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Franek M, Suchánková J, Sehnalová P, Krejčí J, Legartová S, Kozubek S, Večeřa J, Sorokin DV, Bártová E. Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:326-341. [PMID: 26903193 DOI: 10.1017/s1431927616000052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Studies on fixed samples or genome-wide analyses of nuclear processes are useful for generating snapshots of a cell population at a particular time point. However, these experimental approaches do not provide information at the single-cell level. Genome-wide studies cannot assess variability between individual cells that are cultured in vitro or originate from different pathological stages. Immunohistochemistry and immunofluorescence are fundamental experimental approaches in clinical laboratories and are also widely used in basic research. However, the fixation procedure may generate artifacts and prevents monitoring of the dynamics of nuclear processes. Therefore, live-cell imaging is critical for studying the kinetics of basic nuclear events, such as DNA replication, transcription, splicing, and DNA repair. This review is focused on the advanced microscopy analyses of the cells, with a particular focus on live cells. We note some methodological innovations and new options for microscope systems that can also be used to study tissue sections. Cornerstone methods for the biophysical research of living cells, such as fluorescence recovery after photobleaching and fluorescence resonance energy transfer, are also discussed, as are studies on the effects of radiation at the individual cellular level.
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Affiliation(s)
- Michal Franek
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Jana Suchánková
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Petra Sehnalová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Jana Krejčí
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Soňa Legartová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | - Stanislav Kozubek
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
| | | | | | - Eva Bártová
- Institute of Biophysics,Academy of Sciences of the Czech Republic,v.v.i.,Královopolská 135,612 65 Brno,Czech Republic
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102
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Sehgal N, Fritz AJ, Vecerova J, Ding H, Chen Z, Stojkovic B, Bhattacharya S, Xu J, Berezney R. Large-scale probabilistic 3D organization of human chromosome territories. Hum Mol Genet 2016; 25:419-36. [PMID: 26604142 PMCID: PMC4731017 DOI: 10.1093/hmg/ddv479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 11/07/2015] [Accepted: 11/16/2015] [Indexed: 01/13/2023] Open
Abstract
There is growing evidence that chromosome territories (CT) have a probabilistic non-random arrangement within the cell nucleus of mammalian cells including radial positioning and preferred patterns of interchromosomal interactions that are cell-type specific. While it is generally assumed that the three-dimensional (3D) arrangement of genes within the CT is linked to genomic regulation, the degree of non-random organization of individual CT remains unclear. As a first step to elucidating the global 3D organization (topology) of individual CT, we performed multi-color fluorescence in situ hybridization using six probes extending across each chromosome in human WI38 lung fibroblasts. Six CT were selected ranging in size and gene density (1, 4, 12, 17, 18 and X). In-house computational geometric algorithms were applied to measure the 3D distances between every combination of probes and to elucidate data-mined structural patterns. Our findings demonstrate a high degree of non-random arrangement of individual CT that vary from chromosome to chromosome and display distinct changes during the cell cycle. Application of a classic, well-defined data mining and pattern recognition approach termed the 'k-means' generated 3D models for the best fit arrangement of each chromosome. These predicted models correlated well with the detailed distance measurements and analysis. We propose that the unique 3D topology of each CT and characteristic changes during the cell cycle provide the structural framework for the global gene expression programs of the individual chromosomes.
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Affiliation(s)
| | | | | | - Hu Ding
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Zihe Chen
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Branislav Stojkovic
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
| | - Sambit Bhattacharya
- Department of Mathematics and Computer Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
| | - Jinhui Xu
- Department of Computer Science and Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA and
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103
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Maduro C, de Hoon B, Gribnau J. Fitting the Puzzle Pieces: the Bigger Picture of XCI. Trends Biochem Sci 2016; 41:138-147. [DOI: 10.1016/j.tibs.2015.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/08/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023]
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104
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Cheng L, Ming H, Zhu M, Wen B. Long noncoding RNAs as Organizers of Nuclear Architecture. SCIENCE CHINA-LIFE SCIENCES 2016; 59:236-44. [PMID: 26825945 DOI: 10.1007/s11427-016-5012-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/06/2015] [Indexed: 12/25/2022]
Abstract
In the eukaryotic cell nucleus, chromatin and its associated macromolecules must be organized into a higher-ordered conformation to function normally. However, mechanisms underlying the organization and dynamics of the nucleus remain unclear. Long noncoding RNAs (lncRNAs), i.e., transcripts longer than 200 nucleotides with little or no protein-coding capacity, are increasingly recognized as important regulators in diverse biological processes. Recent studies have shown that some lncRNAs are involved in various aspects of genome organization, including the facilitation of chromosomal interactions and establishment of nuclear bodies, suggesting that lncRNAs act as general organizers of the nuclear architecture. Here, we discuss recent advances in this emerging and intriguing field.
