406 DOI: 10.3390/genes14051046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
During embryonic development, stem cells undergo the differentiation process so that they can specialize for different functions within the organism. Complex programs of gene transcription are crucial for this process to happen. Epigenetic modifications and the architecture of chromatin in the nucleus, through the formation of specific regions of active as well as inactive chromatin, allow the coordinated regulation of the genes for each cell fate. In this mini-review, we discuss the current knowledge regarding the regulation of three-dimensional chromatin structure during neuronal differentiation. We also focus on the role the nuclear lamina plays in neurogenesis to ensure the tethering of the chromatin to the nuclear envelope.
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Affiliation(s)
- Salvatore Martino
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
| | - Pietro Salvatore Carollo
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
- Institute of Molecular Bioimaging and Physiology, National Research Council (IBFM-CNR), 90015 Cefalù, Italy
| | - Viviana Barra
- Department of Biological Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
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6
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Das S, Ramanan N. Region-specific heterogeneity in neuronal nuclear morphology in young, aged and in Alzheimer's disease mouse brains. Front Cell Dev Biol 2023; 11:1032504. [PMID: 36819109 PMCID: PMC9929567 DOI: 10.3389/fcell.2023.1032504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
Neurons in the mammalian brain exhibit enormous structural and functional diversity across different brain regions. Compared to our understanding of the morphological diversity of neurons, very little is known about the heterogeneity of neuronal nuclear morphology and how nuclear size changes in aging and diseased brains. Here, we report that the neuronal cell nucleus displays differences in area, perimeter, and circularity across different anatomical regions in the mouse brain. The pyramidal neurons of the hippocampal CA3 region exhibited the largest area whereas the striatal neuronal nuclei were the smallest. These nuclear size parameters also exhibited dichotomous changes with age across brain regions-while the neocortical and striatal neurons showed a decrease in nuclear area and perimeter, the CA3 neurons showed an increase with age. The nucleus of parvalbumin- and calbindin-positive interneurons had comparable morphological features but exhibited differences between brain regions. In the context of activity-dependent transcription in response to a novel environment, there was a decrease in nuclear size and circularity in c-Fos expressing neurons in the somatosensory cortex and hippocampal CA1 and CA3. In an APP/PS1 mutant mouse model of Alzheimer's disease (AD), the neuronal nuclear morphology varies with plaque size and with increasing distance from the plaque. The neuronal nuclear morphology in the immediate vicinity of the plaque was independent of the plaque size and the morphology tends to change away from the plaque. These changes in the neuronal nuclear size and shape at different ages and in AD may be attributed to changes in transcriptional activity. This study provides a detailed report on the differences that exist between neurons in nuclear morphology and can serve as a basis for future studies.
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7
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Brändle F, Frühbauer B, Jagannathan M. Principles and functions of pericentromeric satellite DNA clustering into chromocenters. Semin Cell Dev Biol 2022; 128:26-39. [PMID: 35144860 DOI: 10.1016/j.semcdb.2022.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022]
Abstract
Simple non-coding tandem repeats known as satellite DNA are observed widely across eukaryotes. These repeats occupy vast regions at the centromere and pericentromere of chromosomes but their contribution to cellular function has remained incompletely understood. Here, we review the literature on pericentromeric satellite DNA and discuss its organization and functions across eukaryotic species. We specifically focus on chromocenters, DNA-dense nuclear foci that contain clustered pericentromeric satellite DNA repeats from multiple chromosomes. We first discuss chromocenter formation and the roles that epigenetic modifications, satellite DNA transcripts and sequence-specific satellite DNA-binding play in this process. We then review the newly emerging functions of chromocenters in genome encapsulation, the maintenance of cell fate and speciation. We specifically highlight how the rapid divergence of satellite DNA repeats impacts reproductive isolation between closely related species. Together, we underline the importance of this so-called 'junk DNA' in fundamental biological processes.
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Affiliation(s)
- Franziska Brändle
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Benjamin Frühbauer
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland
| | - Madhav Jagannathan
- Institute of Biochemistry, ETH Zürich, Otto-Stern-Weg 3, Zürich CH-8093, Switzerland.
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8
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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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9
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Takei Y, Zheng S, Yun J, Shah S, Pierson N, White J, Schindler S, Tischbirek CH, Yuan GC, Cai L. Single-cell nuclear architecture across cell types in the mouse brain. Science 2021; 374:586-594. [PMID: 34591592 DOI: 10.1126/science.abj1966] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Diverse cell types in tissues have distinct gene expression programs, chromatin states, and nuclear architectures. To correlate such multimodal information across thousands of single cells in mouse brain tissue sections, we use integrated spatial genomics, imaging thousands of genomic loci along with RNAs and epigenetic markers simultaneously in individual cells. We reveal that cell type–specific association and scaffolding of DNA loci around nuclear bodies organize the nuclear architecture and correlate with differential expression levels in different cell types. At the submegabase level, active and inactive X chromosomes access similar domain structures in single cells despite distinct epigenetic and expression states. This work represents a major step forward in linking single-cell three-dimensional nuclear architecture, gene expression, and epigenetic modifications in a native tissue context.
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Affiliation(s)
- Yodai Takei
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shiwei Zheng
- Department of Genetics and Genomic Sciences and Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jina Yun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sheel Shah
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nico Pierson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jonathan White
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Simone Schindler
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Carsten H Tischbirek
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences and Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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10
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Kishi Y, Gotoh Y. Regulation of Chromatin Structure During Neural Development. Front Neurosci 2018; 12:874. [PMID: 30618540 PMCID: PMC6297780 DOI: 10.3389/fnins.2018.00874] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/09/2018] [Indexed: 11/13/2022] Open
Abstract
The regulation of genome architecture is a key determinant of gene transcription patterns and neural development. Advances in methodologies based on chromatin conformation capture (3C) have shed light on the genome-wide organization of chromatin in developmental processes. Here, we review recent discoveries regarding the regulation of three-dimensional (3D) chromatin conformation, including promoter-enhancer looping, and the dynamics of large chromatin domains such as topologically associated domains (TADs) and A/B compartments. We conclude with perspectives on how these conformational changes govern neural development and may go awry in disease states.
