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Abstract
The high-order structure of mitotic chromosomes remains to be fully elucidated. How nucleosomes compact at various structural levels into a condensed mitotic chromosome is unclear. Cryogenic preservation and imaging have been applied for over three decades, keeping biological structures close to the native in vivo state. Despite being extensively utilized, this field is still wide open for mitotic chromosome research. In this review, we focus specifically on cryogenic efforts for determining the mitotic nanoscale chromatin structures. We describe vitrification methods, current status, and applications of advanced cryo-microscopy including future tools required for resolving the native architecture of these fascinating structures that hold the instructions to life.
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Affiliation(s)
- Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan.
| | - Safana Farooq
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Brookhaven National Lab, Upton, NY, 11973, USA
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, P.O.Box 3500, Karachi, 74800, Pakistan
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Yusuf M, Kaneyoshi K, Fukui K, Robinson I. Use of 3D imaging for providing insights into high-order structure of mitotic chromosomes. Chromosoma 2019; 128:7-13. [PMID: 30175387 DOI: 10.1007/s00412-018-0678-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/17/2018] [Accepted: 07/24/2018] [Indexed: 11/16/2022]
Abstract
The high-order structure of metaphase chromosomes remains still under investigation, especially the 30-nm structure that is still controversial. Advanced 3D imaging has provided useful information for our understanding of this detailed structure. It is evident that new technologies together with improved sample preparations and image analyses should be adequately combined. This mini review highlights 3D imaging used for chromosome analysis so far with future imaging directions also highlighted.
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Estandarte AK, Botchway S, Lynch C, Yusuf M, Robinson I. The use of DAPI fluorescence lifetime imaging for investigating chromatin condensation in human chromosomes. Sci Rep 2016; 6:31417. [PMID: 27526631 PMCID: PMC4985626 DOI: 10.1038/srep31417] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/19/2016] [Indexed: 12/30/2022] Open
Abstract
Chromatin undergoes dramatic condensation and decondensation as cells transition between the different phases of the cell cycle. The organization of chromatin in chromosomes is still one of the key challenges in structural biology. Fluorescence lifetime imaging (FLIM), a technique which utilizes a fluorophore's fluorescence lifetime to probe changes in its environment, was used to investigate variations in chromatin compaction in fixed human chromosomes. Fixed human metaphase and interphase chromosomes were labeled with the DNA minor groove binder, DAPI, followed by measurement and imaging of the fluorescence lifetime using multiphoton excitation. DAPI lifetime variations in metaphase chromosome spreads allowed mapping of the differentially compacted regions of chromatin along the length of the chromosomes. The heteromorphic regions of chromosomes 1, 9, 15, 16, and Y, which consist of highly condensed constitutive heterochromatin, showed statistically significant shorter DAPI lifetime values than the rest of the chromosomes. Differences in the DAPI lifetimes for the heteromorphic regions suggest differences in the structures of these regions. DAPI lifetime variations across interphase nuclei showed variation in chromatin compaction in interphase and the formation of chromosome territories. The successful probing of differences in chromatin compaction suggests that FLIM has enormous potential for application in structural and diagnostic studies.
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Affiliation(s)
- Ana Katrina Estandarte
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, OX11 0FA, UK
| | - Stanley Botchway
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Oxon, OX11 0QX, UK
| | - Christophe Lynch
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, OX11 0FA, UK
| | - Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, OX11 0FA, UK
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, OX11 0FA, UK
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Yan H, Nazaretski E, Lauer K, Huang X, Wagner U, Rau C, Yusuf M, Robinson I, Kalbfleisch S, Li L, Bouet N, Zhou J, Conley R, Chu YS. Multimodality hard-x-ray imaging of a chromosome with nanoscale spatial resolution. Sci Rep 2016; 6:20112. [PMID: 26846188 PMCID: PMC4742846 DOI: 10.1038/srep20112] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/29/2015] [Indexed: 11/17/2022] Open
Abstract
We developed a scanning hard x-ray microscope using a new class of x-ray nano-focusing optic called a multilayer Laue lens and imaged a chromosome with nanoscale spatial resolution. The combination of the hard x-ray’s superior penetration power, high sensitivity to elemental composition, high spatial-resolution and quantitative analysis creates a unique tool with capabilities that other microscopy techniques cannot provide. Using this microscope, we simultaneously obtained absorption-, phase-, and fluorescence-contrast images of Pt-stained human chromosome samples. The high spatial-resolution of the microscope and its multi-modality imaging capabilities enabled us to observe the internal ultra-structures of a thick chromosome without sectioning it.