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Affiliation(s)
- Lu Cheng
- Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hui Ming
- Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Minzhe Zhu
- Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Bo Wen
- Department of Biochemistry and Molecular Biology and Key Laboratory of Metabolism and Molecular Medicine of Ministry of Education & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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105
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RNA binding proteins implicated in Xist-mediated chromosome silencing. Semin Cell Dev Biol 2016; 56:58-70. [PMID: 26816113 DOI: 10.1016/j.semcdb.2016.01.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 11/20/2022]
Abstract
Chromosome silencing by Xist RNA occurs in two steps; localisation in cis within the nuclear matrix to form a domain that corresponds to the territory of the inactive X chromosome elect, and transduction of silencing signals from Xist RNA to the underlying chromatin. Key factors that mediate these processes have been identified in a series of recent studies that harnessed comprehensive proteomic or genetic screening strategies. In this review we discuss these findings in light of prior knowledge both of Xist-mediated silencing and known functions/properties of the novel factors.
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106
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Sharma R, Meister P. Dosage compensation and nuclear organization: cluster to control chromosome-wide gene expression. Curr Opin Genet Dev 2016; 37:9-16. [PMID: 26748388 DOI: 10.1016/j.gde.2015.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 11/18/2015] [Accepted: 11/25/2015] [Indexed: 11/28/2022]
Abstract
In many species, male and female animals differ in the number of X chromosomes they possess. As a consequence, large scale differences in gene dosage exist between sexes; a phenomenon that is rarely tolerated by the organism for changes in autosome dosage. Several strategies have evolved independently to balance X-linked gene dosage between sexes, named dosage compensation (DC). The molecular basis of DC differs among the three best-studied examples: mammals, fruit fly and nematodes. In this short review, we summarize recent microscopic and chromosome conformation capture data that reveal key features of the compensated X chromosome and highlight the events leading to the establishment of a functional, specialized nuclear compartment, the X domain.
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Affiliation(s)
- Rahul Sharma
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland
| | - Peter Meister
- Cell Fate and Nuclear Organization, Institute of Cell Biology, University of Bern, Switzerland.
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107
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Linhoff MW, Garg SK, Mandel G. A high-resolution imaging approach to investigate chromatin architecture in complex tissues. Cell 2015; 163:246-55. [PMID: 26406379 DOI: 10.1016/j.cell.2015.09.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 05/22/2015] [Accepted: 08/11/2015] [Indexed: 01/08/2023]
Abstract
We present ChromATin, a quantitative high-resolution imaging approach for investigating chromatin organization in complex tissues. This method combines analysis of epigenetic modifications by immunostaining, localization of specific DNA sequences by FISH, and high-resolution segregation of nuclear compartments using array tomography (AT) imaging. We then apply this approach to examine how the genome is organized in the mammalian brain using female Rett syndrome mice, which are a mosaic of normal and Mecp2-null cells. Side-by-side comparisons within the same field reveal distinct heterochromatin territories in wild-type neurons that are altered in Mecp2-null nuclei. Mutant neurons exhibit increased chromatin compaction and a striking redistribution of the H4K20me3 histone modification into pericentromeric heterochromatin, a territory occupied normally by MeCP2. These events are not observed in every neuronal cell type, highlighting ChromATin as a powerful in situ method for examining cell-type-specific differences in chromatin architecture in complex tissues.
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Affiliation(s)
- Michael W Linhoff
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Saurabh K Garg
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Gail Mandel
- Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA.
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108
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Hübner B, Lomiento M, Mammoli F, Illner D, Markaki Y, Ferrari S, Cremer M, Cremer T. Remodeling of nuclear landscapes during human myelopoietic cell differentiation maintains co-aligned active and inactive nuclear compartments. Epigenetics Chromatin 2015; 8:47. [PMID: 26579212 PMCID: PMC4647504 DOI: 10.1186/s13072-015-0038-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 01/08/2023] Open
Abstract
Background Previous studies of higher order chromatin organization in nuclei of mammalian species revealed both structural consistency and species-specific differences between cell lines and during early embryonic development. Here, we extended our studies to nuclear landscapes in the human myelopoietic lineage representing a somatic cell differentiation system. Our longterm goal is a search for structural features of nuclei, which are restricted to certain cell types/species, as compared to features, which are evolutionary highly conserved, arguing for their basic functional roles in nuclear organization. Results Common human hematopoietic progenitors, myeloid precursor cells, differentiated monocytes and granulocytes analyzed by super-resolution fluorescence microscopy and electron microscopy revealed profound differences with respect to global chromatin arrangements, the nuclear space occupied by the interchromatin compartment and the distribution of nuclear pores. In contrast, we noted a consistent organization in all cell types with regard to two co-aligned networks, an active (ANC) and an inactive (INC) nuclear compartment delineated by functionally relevant hallmarks. The ANC is enriched in active RNA polymerase II, splicing speckles and histone signatures for transcriptionally competent chromatin (H3K4me3), whereas the INC carries marks for repressed chromatin (H3K9me3). Conclusions Our findings substantiate the conservation of the recently published ANC-INC network model of mammalian nuclear organization during human myelopoiesis irrespective of profound changes of the global nuclear architecture observed during this differentiation process. According to this model, two spatially co-aligned and functionally interacting active and inactive nuclear compartments (ANC and INC) pervade the nuclear space. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0038-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Barbara Hübner
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany ; School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, Singapore
| | - Mariana Lomiento
- Department of Life Sciences, University of Modena (Unimore), Modena, Italy
| | - Fabiana Mammoli
- Department of Life Sciences, University of Modena (Unimore), Modena, Italy
| | - Doris Illner
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany ; Bundeswehr Institute of Radiobiology, Munich, Germany
| | - Yolanda Markaki
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany
| | - Sergio Ferrari
- Department of Life Sciences, University of Modena (Unimore), Modena, Italy
| | - Marion Cremer
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany
| | - Thomas Cremer
- Department Biology II, Biocenter, Ludwig Maximilians University (LMU), Grosshadernerstr. 2, 82152 Martinsried, Germany
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109
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Stuhlmüller M, Schwarz-Finsterle J, Fey E, Lux J, Bach M, Cremer C, Hinderhofer K, Hausmann M, Hildenbrand G. In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing. NANOSCALE 2015; 7:17938-17946. [PMID: 26463479 DOI: 10.1039/c5nr04141d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.