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Affiliation(s)
- Yusuke Kishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
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11
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Cremer T, Cremer M, Cremer C. The 4D Nucleome: Genome Compartmentalization in an Evolutionary Context. BIOCHEMISTRY (MOSCOW) 2018; 83:313-325. [PMID: 29626919 DOI: 10.1134/s000629791804003x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
4D nucleome research aims to understand the impact of nuclear organization in space and time on nuclear functions, such as gene expression patterns, chromatin replication, and the maintenance of genome integrity. In this review we describe evidence that the origin of 4D genome compartmentalization can be traced back to the prokaryotic world. In cell nuclei of animals and plants chromosomes occupy distinct territories, built up from ~1 Mb chromatin domains, which in turn are composed of smaller chromatin subdomains and also form larger chromatin domain clusters. Microscopic evidence for this higher order chromatin landscape was strengthened by chromosome conformation capture studies, in particular Hi-C. This approach demonstrated ~1 Mb sized, topologically associating domains in mammalian cell nuclei separated by boundaries. Mutations, which destroy boundaries, can result in developmental disorders and cancer. Nucleosomes appeared first as tetramers in the Archaea kingdom and later evolved to octamers built up each from two H2A, two H2B, two H3, and two H4 proteins. Notably, nucleosomes were lost during the evolution of the Dinoflagellata phylum. Dinoflagellate chromosomes remain condensed during the entire cell cycle, but their chromosome architecture differs radically from the architecture of other eukaryotes. In summary, the conservation of fundamental features of higher order chromatin arrangements throughout the evolution of metazoan animals suggests the existence of conserved, but still unknown mechanism(s) controlling this architecture. Notwithstanding this conservation, a comparison of metazoans and protists also demonstrates species-specific structural and functional features of nuclear organization.
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Affiliation(s)
- T Cremer
- Biocenter, Department of Biology II, Ludwig Maximilian University (LMU), Munich, Germany.
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12
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Ostromyshenskii DI, Chernyaeva EN, Kuznetsova IS, Podgornaya OI. Mouse chromocenters DNA content: sequencing and in silico analysis. BMC Genomics 2018; 19:151. [PMID: 29458329 PMCID: PMC5819297 DOI: 10.1186/s12864-018-4534-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 02/06/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromocenters are defined as a punctate condensed blocks of chromatin in the interphase cell nuclei of certain cell types with unknown biological significance. In recent years a progress in revealing of chromocenters protein content has been made although the details of DNA content within constitutive heterochromatin still remain unclear. It is known that these regions are enriched in tandem repeats (TR) and transposable elements. Quick improvement of genome sequencing does not help to assemble the heterochromatic regions due to lack of appropriate bioinformatics techniques. RESULTS Chromocenters DNA have been isolated by a biochemical approach from mouse liver cells nuclei and sequenced on the Illumina MiSeq resulting in ChrmC dataset. Analysis of ChrmC dataset by the bioinformatics tools available revealed that the major component of chromocenter DNA are TRs: ~ 66% MaSat and ~ 4% MiSat. Other previously classified TR families constitute ~ 1% of ChrmC dataset. About 6% of chromocenters DNA are mostly unannotated sequences. In the contigs assembled with IDBA_UD there are many fragments of heterochromatic Y-chromosome, rDNA and other pseudo-genes and non-coding DNA. A protein coding sfi1 homolog gene fragment was also found in contigs. The Sfi1 homolog gene is located on the chromosome 11 in the reference genome very close to the Golden Pass Gap (a ~ 3 Mb empty region reserved to the pericentromeric region) and proves the purity of chromocenters isolation. The second major fraction are non-LTR retroposons (SINE and LINE) with overwhelming majority of LINE - ~ 11% of ChrmC. Most of the LINE fragments are from the ~ 2 kb region at the end of the 2nd ORF and its' flanking region. The precise LINEs' segment of ~ 2 kb is the necessary mouse constitutive heterohromatin component together with TR. The third most abundant fraction are ERVs. The ERV distribution in chromocenters differs from the whole genome: IAP (ERV2 class) is the most numerous in ChrmC while MaLR (ERV3 class) prevails in the reference genome. IAP and its LTR also prevail in TR containing contigs extracted from the WGS dataset. In silico prediction of IAP and LINE fragments in chromocenters was confirmed by direct fluorescent in situ hybridization (FISH). CONCLUSION Our data of chromocenters' DNA (ChrmC) sequencing demonstrate that IAP with LTR and a precise ~ 2 kb fragment of LINE represent a substantial fraction of mouse chromocenters (constitutive heteroсhromatin) along with TRs.
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Affiliation(s)
- Dmitrii I Ostromyshenskii
- Institute of Cytology RAS, St.-Petersburg, 194064, Russia.
- Far Eastern Federal University, Vladivostok, 690922, Russia.
| | | | - Inna S Kuznetsova
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Olga I Podgornaya
- Institute of Cytology RAS, St.-Petersburg, 194064, Russia
- Far Eastern Federal University, Vladivostok, 690922, Russia
- St Petersburg State University, St Petersburg, 199034, Russia
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13
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van de Werken HJG, Haan JC, Feodorova Y, Bijos D, Weuts A, Theunis K, Holwerda SJB, Meuleman W, Pagie L, Thanisch K, Kumar P, Leonhardt H, Marynen P, van Steensel B, Voet T, de Laat W, Solovei I, Joffe B. Small chromosomal regions position themselves autonomously according to their chromatin class. Genome Res 2017; 27:922-933. [PMID: 28341771 PMCID: PMC5453326 DOI: 10.1101/gr.213751.116] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/22/2017] [Indexed: 11/24/2022]
Abstract
The spatial arrangement of chromatin is linked to the regulation of nuclear processes. One striking aspect of nuclear organization is the spatial segregation of heterochromatic and euchromatic domains. The mechanisms of this chromatin segregation are still poorly understood. In this work, we investigated the link between the primary genomic sequence and chromatin domains. We analyzed the spatial intranuclear arrangement of a human artificial chromosome (HAC) in a xenospecific mouse background in comparison to an orthologous region of native mouse chromosome. The two orthologous regions include segments that can be assigned to three major chromatin classes according to their gene abundance and repeat repertoire: (1) gene-rich and SINE-rich euchromatin; (2) gene-poor and LINE/LTR-rich heterochromatin; and (3) gene-depleted and satellite DNA-containing constitutive heterochromatin. We show, using fluorescence in situ hybridization (FISH) and 4C-seq technologies, that chromatin segments ranging from 0.6 to 3 Mb cluster with segments of the same chromatin class. As a consequence, the chromatin segments acquire corresponding positions in the nucleus irrespective of their chromosomal context, thereby strongly suggesting that this is their autonomous property. Interactions with the nuclear lamina, although largely retained in the HAC, reveal less autonomy. Taken together, our results suggest that building of a functional nucleus is largely a self-organizing process based on mutual recognition of chromosome segments belonging to the major chromatin classes.