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Affiliation(s)
- Hanfei Yan
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Evgeny Nazaretski
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kenneth Lauer
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Xiaojing Huang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ulrich Wagner
- Diamond Light Source Ltd, Didcot, Oxfordshire, OX11 0DE, UK
| | - Christoph Rau
- Diamond Light Source Ltd, Didcot, Oxfordshire, OX11 0DE, UK
| | - Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.,Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Sebastian Kalbfleisch
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Li Li
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Nathalie Bouet
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Juan Zhou
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Ray Conley
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Yong S Chu
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
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Shemilt L, Verbanis E, Schwenke J, Estandarte AK, Xiong G, Harder R, Parmar N, Yusuf M, Zhang F, Robinson IK. Karyotyping human chromosomes by optical and X-ray ptychography methods. Biophys J 2015; 108:706-13. [PMID: 25650937 PMCID: PMC4317545 DOI: 10.1016/j.bpj.2014.11.3456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/27/2014] [Accepted: 11/14/2014] [Indexed: 11/16/2022] Open
Abstract
Sorting and identifying chromosomes, a process known as karyotyping, is widely used to detect changes in chromosome shapes and gene positions. In a karyotype the chromosomes are identified by their size and therefore this process can be performed by measuring macroscopic structural variables. Chromosomes contain a specific number of basepairs that linearly correlate with their size; therefore, it is possible to perform a karyotype on chromosomes using their mass as an identifying factor. Here, we obtain the first images, to our knowledge, of chromosomes using the novel imaging method of ptychography. We can use the images to measure the mass of chromosomes and perform a partial karyotype from the results. We also obtain high spatial resolution using this technique with synchrotron source x-rays.
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Affiliation(s)
- Laura Shemilt
- London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom.
| | - Ephanielle Verbanis
- London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
| | - Joerg Schwenke
- London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
| | - Ana K Estandarte
- London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
| | - Gang Xiong
- London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Ross Harder
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois
| | - Neha Parmar
- London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
| | - Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
| | - Fucai Zhang
- London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
| | - Ian K Robinson
- London Centre for Nanotechnology, University College London, London, United Kingdom; Research Complex at Harwell (RCaH), Rutherford Appleton Laboratory, Harwell Oxford, Didcot, United Kingdom
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Yusuf M, Chen B, Hashimoto T, Estandarte AK, Thompson G, Robinson I. Staining and embedding of human chromosomes for 3-d serial block-face scanning electron microscopy. Biotechniques 2014; 57:302-7. [PMID: 25495730 DOI: 10.2144/000114236] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/21/2014] [Indexed: 11/23/2022] Open
Abstract
The high-order structure of human chromosomes is an important biological question that is still under investigation. Studies have been done on imaging human mitotic chromosomes using mostly 2-D microscopy methods. To image micron-sized human chromosomes in 3-D, we developed a procedure for preparing samples for serial block-face scanning electron microscopy (SBFSEM). Polyamine chromosomes are first separated using a simple filtration method and then stained with heavy metal. We show that the DNA-specific platinum blue provides higher contrast than osmium tetroxide. A two-step procedure for embedding chromosomes in resin is then used to concentrate the chromosome samples. After stacking the SBFSEM images, a familiar X-shaped chromosome was observed in 3-D.
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Affiliation(s)
- Mohammed Yusuf
- London Centre for Nanotechnology, University College London, London, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, UK
| | - Bo Chen
- London Centre for Nanotechnology, University College London, London, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, UK
| | - Teruo Hashimoto
- Corrosion & Protection Centre, School of Materials, The University of Manchester, Manchester, UK
| | - Ana Katrina Estandarte
- London Centre for Nanotechnology, University College London, London, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, UK
| | - George Thompson
- Corrosion & Protection Centre, School of Materials, The University of Manchester, Manchester, UK
| | - Ian Robinson
- London Centre for Nanotechnology, University College London, London, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Oxon, UK
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Tůmová P, Uzlíková M, Wanner G, Nohýnková E. Structural organization of very small chromosomes: study on a single-celled evolutionary distant eukaryote Giardia intestinalis. Chromosoma 2015; 124:81-94. [DOI: 10.1007/s00412-014-0486-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/05/2014] [Accepted: 08/18/2014] [Indexed: 12/30/2022]
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