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Affiliation(s)
- M Stuhlmüller
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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110
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Kirmes I, Szczurek A, Prakash K, Charapitsa I, Heiser C, Musheev M, Schock F, Fornalczyk K, Ma D, Birk U, Cremer C, Reid G. A transient ischemic environment induces reversible compaction of chromatin. Genome Biol 2015; 16:246. [PMID: 26541514 PMCID: PMC4635527 DOI: 10.1186/s13059-015-0802-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
Background Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. Results Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40–700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. Conclusions These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0802-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ina Kirmes
- Institute for Molecular Biology, 55128, Mainz, Germany
| | | | - Kirti Prakash
- Institute for Molecular Biology, 55128, Mainz, Germany.,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany
| | | | | | | | | | - Karolina Fornalczyk
- Institute for Molecular Biology, 55128, Mainz, Germany.,Department of Molecular Biophysics, University of Łódź, Łódź, Poland
| | - Dongyu Ma
- Institute for Molecular Biology, 55128, Mainz, Germany.,Centre for Biomedicine and Medical Technology Mannheim (CBTM), University of Heidelberg, 68167, Mannheim, Germany
| | - Udo Birk
- Institute for Molecular Biology, 55128, Mainz, Germany
| | - Christoph Cremer
- Institute for Molecular Biology, 55128, Mainz, Germany. .,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany.
| | - George Reid
- Institute for Molecular Biology, 55128, Mainz, Germany.
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111
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SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy. Sci Rep 2015; 5:15915. [PMID: 26525406 PMCID: PMC4648340 DOI: 10.1038/srep15915] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 10/01/2015] [Indexed: 11/30/2022] Open
Abstract
Three-dimensional structured illumination microscopy (3D-SIM) is a versatile and accessible method for super-resolution fluorescence imaging, but generating high-quality data is challenging, particularly for non-specialist users. We present SIMcheck, a suite of ImageJ plugins enabling users to identify and avoid common problems with 3D-SIM data, and assess resolution and data quality through objective control parameters. Additionally, SIMcheck provides advanced calibration tools and utilities for common image processing tasks. This open-source software is applicable to all commercial and custom platforms, and will promote routine application of super-resolution SIM imaging in cell biology.
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112
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Ulianov SV, Khrameeva EE, Gavrilov AA, Flyamer IM, Kos P, Mikhaleva EA, Penin AA, Logacheva MD, Imakaev MV, Chertovich A, Gelfand MS, Shevelyov YY, Razin SV. Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains. Genome Res 2015; 26:70-84. [PMID: 26518482 PMCID: PMC4691752 DOI: 10.1101/gr.196006.115] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/26/2015] [Indexed: 01/06/2023]
Abstract
Recent advances enabled by the Hi-C technique have unraveled many principles of chromosomal folding that were subsequently linked to disease and gene regulation. In particular, Hi-C revealed that chromosomes of animals are organized into topologically associating domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. Mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principles of TAD folding in Drosophila melanogaster, we performed Hi-C and poly(A)+ RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e., the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predicts TAD boundaries much worse than active chromatin marks do. Interestingly, inter-TADs correspond to decompacted inter-bands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin. We propose the mechanism of TAD self-assembly based on the ability of nucleosomes from inactive chromatin to aggregate, and lack of this ability in acetylated nucleosomal arrays. Finally, we test this hypothesis by polymer simulations and find that TAD partitioning may be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ekaterina E Khrameeva
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia; Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia
| | | | - Ilya M Flyamer
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Pavel Kos
- Physics Department, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A Mikhaleva
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, RAS, 123182 Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Maxim V Imakaev
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Mikhail S Gelfand
- Institute for Information Transmission Problems (Kharkevich Institute), RAS, 127051 Moscow, Russia; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Yuri Y Shevelyov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, RAS, 123182 Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, RAS, 119334 Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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113
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Abstract
X chromosome inactivation (XCI) is the dosage compensation mechanism that evolved in female mammals to correct the genetic imbalance of X-linked genes between sexes. X chromosome inactivation occurs in early development when one of the two X chromosomes of females is nearly-completely silenced. Differentiating Embryonic Stem cells (ESC) are regarded as a useful tool to study XCI, since they recapitulate many events occurring during early development. In this review we aim to summarise the advances in the field and to discuss the close connection between cell differentiation and X chromosome inactivation, with a particular focus on mouse ESCs.