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Affiliation(s)
- Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC Cancer Institute & Department of Urology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands.,Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Josien C Haan
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Dominika Bijos
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - An Weuts
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Koen Theunis
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Sjoerd J B Holwerda
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Wouter Meuleman
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Parveen Kumar
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Heinrich Leonhardt
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Thierry Voet
- Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Wouter de Laat
- Hubrecht Institute-KNAW & University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands
| | - Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Boris Joffe
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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14
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Borsos M, Torres-Padilla ME. Building up the nucleus: nuclear organization in the establishment of totipotency and pluripotency during mammalian development. Genes Dev 2016; 30:611-21. [PMID: 26980186 PMCID: PMC4803048 DOI: 10.1101/gad.273805.115] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In mammals, epigenetic reprogramming, the acquisition and loss of totipotency, and the first cell fate decision all occur within a 3-d window after fertilization from the one-cell zygote to the formation of the blastocyst. These processes are poorly understood in molecular detail, yet this is an essential prerequisite to uncover principles of stem cells, chromatin biology, and thus regenerative medicine. A unique feature of preimplantation development is the drastic genome-wide changes occurring to nuclear architecture. From studying somatic and in vitro cultured embryonic stem cells (ESCs) it is becoming increasingly established that the three-dimensional (3D) positions of genomic loci relative to each other and to specific compartments of the nucleus can act on the regulation of gene expression, potentially driving cell fate. However, the functionality, mechanisms, and molecular characteristics of the changes in nuclear organization during preimplantation development are only now beginning to be unraveled. Here, we discuss the peculiarities of nuclear compartments and chromatin organization during mammalian preimplantation development in the context of the transition from totipotency to pluripotency.
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Affiliation(s)
- Máté Borsos
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, U964, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale F-67404 Illkirch, France; Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, U964, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale F-67404 Illkirch, France; Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München D-81377 München, Germany
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15
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Solovei I, Thanisch K, Feodorova Y. How to rule the nucleus: divide et impera. Curr Opin Cell Biol 2016; 40:47-59. [PMID: 26938331 DOI: 10.1016/j.ceb.2016.02.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/04/2016] [Accepted: 02/14/2016] [Indexed: 01/14/2023]
Abstract
Genome-wide molecular studies have provided new insights into the organization of nuclear chromatin by revealing the presence of chromatin domains of differing transcriptional activity, frequency of cis-interactions, proximity to scaffolding structures and replication timing. These studies have not only brought our understanding of genome function to a new level, but also offered functional insight for many phenomena observed in microscopic studies. In this review, we discuss the major principles of nuclear organization based on the spatial segregation of euchromatin and heterochromatin, as well as the dynamic genome rearrangements occurring during cell differentiation and development. We hope to unite the existing molecular and microscopic data on genome organization to get a holistic view of the nucleus, and propose a model, in which repeat repertoire together with scaffolding structures blueprint the functional nuclear architecture.
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Affiliation(s)
- Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany.
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany; Department of Medical Biology, Medical University-Plovdiv, Boulevard Vasil Aprilov 15A, Plovdiv 4000, Bulgaria
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16
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Wilczynski GM. Significance of higher-order chromatin architecture for neuronal function and dysfunction. Neuropharmacology 2014; 80:28-33. [PMID: 24456745 DOI: 10.1016/j.neuropharm.2014.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/08/2014] [Accepted: 01/09/2014] [Indexed: 02/08/2023]
Abstract
Recent studies in neurons indicate that the large-scale chromatin architectural framework, including chromosome territories or lamina-associated chromatin, undergoes dynamic changes that represent an emergent level of regulation of neuronal gene-expression. This phenomenon has been implicated in neuronal differentiation, long-term potentiation, seizures, and disorders of neural plasticity such as Rett syndrome and epilepsy.
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Affiliation(s)
- Grzegorz M Wilczynski
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland.
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17
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Insights into chromatin structure and dynamics in plants. BIOLOGY 2013; 2:1378-410. [PMID: 24833230 PMCID: PMC4009787 DOI: 10.3390/biology2041378] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/15/2013] [Accepted: 11/18/2013] [Indexed: 11/17/2022]
Abstract
The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.
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18
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Abstract
This review highlights recent discoveries that have shaped the emerging viewpoints in the field of epigenetic influences in the central nervous system (CNS), focusing on the following questions: (i) How is the CNS shaped during development when precursor cells transition into morphologically and molecularly distinct cell types, and is this event driven by epigenetic alterations?; ii) How do epigenetic pathways control CNS function?; (iii) What happens to "epigenetic memory" during aging processes, and do these alterations cause CNS dysfunction?; (iv) Can one restore normal CNS function by manipulating the epigenome using pharmacologic agents, and will this ameliorate aging-related neurodegeneration? These and other still unanswered questions remain critical to understanding the impact of multifaceted epigenetic machinery on the age-related dysfunction of CNS.
