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Zhou Z, Li K, Yan R, Yu G, Gilpin CJ, Jiang W, Irudayaraj JMK. The transition structure of chromatin fibers at the nanoscale probed by cryogenic electron tomography. NANOSCALE 2019; 11:13783-13789. [PMID: 31211313 PMCID: PMC6688845 DOI: 10.1039/c9nr02042j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The naked DNA inside the nucleus interacts with proteins and RNAs forming a higher order chromatin structure to spatially and temporally control transcription in eukaryotic cells. The 30 nm chromatin fiber is one of the most important determinants of the regulation of eukaryotic transcription. However, the transition of chromatin from the 30 nm inactive higher order structure to the actively transcribed lower order nucleosomal arrays is unclear, which limits our understanding of eukaryotic transcription. Using a method to extract near-native eukaryotic chromatin, we revealed the chromatin structure at the transitional state from the 30 nm chromatin to multiple nucleosomal arrays by cryogenic electron tomography (cryo-ET). Reproducible electron microscopy images revealed that the transitional structure is a branching structure that the 30 nm chromatin hierarchically branches into lower order nucleosomal arrays, indicating chromatin compaction at different levels to control its accessibility during the interphase. We further observed that some of the chromatin fibers on the branching structure have a helix ribbon structure, while the others randomly twist together. Our finding of the chromatin helix ribbon structure on the extracted native chromatin revealed by cryo-ET indicates a complex higher order chromatin organization beyond the beads-on-a-string structure. The hierarchical branching and helix ribbon structure may provide mechanistic insights into how chromatin organization plays a central role in transcriptional regulation and other DNA-related biological processes during diseases such as cancer.
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Affiliation(s)
- Zhongwu Zhou
- Bindley Bioscience Center, Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA.
| | - Kunpeng Li
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN 47907, USA
| | - Rui Yan
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN 47907, USA
| | - Guimei Yu
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN 47907, USA
| | - Christopher J Gilpin
- Life Science Microscopy Facility, Purdue University, West Lafayette, IN 47907, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Science, Purdue University, West Lafayette, IN 47907, USA
| | - Joseph M K Irudayaraj
- Bindley Bioscience Center, Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN 47907, USA. and Department of Bioengineering, College of Engineering, 1103 Everitt Laboratory, 1406 W. Greet Street, Urbana, IL 61801, USA
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Hémonnot CYJ, Ranke C, Saldanha O, Graceffa R, Hagemann J, Köster S. Following DNA Compaction During the Cell Cycle by X-ray Nanodiffraction. ACS NANO 2016; 10:10661-10670. [PMID: 28024349 DOI: 10.1021/acsnano.6b05034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
X-ray imaging of intact biological cells is emerging as a complementary method to visible light or electron microscopy. Owing to the high penetration depth and small wavelength of X-rays, it is possible to resolve subcellular structures at a resolution of a few nanometers. Here, we apply scanning X-ray nanodiffraction in combination with time-lapse bright-field microscopy to nuclei of 3T3 fibroblasts and thus relate the observed structures to specific phases in the cell division cycle. We scan the sample at a step size of 250 nm and analyze the individual diffraction patterns according to a generalized Porod's law. Thus, we obtain information on the aggregation state of the nuclear DNA at a real space resolution on the order of the step size and in parallel structural information on the order of few nanometers. We are able to distinguish nucleoli, heterochromatin, and euchromatin in the nuclei and follow the compaction and decompaction during the cell division cycle.
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Affiliation(s)
- Clément Y J Hémonnot
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Christiane Ranke
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Oliva Saldanha
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Rita Graceffa
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Johannes Hagemann
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
| | - Sarah Köster
- Institute for X-ray Physics, University of Göttingen , Friedrich-Hund-Platz 1, Göttingen 37077, Germany
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Xu W, Wang F, Yu Z, Xin F. Epigenetics and Cellular Metabolism. GENETICS & EPIGENETICS 2016; 8:43-51. [PMID: 27695375 PMCID: PMC5038610 DOI: 10.4137/geg.s32160] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/25/2016] [Accepted: 08/01/2016] [Indexed: 01/03/2023]
Abstract
Living eukaryotic systems evolve delicate cellular mechanisms for responding to various environmental signals. Among them, epigenetic machinery (DNA methylation, histone modifications, microRNAs, etc.) is the hub in transducing external stimuli into transcriptional response. Emerging evidence reveals the concept that epigenetic signatures are essential for the proper maintenance of cellular metabolism. On the other hand, the metabolite, a main environmental input, can also influence the processing of epigenetic memory. Here, we summarize the recent research progress in the epigenetic regulation of cellular metabolism and discuss how the dysfunction of epigenetic machineries influences the development of metabolic disorders such as diabetes and obesity; then, we focus on discussing the notion that manipulating metabolites, the fuel of cell metabolism, can function as a strategy for interfering epigenetic machinery and its related disease progression as well.
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Affiliation(s)
- Wenyi Xu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fengzhong Wang
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhongsheng Yu
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Fengjiao Xin
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Serra F, Di Stefano M, Spill YG, Cuartero Y, Goodstadt M, Baù D, Marti-Renom MA. Restraint-based three-dimensional modeling of genomes and genomic domains. FEBS Lett 2015; 589:2987-95. [PMID: 25980604 DOI: 10.1016/j.febslet.2015.05.012] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/05/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
Chromosomes are large polymer molecules composed of nucleotides. In some species, such as humans, this polymer can sum up to meters long and still be properly folded within the nuclear space of few microns in size. The exact mechanisms of how the meters long DNA is folded into the nucleus, as well as how the regulatory machinery can access it, is to a large extend still a mystery. However, and thanks to newly developed molecular, genomic and computational approaches based on the Chromosome Conformation Capture (3C) technology, we are now obtaining insight on how genomes are spatially organized. Here we review a new family of computational approaches that aim at using 3C-based data to obtain spatial restraints for modeling genomes and genomic domains.
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Affiliation(s)
- François Serra
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Marco Di Stefano
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Yannick G Spill
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Yasmina Cuartero
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Michael Goodstadt
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Davide Baù
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain
| | - Marc A Marti-Renom
- Genome Biology Group, Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain; Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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