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Affiliation(s)
- Greta Pintacuda
- />Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
| | - Andrea Cerase
- />EMBL Mouse Biology Unit, Monterotondo, 00015 RM Italy
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114
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Popken J, Koehler D, Brero A, Wuensch A, Guengoer T, Thormeyer T, Wolf E, Cremer T, Zakhartchenko V. Positional changes of a pluripotency marker gene during structural reorganization of fibroblast nuclei in cloned early bovine embryos. Nucleus 2015; 5:542-54. [PMID: 25495180 PMCID: PMC4615807 DOI: 10.4161/19491034.2014.970107] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cloned bovine preimplantation embryos were generated by somatic cell nuclear transfer (SCNT) of bovine fetal fibroblasts with a silent copy of the pluripotency reporter gene GOF, integrated at a single site of a chromosome 13. GOF combines the regulatory Oct4/Pou5f1 sequence with the coding sequence for EGFP. EGFP expression served as a marker for pluripotency gene activation and was consistently detected in preimplantation embryos with 9 and more cells. Three-dimensional radial nuclear positions of GOF, its carrier chromosome territory and non-carrier homolog were measured in nuclei of fibroblasts, and of day 2 and day 4 embryos, carrying 2 to 9 and 15 to 22 cells, respectively. We tested, whether transcriptional activation was correlated with repositioning of GOF toward the nuclear interior either with a corresponding movement of its carrier chromosome territory 13 or via the formation of a giant chromatin loop. A significant shift of GOF away from the nuclear periphery was observed in day 2 embryos together with both carrier and non-carrier chromosome territories. At day 4, GOF, its carrier chromosome territory 13 and the non-carrier homolog had moved back toward the nuclear periphery. Similar movements of both chromosome territories ruled out a specific GOF effect. Pluripotency gene activation was preceded by a transient, radial shift of GOF toward the nuclear interior. The persistent co-localization of GOF with its carrier chromosome territory rules out the formation of a giant chromatin loop during GOF activation.
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Key Words
- (bovine) preimplantation embryos, chromosome territories, nuclear architecture, nuclear reprogramming, pluripotency gene activation, somatic cell nuclear transfer
- BFF, bovine fetal fibroblasts; BTA, Bos taurus; CLSM, confocal laser scanning microscopy; CT, chromosome territory; eADS, enhanced absolute 3D distances to surfaces; IVF, in vitro fertilization; MGA, major embryonic genome activation; GOF, Oct4/Pou5f1-EGF
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Affiliation(s)
- Jens Popken
- a Division of Anthropology and Human Genetics Biocenter ; LMU Munich ; Martinsried , Germany
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115
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Popken J, Brero A, Koehler D, Schmid VJ, Strauss A, Wuensch A, Guengoer T, Graf A, Krebs S, Blum H, Zakhartchenko V, Wolf E, Cremer T. Reprogramming of fibroblast nuclei in cloned bovine embryos involves major structural remodeling with both striking similarities and differences to nuclear phenotypes of in vitro fertilized embryos. Nucleus 2015; 5:555-89. [PMID: 25482066 PMCID: PMC4615760 DOI: 10.4161/19491034.2014.979712] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nuclear landscapes were studied during preimplantation development of bovine embryos, generated either by in vitro fertilization (IVF), or generated as cloned embryos by somatic cell nuclear transfer (SCNT) of bovine fetal fibroblasts, using 3-dimensional confocal laser scanning microscopy (3D-CLSM) and structured illumination microscopy (3D-SIM). Nuclear landscapes of IVF and SCNT embryonic nuclei were compared with each other and with fibroblast nuclei. We demonstrate that reprogramming of fibroblast nuclei in cloned embryos requires changes of their landscapes similar to nuclei of IVF embryos. On the way toward the 8-cell stage, where major genome activation occurs, a major lacuna, enriched with splicing factors, was formed in the nuclear interior and chromosome territories (CTs) were shifted toward the nuclear periphery. During further development the major lacuna disappeared and CTs were redistributed throughout the nuclear interior forming a contiguous higher order chromatin network. At all stages of development CTs of IVF and SCNT embryonic nuclei were built up from chromatin domain clusters (CDCs) pervaded by interchromatin compartment (IC) channels. Quantitative analyses revealed a highly significant enrichment of RNA polymerase II and H3K4me3, a marker for transcriptionally competent chromatin, at the periphery of CDCs. In contrast, H3K9me3, a marker for silent chromatin, was enriched in the more compacted interior of CDCs. Despite these striking similarities, we also detected major differences between nuclear landscapes of IVF and cloned embryos. Possible implications of these differences for the developmental potential of cloned animals remain to be investigated. We present a model, which integrates generally applicable structural and functional features of the nuclear landscape.