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Affiliation(s)
- Yue-Qiang Zhao
- />Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400 USA
- />Department of Plastic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - I. King Jordan
- />School of Biology, Georgia Institute of Technology, Atlanta, GA USA
- />PanAmerican Bioinformatics Institute, Santa Marta, Magdalena Colombia
| | - Victoria V. Lunyak
- />Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945-1400 USA
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19
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Purkartová Z, Vožeh F. Cerebellar degeneration in Lurcher mice under confocal laser scanning microscope. Microsc Res Tech 2013; 76:545-51. [PMID: 23463661 DOI: 10.1002/jemt.22198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 01/28/2013] [Accepted: 02/05/2013] [Indexed: 12/19/2022]
Abstract
Lurcher mutant mice represent a natural model of genetically-determined olivocerebellar degeneration caused by a mutation in the δ2 glutamate receptor gene. They suffer from progressive postnatal loss of cerebellar Purkinje cells and a decrease of granule cells and inferior olive neurons. Their wild type littermates serve as healthy controls. A confocal laser scanning microscope was used aiming investigation the dynamics of changes in the cerebellar cortex of Lurcher and wild type mice derived from two strains during the period of 8-21 postnatal days. Fluorescent double-staining was used to visualize mainly the Purkinje cells in cerebellar slices. In wild types, only normal Purkinje cells of round or regular drop-shaped were present, when staining intensity of other individual cell structures differed in dependence on the age of the animal. In Lurcher mutants, there were still some normal-shaped cells. Nevertheless, depending on the animal's age, a wide variety of stages of the cell degeneration were depicted. The main characteristics of Purkinje cell degeneration in the early stage are: disruption of the continuity of the Purkinje cell layer, dark spots in cell nuclei and an irregular coloring of the cytoplasm. Later, the cells and their nuclei were deformed, often with two main dendrites sprouting from the cell body. Finally, the cell and nucleus margins were unclear, dendrites were significantly thickened, showing signs of shrinkage and fragmentation. Cell nucleoli underwent changes in number and appearance. No differences between the Lurcher mice of both strains (C3H and B6CBA) under examination were found.
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Affiliation(s)
- Zdeňka Purkartová
- Department of Pathophysiology, Medical Faculty in Pilsen, Charles University, Pilsen, Czech Republic
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20
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Remodeling of three-dimensional organization of the nucleus during terminal keratinocyte differentiation in the epidermis. J Invest Dermatol 2013; 133:2191-201. [PMID: 23407401 DOI: 10.1038/jid.2013.66] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/19/2012] [Accepted: 01/09/2013] [Indexed: 01/01/2023]
Abstract
The nucleus of epidermal keratinocytes (KCs) is a complex and highly compartmentalized organelle, whose structure is markedly changed during terminal differentiation and transition of the genome from a transcriptionally active state seen in the basal and spinous epidermal cells to a fully inactive state in the keratinized cells of the cornified layer. Here, using multicolor confocal microscopy, followed by computational image analysis and mathematical modeling, we demonstrate that in normal mouse footpad epidermis, transition of KCs from basal epidermal layer to the granular layer is accompanied by marked differences in nuclear architecture and microenvironment including the following: (i) decrease in the nuclear volume; (ii) decrease in expression of the markers of transcriptionally active chromatin; (iii) internalization and decrease in the number of nucleoli; (iv) increase in the number of pericentromeric heterochromatic clusters; and (v) increase in the frequency of associations between the pericentromeric clusters, chromosomal territory 3, and nucleoli. These data suggest a role for nucleoli and pericentromeric heterochromatin clusters as organizers of nuclear microenvironment required for proper execution of gene expression programs in differentiating KCs, and provide important background information for further analyses of alterations in the topological genome organization seen in pathological skin conditions, including disorders of epidermal differentiation and epidermal tumors.
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21
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Kishi Y, Kondo S, Gotoh Y. Transcriptional activation of mouse major satellite regions during neuronal differentiation. Cell Struct Funct 2012; 37:101-10. [PMID: 22976370 DOI: 10.1247/csf.12009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Recent studies have revealed various biological functions for repetitive sequences, which make up about half of the human genome. One such sequence, major satellites, which are tandem repetitive sequences adjacent to the centromere, have been shown to be a kinetochore component that plays a role in the formation and function of the pericentric heterochromatin necessary for mitosis. However, it is unknown whether these regions also play a role in post-mitotic cells. Here, we show that, during neuronal differentiation, the heterochromatin domains that include major satellite regions become both enriched with the active histone modification lysine-4 trimethylation of histone H3, and more sensitive to nuclease, both of which suggest increased activation of this area. Further supporting this notion, we also found that transcription from major satellite regions is significantly increased during neuronal differentiation both in vitro and in vivo. These results together suggest that the structural and transcriptional state of major satellite regions changes dramatically during neuronal differentiation, implying that this region might play a role in differentiating neurons.
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Affiliation(s)
- Yusuke Kishi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan.
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22
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Baltanás FC, Casafont I, Lafarga V, Weruaga E, Alonso JR, Berciano MT, Lafarga M. Purkinje cell degeneration in pcd mice reveals large scale chromatin reorganization and gene silencing linked to defective DNA repair. J Biol Chem 2011; 286:28287-302. [PMID: 21700704 DOI: 10.1074/jbc.m111.246041] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA repair protects neurons against spontaneous or disease-associated DNA damage. Dysfunctions of this mechanism underlie a growing list of neurodegenerative disorders. The Purkinje cell (PC) degeneration mutation causes the loss of nna1 expression and is associated with the postnatal degeneration of PCs. This PC degeneration dramatically affects nuclear architecture and provides an excellent model to elucidate the nuclear mechanisms involved in a whole array of neurodegenerative disorders. We used immunocytochemistry for histone variants and components of the DNA damage response, an in situ transcription assay, and in situ hybridization for telomeres to analyze changes in chromatin architecture and function. We demonstrate that the phosphorylation of H2AX, a DNA damage signal, and the trimethylation of the histone H4K20, a repressive mark, in extensive domains of genome are epigenetic hallmarks of chromatin in degenerating PCs. These histone modifications are associated with a large scale reorganization of chromatin, telomere clustering, and heterochromatin-induced gene silencing, all of them key factors in PC degeneration. Furthermore, ataxia telangiectasia mutated and 53BP1, two components of the DNA repair pathway, fail to be concentrated in the damaged chromatin compartments, even though the expression levels of their coding genes were slightly up-regulated. Although the mechanism by which Nna1 loss of function leads to PC neurodegeneration is undefined, the progressive accumulation of DNA damage in chromosome territories irreversibly compromises global gene transcription and seems to trigger PC degeneration and death.