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Key Words
- 3D-CLSM, 3-dimensional confocal laser scanning microscopy
- 3D-SIM, 3-dimensional structured illumination microscopy
- B23, nucleophosmin B23
- BTA, Bos taurus
- CDC, chromatin domain cluster
- CT, chromosome territory
- EM, electron microscopy
- ENC, embryonic nuclei with conventional nuclear architecture
- ENP, embryonic nuclei with peripheral CT distribution
- H3K4me3
- H3K4me3, histone H3 with tri-methylated lysine 4
- H3K9me3
- H3K9me3, histone H3 with tri-methylated lysine 9
- H3S10p, histone H3 with phosphorylated serine 10
- IC, interchromatin compartment
- IVF, in vitro fertilization
- MCB, major chromatin body
- PR, perichromatin region
- RNA polymerase II
- RNA polymerase II-S2p, RNA polymerase II with phosphorylated serine 2 of its CTD domain
- RNA polymerase II-S5p, RNA polymerase II with phosphorylated serine 5 of its CTD domain
- SC-35, splicing factor SC-35
- SCNT, somatic cell nuclear transfer.
- bovine preimplantation development
- chromatin domain
- chromosome territory
- embryonic genome activation
- in vitro fertilization (IVF)
- interchromatin compartment
- major EGA, major embryonic genome activation
- somatic cell nuclear transfer (SCNT)
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Affiliation(s)
- Jens Popken
- a Division of Anthropology and Human Genetics ; Biocenter; LMU Munich ; Munich , Germany
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116
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Fraser J, Williamson I, Bickmore WA, Dostie J. An Overview of Genome Organization and How We Got There: from FISH to Hi-C. Microbiol Mol Biol Rev 2015; 79:347-72. [PMID: 26223848 PMCID: PMC4517094 DOI: 10.1128/mmbr.00006-15] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In humans, nearly two meters of genomic material must be folded to fit inside each micrometer-scale cell nucleus while remaining accessible for gene transcription, DNA replication, and DNA repair. This fact highlights the need for mechanisms governing genome organization during any activity and to maintain the physical organization of chromosomes at all times. Insight into the functions and three-dimensional structures of genomes comes mostly from the application of visual techniques such as fluorescence in situ hybridization (FISH) and molecular approaches including chromosome conformation capture (3C) technologies. Recent developments in both types of approaches now offer the possibility of exploring the folded state of an entire genome and maybe even the identification of how complex molecular machines govern its shape. In this review, we present key methodologies used to study genome organization and discuss what they reveal about chromosome conformation as it relates to transcription regulation across genomic scales in mammals.
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Affiliation(s)
- James Fraser
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Iain Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Josée Dostie
- Department of Biochemistry, and Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
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117
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Cerase A, Pintacuda G, Tattermusch A, Avner P. Xist localization and function: new insights from multiple levels. Genome Biol 2015; 16:166. [PMID: 26282267 PMCID: PMC4539689 DOI: 10.1186/s13059-015-0733-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/29/2015] [Indexed: 12/21/2022] Open
Abstract
In female mammals, one of the two X chromosomes in each cell is transcriptionally silenced in order to achieve dosage compensation between the genders in a process called X chromosome inactivation. The master regulator of this process is the long non-coding RNA Xist. During X-inactivation, Xist accumulates in cis on the future inactive X chromosome, triggering a cascade of events that provoke the stable silencing of the entire chromosome, with relatively few genes remaining active. How Xist spreads, what are its binding sites, how it recruits silencing factors and how it induces a specific topological and nuclear organization of the chromatin all remain largely unanswered questions. Recent studies have improved our understanding of Xist localization and the proteins with which it interacts, allowing a reappraisal of ideas about Xist function. We discuss recent advances in our knowledge of Xist-mediated silencing, focusing on Xist spreading, the nuclear organization of the inactive X chromosome, recruitment of the polycomb complex and the role of the nuclear matrix in the process of X chromosome inactivation.
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Affiliation(s)
- Andrea Cerase
- EMBL Mouse Biology Unit, Monterotondo, 00015 (RM), Italy.
| | - Greta Pintacuda
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Anna Tattermusch
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Philip Avner
- EMBL Mouse Biology Unit, Monterotondo, 00015 (RM), Italy. .,Institut Pasteur, Unite de Genetique Moleculaire Murine, CNRS, URA2578, Paris, France.
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118
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The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells. Proc Natl Acad Sci U S A 2015. [PMID: 26195790 DOI: 10.1073/pnas.1503690112] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-chromosome inactivation (XCI) is initiated by the long noncoding RNA Xist, which coats the inactive X (Xi) and targets Polycomb repressive complex 2 (PRC2) in cis. Epigenomic analyses have provided significant insight into Xist binding patterns and chromatin organization of the Xi. However, such epigenomic analyses are limited by averaging of population-wide dynamics and do not inform behavior of single cells. Here we view Xist RNA and the Xi at 20-nm resolution using STochastic Optical Reconstruction Microscopy (STORM) in mouse cells. We observe dynamics at the single-cell level not predicted by epigenomic analysis. Only ∼50 hubs of Xist RNA occur on the Xi in the maintenance phase, corresponding to 50-100 Xist molecules per Xi and contrasting with the chromosome-wide "coat" observed by deep sequencing and conventional microscopy. Likewise, only ∼50 hubs PRC2 are observed. PRC2 and Xist foci are not randomly distributed but showed statistically significant spatial association. Knock-off experiments enable visualization of the dynamics of dissociation and relocalization onto the Xi and support a functional tethering of Xist and PRC2. Our analysis reveals that Xist-PRC2 complexes are less numerous than expected and suggests methylation of nucleosomes in a hit-and-run model.
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119
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Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming. Genes (Basel) 2015; 6:641-61. [PMID: 26193323 PMCID: PMC4584322 DOI: 10.3390/genes6030641] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/08/2015] [Accepted: 07/10/2015] [Indexed: 12/15/2022] Open
Abstract
Dynamic structural properties of chromatin play an essential role in defining cell identity and function. Transcription factors and chromatin modifiers establish and maintain cell states through alteration of DNA accessibility and histone modifications. This activity is focused at both gene-proximal promoter regions and distally located regulatory elements. In the three-dimensional space of the nucleus, distal elements are localized in close physical proximity to the gene-proximal regulatory sequences through the formation of chromatin loops. These looping features in the genome are highly dynamic as embryonic stem cells differentiate and commit to specific lineages, and throughout reprogramming as differentiated cells reacquire pluripotency. Identifying these functional distal regulatory regions in the genome provides insight into the regulatory processes governing early mammalian development and guidance for improving the protocols that generate induced pluripotent cells.
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120
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A Pooled shRNA Screen Identifies Rbm15, Spen, and Wtap as Factors Required for Xist RNA-Mediated Silencing. Cell Rep 2015; 12:562-72. [PMID: 26190105 PMCID: PMC4534822 DOI: 10.1016/j.celrep.2015.06.053] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/21/2015] [Accepted: 06/15/2015] [Indexed: 11/24/2022] Open
Abstract
X-chromosome inactivation is the process that evolved in mammals to equalize levels of X-linked gene expression in XX females relative to XY males. Silencing of a single X chromosome in female cells is mediated by the non-coding RNA Xist. Although progress has been made toward identifying factors that function in the maintenance of X inactivation, the primary silencing factors are largely undefined. We developed an shRNA screening strategy to produce a ranked list of candidate primary silencing factors. Validation experiments performed on several of the top hits identified the SPOC domain RNA binding proteins Rbm15 and Spen and Wtap, a component of the m6A RNA methyltransferase complex, as playing an important role in the establishment of Xist-mediated silencing. Localization analysis using super-resolution 3D-SIM microscopy demonstrates that these factors co-localize with Xist RNA within the nuclear matrix subcompartment, consistent with a direct interaction. An shRNA screen identifies factors implicated in chromosome silencing by Xist RNA Rbm15, Wtap, and Spen are required for Xist-mediated silencing Rbm15 is important for efficient deposition of H3K27me3 on the inactive chromosome Rbm15, Wtap, and Spen co-localize with Xist RNA in perichromatin spaces
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121
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Dixon-McDougall T, Brown C. The making of a Barr body: the mosaic of factors that eXIST on the mammalian inactive X chromosome. Biochem Cell Biol 2015; 94:56-70. [PMID: 26283003 DOI: 10.1139/bcb-2015-0016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
During X-chromosome inactivation (XCI), nearly an entire X chromosome is permanently silenced and converted into a Barr body, providing dosage compensation for eutherians between the sexes. XCI is facilitated by the upregulation of the long non-coding RNA gene, XIST, which coats its chromosome of origin, recruits heterochromatin factors, and silences gene expression. During XCI, at least two distinct types of heterochromatin are established, and in this review we discuss the enrichment of facultative heterochromatin marks such as H3K27me3, H2AK119ub, and macroH2A as well as pericentric heterochromatin marks such as HP1, H3K9me3, and H4K20me3. The extremely stable maintenance of silencing is a product of reinforcing interactions within and between these domains. This paper "Xplores" the current knowledge of the pathways involved in XCI, how the pathways interact, and the gaps in our understanding that need to be filled.