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Affiliation(s)
- Fernando C Baltanás
- Laboratory of Neural Plasticity and Neurorepair, Institute for Neuroscience of Castilla y León, Universidad de Salamanca, E-37007 Salamanca, Spain
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23
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Singleton MK, Gonzales ML, Leung KN, Yasui DH, Schroeder DI, Dunaway K, LaSalle JM. MeCP2 is required for global heterochromatic and nucleolar changes during activity-dependent neuronal maturation. Neurobiol Dis 2011; 43:190-200. [PMID: 21420494 DOI: 10.1016/j.nbd.2011.03.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 01/24/2011] [Accepted: 03/11/2011] [Indexed: 10/18/2022] Open
Abstract
Mutations in MECP2, encoding methyl CpG binding protein 2, cause the neurodevelopmental disorder Rett syndrome. MeCP2 is an abundant nuclear protein that binds to chromatin and modulates transcription in response to neuronal activity. Prior studies of MeCP2 function have focused on specific gene targets of MeCP2, but a more global role for MeCP2 in neuronal nuclear maturation has remained unexplored. MeCP2 levels increase during postnatal brain development, coinciding with dynamic changes in neuronal chromatin architecture, particularly detectable as changes in size, number, and location of nucleoli and perinucleolar heterochromatic chromocenters. To determine a potential role for MeCP2 in neuronal chromatin maturational changes, we measured nucleoli and chromocenters in developing wild-type and Mecp2-deficient mouse cortical sections, as well as mouse primary cortical neurons and a human neuronal cell line following induced maturation. Mecp2-deficient mouse neurons exhibited significant differences in nucleolar and chromocenter number and size, as more abundant, smaller nucleoli in brain and primary neurons compared to wild-type, consistent with delayed neuronal nuclear maturation in the absence of MeCP2. Primary neurons increased chromocenter size following depolarization in wild-type, but not Mecp2-deficient cultures. Wild-type MECP2e1 over-expression in human SH-SY5Y cells was sufficient to induce significantly larger nucleoli, but not a T158M mutation of the methyl-binding domain. These results suggest that, in addition to the established role of MeCP2 in transcriptional regulation of specific target genes, the global chromatin-binding function of MeCP2 is essential for activity-dependent global chromatin dynamics during postnatal neuronal maturation.
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Affiliation(s)
- Malaika K Singleton
- Department of Medical Microbiology and Immunology, School of Medicine, Genome Center, and MIND Institute, University of California, Davis, CA 95616, USA
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24
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Jordan BA, Kreutz MR. Nucleocytoplasmic protein shuttling: the direct route in synapse-to-nucleus signaling. Trends Neurosci 2009; 32:392-401. [PMID: 19524307 DOI: 10.1016/j.tins.2009.04.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2008] [Revised: 04/16/2009] [Accepted: 04/24/2009] [Indexed: 02/06/2023]
Abstract
In neurons multiple signaling pathways converge in the nucleus to regulate the expression of genes associated with long-term structural changes of synapto-dendritic input. Of pivotal importance for this type of transcriptional regulation is synapse-to-nucleus communication. Several studies suggest that the nuclear transport of proteins from synapses is involved in this signaling process, including evidence that synapses contain proteins with nuclear localization sequences and components of the nuclear import machinery. Here, we review the evidence for synapse-to-nucleus signaling by means of retrograde transport of proteins from distal processes. We discuss the mechanisms involved in their translocation and their role in the control of nuclear gene expression. Finally, we summarize the current thinking regarding the functional implications of nuclear signaling and address open questions in this evolving area of neuroscience.
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Affiliation(s)
- Bryen A Jordan
- Albert Einstein College of Medicine, Dominick P. Purpura Department of Neuroscience, Bronx, NY 10461, USA
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25
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de Nooijer S, Wellink J, Mulder B, Bisseling T. Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei. Nucleic Acids Res 2009; 37:3558-68. [PMID: 19359359 PMCID: PMC2699506 DOI: 10.1093/nar/gkp219] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The organization of the eukaryote nucleus into functional compartments arises by self-organization both through specific protein-protein and protein-DNA interactions and non-specific interactions that lead to entropic effects, such as e.g. depletion attraction. While many specific interactions have so far been demonstrated, the contributions of non-specific interactions are still unclear. We used coarse-grained molecular dynamics simulations of previously published models for Arabidopsis thaliana chromatin organization to show that non-specific interactions can explain the in vivo localization of nucleoli and chromocenters. Also, we quantitatively demonstrate that chromatin looping contributes to the formation of chromosome territories. Our results are consistent with the previously published Rosette model for Arabidopsis chromatin organization and suggest that chromocenter-associated loops play a role in suppressing chromocenter clustering.
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Affiliation(s)
- S de Nooijer
- Laboratory for Molecular Biology, Wageningen University, Drovendaalsesteeg 1, 6708PB Wageningen, Netherlands
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26
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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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27
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Mateos-Langerak J, Goetze S, Leonhardt H, Cremer T, van Driel R, Lanctôt C. Nuclear architecture: Is it important for genome function and can we prove it? J Cell Biochem 2008; 102:1067-75. [PMID: 17786936 DOI: 10.1002/jcb.21521] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Gene regulation in higher eukaryotes has been shown to involve regulatory sites, such as promoters and enhancers which act at the level of individual genes, and mechanisms which control the functional state of gene clusters. A fundamental question is whether additional levels of genome control exist. Nuclear organization and large-scale chromatin structure may constitute such a level and play an important role in the cell-type specific orchestration of the expression of thousands of genes in eukaryotic cells. Numerous observations indicate a tight correlation between genome activity and nuclear and large-scale chromatin structure. However, causal relationships are rare. Here we explore how these might be uncovered.