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Affiliation(s)
- Thomas Dixon-McDougall
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Carolyn Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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122
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MacDonald WA, Sachani SS, White CR, Mann MRW. A role for chromatin topology in imprinted domain regulation. Biochem Cell Biol 2015. [PMID: 26222733 DOI: 10.1139/bcb-2015-0032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.
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Affiliation(s)
- William A MacDonald
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Saqib S Sachani
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Carlee R White
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
| | - Mellissa R W Mann
- a Departments of Obstetrics & Gynecology, and Biochemistry, University of Western Ontario, Schulich School of Medicine and Dentistry, London, Ontario, Canada.,b Children's Health Research Institute, 4th Floor, Victoria Research Laboratories, A4-130a, 800 Commissioners Rd E, London, ON N6C 2V5, Canada
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123
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Cremer T, Cremer M, Hübner B, Strickfaden H, Smeets D, Popken J, Sterr M, Markaki Y, Rippe K, Cremer C. The 4D nucleome: Evidence for a dynamic nuclear landscape based on co-aligned active and inactive nuclear compartments. FEBS Lett 2015; 589:2931-43. [PMID: 26028501 DOI: 10.1016/j.febslet.2015.05.037] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/19/2015] [Accepted: 05/20/2015] [Indexed: 02/04/2023]
Abstract
Recent methodological advancements in microscopy and DNA sequencing-based methods provide unprecedented new insights into the spatio-temporal relationships between chromatin and nuclear machineries. We discuss a model of the underlying functional nuclear organization derived mostly from electron and super-resolved fluorescence microscopy studies. It is based on two spatially co-aligned, active and inactive nuclear compartments (ANC and INC). The INC comprises the compact, transcriptionally inactive core of chromatin domain clusters (CDCs). The ANC is formed by the transcriptionally active periphery of CDCs, called the perichromatin region (PR), and the interchromatin compartment (IC). The IC is connected to nuclear pores and serves nuclear import and export functions. The ANC is the major site of RNA synthesis. It is highly enriched in epigenetic marks for transcriptionally competent chromatin and RNA Polymerase II. Marks for silent chromatin are enriched in the INC. Multi-scale cross-correlation spectroscopy suggests that nuclear architecture resembles a random obstacle network for diffusing proteins. An increased dwell time of proteins and protein complexes within the ANC may help to limit genome scanning by factors or factor complexes to DNA exposed within the ANC.
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Affiliation(s)
- Thomas Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany.
| | - Marion Cremer
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Barbara Hübner
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Hilmar Strickfaden
- University of Alberta, Cross Cancer Institute Dept. of Oncology, Edmonton, AB, Canada
| | - Daniel Smeets
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Jens Popken
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Michael Sterr
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Yolanda Markaki
- Biocenter, Department Biology II, Ludwig Maximilians University (LMU), Martinsried, Germany
| | - Karsten Rippe
- German Cancer Research Center (DKFZ) & BioQuant Center, Research Group Genome Organization & Function, Heidelberg, Germany.
| | - Christoph Cremer
- Institute of Molecular Biology (IMB), Mainz and Institute of Pharmacy and Molecular Biotechnology (IPMB), University of Heidelberg, Germany.
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124
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Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Commun 2015; 6:7147. [PMID: 25962338 PMCID: PMC4430122 DOI: 10.1038/ncomms8147] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 04/09/2015] [Indexed: 01/06/2023] Open
Abstract
Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying nuclear structure and organization. Here we report two advances in FISH-based imaging. We first describe the in situ visualization of single-copy regions of the genome using two single-molecule super-resolution methodologies. We then introduce a robust and reliable system that harnesses single-nucleotide polymorphisms (SNPs) to visually distinguish the maternal and paternal homologous chromosomes in mammalian and insect systems. Both of these new technologies are enabled by renewable, bioinformatically designed, oligonucleotide-based Oligopaint probes, which we augment with a strategy that uses secondary oligonucleotides (oligos) to produce and enhance fluorescent signals. These advances should substantially expand the capability to query parent-of-origin-specific chromosome positioning and gene expression on a cell-by-cell basis.