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Affiliation(s)
- Julio Mateos-Langerak
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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28
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Rauch J, Knoch TA, Solovei I, Teller K, Stein S, Buiting K, Horsthemke B, Langowski J, Cremer T, Hausmann M, Cremer C. Light optical precision measurements of the active and inactive Prader-Willi syndrome imprinted regions in human cell nuclei. Differentiation 2007; 76:66-82. [PMID: 18039333 DOI: 10.1111/j.1432-0436.2007.00237.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Despite the major advancements during the last decade with respect to both knowledge of higher order chromatin organization in the cell nucleus and the elucidation of epigenetic mechanisms of gene control, the true three-dimensional (3D) chromatin structure of endogenous active and inactive gene loci is not known. The present study was initiated as an attempt to close this gap. As a model case, we compared the chromatin architecture between the genetically active and inactive domains of the imprinted Prader-Willi syndrome (PWS) locus in human fibroblast and lymphoblastoid cell nuclei by 3D fluorescence in situ hybridization and quantitative confocal laser scanning microscopy. The volumes and 3D compactions of identified maternal and paternal PWS domains were determined in stacks of light optical serial sections using a novel threshold-independent approach. Our failure to detect volume and compaction differences indicates that possible differences are below the limits of light optical resolution. To overcome this limitation, spectral precision distance microscopy, a method of localization microscopy at the nanometer scale, was used to measure 3D distances between differentially labeled probes located both within the PWS region and in its neighborhood. This approach allows the detection of intranuclear differences between 3D distances down to about 70-90 nm, but again did not reveal clearly detectable differences between active and inactive PWS domains. Despite this failure, a comparison of the experimental 3D distance measurements with computer simulations of chromatin folding strongly supports a non-random higher order chromatin configuration of the PWS locus and argues against 3D configurations based on giant chromatin loops. Our results indicate that the search for differences between endogenous active and inactive PWS domains must be continued at still smaller scales than hitherto possible with conventional light microscopic procedures. The possibilities to achieve this goal are discussed.
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Affiliation(s)
- Joachim Rauch
- Kirchhoff Institute of Physics, University of Heidelberg, Im Neuenheimer Feld 227, D-69120 Heidelberg, Germany
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29
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Teller K, Solovei I, Buiting K, Horsthemke B, Cremer T. Maintenance of imprinting and nuclear architecture in cycling cells. Proc Natl Acad Sci U S A 2007; 104:14970-5. [PMID: 17848516 PMCID: PMC1986597 DOI: 10.1073/pnas.0704285104] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Indexed: 12/16/2022] Open
Abstract
Dynamic gene repositioning has emerged as an additional level of epigenetic gene regulation. An early example was the report of a transient, spatial convergence (< or =2 microm) of oppositely imprinted regions ("kissing"), including the Angelman syndrome/Prader-Willi syndrome (AS/PWS) locus and the Beckwith-Wiedemann syndrome locus in human lymphocytes during late S phase. It was argued that kissing is required for maintaining opposite imprints in cycling cells. Employing 3D-FISH with a BAC contig covering the AS/PWS region, light optical, serial sectioning, and quantitative 3D-image analysis, we observed that both loci always retained a compact structure and did not form giant loops. Three-dimensional distances measured among various, homologous AS/PWS segments in 393 human lymphocytes, 132 human fibroblasts, and 129 lymphoblastoid cells from Gorilla gorilla revealed a wide range of distances at any stage of interphase and in G(0). At late S phase, 4% of nuclei showed distances < or =2 microm, 49% showed distances >6 microm, and 18% even showed distances >8 microm. A similar distance variability was found for Homo sapiens (HSA) 15 centromeres in a PWS patient with a deletion of the maternal AS/PWS locus and for the Beckwith-Wiedemann syndrome loci in human lymphocytes. A transient kiss during late S phase between loci widely separated at other stages of the cell cycle seems incompatible with known global constraints of chromatin movements in cycling cells. Further experiments suggest that the previously observed convergence of AS/PWS loci during late S phase was most likely a side effect of the convergence of nucleolus organizer region-bearing acrocentric human chromosomes, including HSA 15.
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Affiliation(s)
- Kathrin Teller
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Irina Solovei
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
| | - Karin Buiting
- Institut für Humangenetik, Universitaetsklinikum Essen, Hufelandstrasse 55, 45122 Essen, Germany; and
| | - Bernhard Horsthemke
- Institut für Humangenetik, Universitaetsklinikum Essen, Hufelandstrasse 55, 45122 Essen, Germany; and
| | - Thomas Cremer
- *Department of Biology II, Ludwig Maximilians University, Grosshadernerstrasse 2, 82152 Planegg-Martinsried, Germany
- Munich Center for Integrated Protein Science, 81377 Munich, Germany
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30
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Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet 2007; 8:104-15. [PMID: 17230197 DOI: 10.1038/nrg2041] [Citation(s) in RCA: 585] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The regulation of gene expression is mediated by interactions between chromatin and protein complexes. The importance of where and when these interactions take place in the nucleus is currently a subject of intense investigation. Increasing evidence indicates that gene activation or silencing is often associated with repositioning of the locus relative to nuclear compartments and other genomic loci. At the same time, however, structural constraints impose limits on chromatin mobility. Understanding how the dynamic nature of the positioning of genetic material in the nuclear space and the higher-order architecture of the nucleus are integrated is therefore essential to our overall understanding of gene regulation.
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Affiliation(s)
- Christian Lanctôt
- Department Biologie II, Ludwig-Maximilians Universität, Grosshadernerstr. 2, Planegg-Martinsried, Germany.