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Affiliation(s)
- Brian J. Beliveau
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alistair N. Boettiger
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, USA
| | - Maier S. Avendaño
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ralf Jungmann
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Ruth B. McCole
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eric F. Joyce
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Caroline Kim-Kiselak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Frédéric Bantignies
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Institut de Génétique Humaine, CNRS UPR 1142, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Chamith Y. Fonseka
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Jelena Erceg
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mohammed A. Hannan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hien G. Hoang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Colognori
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jeannie T. Lee
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - William M. Shih
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xiaowei Zhuang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Howard Hughes Medical Institute, Cambridge, Massachusetts 02138, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Chao-ting Wu
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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125
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Popken J, Graf A, Krebs S, Blum H, Schmid VJ, Strauss A, Guengoer T, Zakhartchenko V, Wolf E, Cremer T. Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications. PLoS One 2015; 10:e0124619. [PMID: 25932910 PMCID: PMC4416817 DOI: 10.1371/journal.pone.0124619] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 03/17/2015] [Indexed: 11/19/2022] Open
Abstract
The present study demonstrates a major remodeling of the nuclear envelope and its underlying lamina during bovine preimplantation development. Up to the onset of major embryonic genome activation (MGA) at the 8-cell stage nuclei showed a non-uniform distribution of nuclear pore complexes (NPCs). NPCs were exclusively present at sites where DNA contacted the nuclear lamina. Extended regions of the lamina, which were not contacted by DNA, lacked NPCs. In post-MGA nuclei the whole lamina was contacted rather uniformly by DNA. Accordingly, NPCs became uniformly distributed throughout the entire nuclear envelope. These findings shed new light on the conditions which control the integration of NPCs into the nuclear envelope. The switch from maternal to embryonic production of mRNAs was accompanied by multiple invaginations covered with NPCs, which may serve the increased demands of mRNA export and protein import. Other invaginations, as well as interior nuclear segments and vesicles without contact to the nuclear envelope, were exclusively positive for lamin B. Since the abundance of these invaginations and vesicles increased in concert with a massive nuclear volume reduction, we suggest that they reflect a mechanism for fitting the nuclear envelope and its lamina to a shrinking nuclear size during bovine preimplantation development. In addition, a deposit of extranuclear clusters of NUP153 (a marker for NPCs) without associated lamin B was frequently observed from the zygote stage up to MGA. Corresponding RNA-Seq data revealed deposits of spliced, maternally provided NUP153 mRNA and little unspliced, newly synthesized RNA prior to MGA, which increased strongly at the initiation of embryonic expression of NUP153 at MGA.
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Affiliation(s)
- Jens Popken
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
- * E-mail: (JP); (EW); (TC)
| | - Alexander Graf
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | | | - Axel Strauss
- Division of Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
| | - Tuna Guengoer
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
| | - Valeri Zakhartchenko
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center, LMU Munich, Munich, Germany
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
- * E-mail: (JP); (EW); (TC)
| | - Thomas Cremer
- Division of Anthropology and Human Genetics, Biocenter, LMU Munich, Planegg-Martinsried, Germany
- * E-mail: (JP); (EW); (TC)
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126
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Lakadamyali M, Cosma MP. Advanced microscopy methods for visualizing chromatin structure. FEBS Lett 2015; 589:3023-30. [PMID: 25896023 DOI: 10.1016/j.febslet.2015.04.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 12/29/2022]
Abstract
In the recent years it has become clear that our genome is not randomly organized and its architecture is tightly linked to its function. While genomic studies have given much insight into genome organization, they mostly rely on averaging over large populations of cells, are not compatible with living cells and have limited resolution. For studying genome organization in single living cells, microscopy is indispensable. In addition, the visualization of biological structures helps to understand their function. Up to now, fluorescence microscopy has allowed us to probe the larger scale organization of chromosome territories in the micron length scales, however, the smaller length scales remained invisible due to the diffraction limited spatial resolution of fluorescence microscopy. Thanks to the advent of super-resolution microscopy methods, we are finally starting to be able to probe the nanoscale organization of chromatin in vivo and these methods have the potential to greatly advance our knowledge about chromatin structure and function relationship.
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Affiliation(s)
- Melike Lakadamyali
- ICFO-Institut de Ciències Fotòniques, Mediterranean Technology Park, 08860 Barcelona, Spain.
| | - Maria Pia Cosma
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain.
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127
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Fornasiero EF, Opazo F. Super-resolution imaging for cell biologists: concepts, applications, current challenges and developments. Bioessays 2015; 37:436-51. [PMID: 25581819 DOI: 10.1002/bies.201400170] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The recent 2014 Nobel Prize in chemistry honored an era of discoveries and technical advancements in the field of super-resolution microscopy. However, the applications of diffraction-unlimited imaging in biology have a long road ahead and persistently engage scientists with new challenges. Some of the bottlenecks that restrain the dissemination of super-resolution techniques are tangible, and include the limited performance of affinity probes and the yet not capillary diffusion of imaging setups. Likewise, super-resolution microscopy has introduced new paradigms in the design of projects that require imaging with nanometer-resolution and in the interpretation of biological images. Besides structural or morphological characterization, super-resolution imaging is quickly expanding towards interaction mapping, multiple target detection and live imaging. Here we review the recent progress of biologists employing super-resolution imaging, some pitfalls, implications and new trends, with the purpose of animating the field and spurring future developments.
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Affiliation(s)
- Eugenio F Fornasiero
- STED Microscopy Group, European Neuroscience Institute, Göttingen, Germany; Department of Neuro- and Sensory-physiology, University of Göttingen, Göttingen, Germany
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