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Jordan BA, Fernholz BD, Khatri L, Ziff EB. Activity-dependent AIDA-1 nuclear signaling regulates nucleolar numbers and protein synthesis in neurons. Nat Neurosci 2007; 10:427-35. [PMID: 17334360 DOI: 10.1038/nn1867] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2006] [Accepted: 02/08/2007] [Indexed: 11/08/2022]
Abstract
Neuronal development, plasticity and survival require activity-dependent synapse-to-nucleus signaling. Most studies implicate an activity-dependent regulation of gene expression in this phenomenon. However, little is known about other nuclear functions that are regulated by synaptic activity. Here we show that a newly identified component of rat postsynaptic densities (PSDs), AIDA-1d, can regulate global protein synthesis by altering nucleolar numbers. AIDA-1d binds to the first two postsynaptic density-95/Discs large/zona occludens-1 (PDZ) domains of the scaffolding protein PSD-95 via its C-terminal three amino acids. Stimulation of NMDA receptors (NMDARs), which are also bound to PSD-95, results in a Ca2+-independent translocation of AIDA-1d to the nucleus, where it couples to Cajal bodies and induces Cajal body-nucleolar association. Long-term neuronal stimulation results in an AIDA-1-dependent increase in nucleolar numbers and protein synthesis. We propose that AIDA-1d mediates a link between synaptic activity and control of protein biosynthetic capacity by regulating nucleolar assembly.
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Affiliation(s)
- Bryen A Jordan
- Department of Biochemistry, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA.
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Albiez H, Cremer M, Tiberi C, Vecchio L, Schermelleh L, Dittrich S, Küpper K, Joffe B, Thormeyer T, von Hase J, Yang S, Rohr K, Leonhardt H, Solovei I, Cremer C, Fakan S, Cremer T. Chromatin domains and the interchromatin compartment form structurally defined and functionally interacting nuclear networks. Chromosome Res 2006; 14:707-33. [PMID: 17115328 DOI: 10.1007/s10577-006-1086-x] [Citation(s) in RCA: 194] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 08/04/2006] [Accepted: 08/04/2006] [Indexed: 11/28/2022]
Abstract
In spite of strong evidence that the nucleus is a highly organized organelle, a consensus on basic principles of the global nuclear architecture has not so far been achieved. The chromosome territory-interchromatin compartment (CT-IC) model postulates an IC which expands between chromatin domains both in the interior and the periphery of CT. Other models, however, dispute the existence of the IC and claim that numerous chromatin loops expand between and within CTs. The present study was undertaken to resolve these conflicting views. (1) We demonstrate that most chromatin exists in the form of higher-order chromatin domains with a compaction level at least 10 times above the level of extended 30 nm chromatin fibers. A similar compaction level was obtained in a detailed analysis of a particularly gene-dense chromosome region on HSA 11, which often expanded from its CT as a finger-like chromatin protrusion. (2) We further applied an approach which allows the experimental manipulation of both chromatin condensation and the width of IC channels in a fully reversible manner. These experiments, together with electron microscopic observations, demonstrate the existence of the IC as a dynamic, structurally distinct nuclear compartment, which is functionally linked with the chromatin compartment.
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Affiliation(s)
- Heiner Albiez
- Department of Biology II, LMU Biozentrum, Grosshaderner Strasse 2, 82152, Planegg-Martinsried, Germany
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Vadakkan KI, Li B, De Boni U. Cell-type specific proximity of centromeric domains of one homologue each of chromosomes 2 and 11 in nuclei of cerebellar Purkinje neurons. Chromosoma 2006; 115:395-402. [PMID: 16741706 DOI: 10.1007/s00412-006-0069-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2006] [Revised: 04/15/2006] [Accepted: 04/18/2006] [Indexed: 10/24/2022]
Abstract
In Purkinje neurons of the mouse cerebellum, the centromeres of several chromosomes are placed in close proximity to form a distinct pattern of clusters and exhibit reproducible spatial redistributions during development. In granule neurons, an adjacent cell type in the cerebellum, the pattern, size, and number of centromeric aggregations are different from those of Purkinje neurons. The present work was undertaken to test the hypothesis that the same chromosomes form part of one aggregate in a cell-type-specific manner. Fluorescence in situ hybridization (FISH) with chromosome-specific paracentromeric probes was used to identify centromeric regions of individual chromosomes in cerebellar Purkinje and granule neurons of the adult mouse. When pairs of centromeric probes were used in two-color FISH, one homologue each of chromosomes 2 and 11 were routinely found close to each other in Purkinje neurons but not in granule neurons. This finding of specific proximity was limited to the pair 2 and 11, out of the ten chromosome pairs that were randomly selected and studied. Our results indicate that, in adult Purkinje neurons, a cell-type-specific spatial proximity is present between centromeric domains of one homologue each of chromosomes 2 and 11.
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Affiliation(s)
- Kunjumon I Vadakkan
- Department of Physiology, Faculty of Medicine, University of Toronto, M5S 1A8 Toronto, ON, Canada
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Mayer R, Brero A, von Hase J, Schroeder T, Cremer T, Dietzel S. Common themes and cell type specific variations of higher order chromatin arrangements in the mouse. BMC Cell Biol 2005; 6:44. [PMID: 16336643 PMCID: PMC1325247 DOI: 10.1186/1471-2121-6-44] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 12/07/2005] [Indexed: 11/10/2022] Open
Abstract
Background Similarities as well as differences in higher order chromatin arrangements of human cell types were previously reported. For an evolutionary comparison, we now studied the arrangements of chromosome territories and centromere regions in six mouse cell types (lymphocytes, embryonic stem cells, macrophages, fibroblasts, myoblasts and myotubes) with fluorescence in situ hybridization and confocal laser scanning microscopy. Both species evolved pronounced differences in karyotypes after their last common ancestors lived about 87 million years ago and thus seem particularly suited to elucidate common and cell type specific themes of higher order chromatin arrangements in mammals. Results All mouse cell types showed non-random correlations of radial chromosome territory positions with gene density as well as with chromosome size. The distribution of chromosome territories and pericentromeric heterochromatin changed during differentiation, leading to distinct cell type specific distribution patterns. We exclude a strict dependence of these differences on nuclear shape. Positional differences in mouse cell nuclei were less pronounced compared to human cell nuclei in agreement with smaller differences in chromosome size and gene density. Notably, the position of chromosome territories relative to each other was very variable. Conclusion Chromosome territory arrangements according to chromosome size and gene density provide common, evolutionary conserved themes in both, human and mouse cell types. Our findings are incompatible with a previously reported model of parental genome separation.
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Affiliation(s)
- Robert Mayer
- Ludwig-Maximilians-Universität München, Department Biologie II, Groβhaderner Str 2, 82152 Planegg-Martinsried, Germany
| | - Alessandro Brero
- Ludwig-Maximilians-Universität München, Department Biologie II, Groβhaderner Str 2, 82152 Planegg-Martinsried, Germany
| | - Johann von Hase
- Kirchhoff Institut für Physik, Universität Heidelberg, Germany
| | - Timm Schroeder
- Institute of Stem Cell Research, GSF – National Research Center for Environment and Health, Neuherberg, Germany
| | - Thomas Cremer
- Ludwig-Maximilians-Universität München, Department Biologie II, Groβhaderner Str 2, 82152 Planegg-Martinsried, Germany
| | - Steffen Dietzel
- Ludwig-Maximilians-Universität München, Department Biologie II, Groβhaderner Str 2, 82152 Planegg-Martinsried, Germany
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Kuznetsova IS, Prusov AN, Enukashvily NI, Podgornaya OI. New types of mouse centromeric satellite DNAs. Chromosome Res 2005; 13:9-25. [PMID: 15791408 DOI: 10.1007/s10577-005-2346-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Revised: 10/15/2004] [Accepted: 10/15/2004] [Indexed: 11/28/2022]
Abstract
Genomic databases do not contain complete sequences of the centromeric regions. We created a pUC19-based library of DNA fragments from isolated chromocentres of interphase nuclei. In this library we have found major satellite (MaSat) and two new satellite sequences - MS3 and MS4. The computer analysis of MS3 and MS4 sequences by alignment, fragment curved state and search for MAR motifs in comparison with the mouse major and minor satellite (MiSat) DNA has shown them to be new satellite fragments. Southern blot of MS3 and MS4 with total DNA digested by restriction enzymes shows the ladder characteristic of satellite DNA. 2.2% of the total DNA consists of MS3, the monomer of which is 150 bp long. The MS4 monomer is 300 bp long and accounts for 1.6% of the total DNA. On metaphase chromosomes MS3 and MS4 are located at the centromeric region. FISH analysis of L929 nuclei during the cell cycle showed relative positions of MaSat, MiSat, MS3, and MS4. All mapped satDNA fragments except MaSat belong to the outer layer of the chromocentres in the G0/G1 phase. MS3 is likely to be involved in the centromere formation. The mouse genome contains at least four satDNA types: AT-rich (MaSat and MiSat), and CG-rich (MS3 and MS4).
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Affiliation(s)
- Inna S Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
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Brero A, Easwaran HP, Nowak D, Grunewald I, Cremer T, Leonhardt H, Cardoso MC. Methyl CpG-binding proteins induce large-scale chromatin reorganization during terminal differentiation. ACTA ACUST UNITED AC 2005; 169:733-43. [PMID: 15939760 PMCID: PMC2171616 DOI: 10.1083/jcb.200502062] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Pericentric heterochromatin plays an important role in epigenetic gene regulation. We show that pericentric heterochromatin aggregates during myogenic differentiation. This clustering leads to the formation of large chromocenters and correlates with increased levels of the methyl CpG–binding protein MeCP2 and pericentric DNA methylation. Ectopic expression of fluorescently tagged MeCP2 mimicked this effect, causing a dose-dependent clustering of chromocenters in the absence of differentiation. MeCP2-induced rearrangement of heterochromatin occurred throughout interphase, did not depend on the H3K9 histone methylation pathway, and required the methyl CpG–binding domain (MBD) only. Similar to MeCP2, another methyl CpG–binding protein, MBD2, also increased during myogenic differentiation and could induce clustering of pericentric regions, arguing for functional redundancy. This MeCP2- and MBD2-mediated chromatin reorganization may thus represent a molecular link between nuclear genome topology and the epigenetic maintenance of cellular differentiation.
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MESH Headings
- Animals
- Cell Differentiation/genetics
- Cells, Cultured
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- DNA Methylation
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Epigenesis, Genetic/genetics
- Gene Expression Regulation, Developmental/genetics
- Heterochromatin/genetics
- Heterochromatin/metabolism
- Heterochromatin/ultrastructure
- Histones/genetics
- Histones/metabolism
- Male
- Methyl-CpG-Binding Protein 2
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Muscle, Skeletal/embryology
- Muscle, Skeletal/metabolism
- Muscle, Skeletal/ultrastructure
- Myoblasts, Skeletal/metabolism
- Myoblasts, Skeletal/ultrastructure
- Protein Structure, Tertiary/genetics
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
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Affiliation(s)
- Alessandro Brero
- Department of Biology II, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
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Garagna S, Merico V, Sebastiano V, Monti M, Orlandini G, Gatti R, Scandroglio R, Redi CA, Zuccotti M. Three-dimensional localization and dynamics of centromeres in mouse oocytes during folliculogenesis. J Mol Histol 2005; 35:631-8. [PMID: 15614617 DOI: 10.1007/s10735-004-2190-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: 12/04/2003] [Revised: 01/19/2004] [Indexed: 12/13/2022]
Abstract
Very little is known about oocyte nuclear architecture during folliculogenesis. Using antibodies to reveal centromeres, Hoechst-staining to detect the AT-rich pericentromeric heterochromatin (chromocenters), combined with confocal microscopy for the three-dimensional analysis of the nucleus, we demonstrate that during mouse folliculogenesis the oocyte nuclear architecture undergoes dynamic changes. In oocytes isolated from primordial and primary follicles, centromeres and chromocenters were preferentially located at the periphery of the nucleus. During oocyte growth, centromeres and chromocenters were initially found spread within the nucleus and then progressively clustered around the periphery of the nucleolus. Our results indicate that the oocyte nuclear achitecture is developmentally regulated and they contribute to a further understanding of the role of nuclear organization in the regulation of genome functioning during differentiation and development.
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Affiliation(s)
- Silvia Garagna
- Laboratorio di Biologia dello Sviluppo e Centro di Eccellenza in Biologia Applicata, Universita' degli Studi di Pavia, 27100 Pavia, Italy
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