1
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Zhang L, Hu C, Xu Z, Li H, Ye B, Li X, Czajkowsky DM, Shao Z. Quantitative catalogue of mammalian mitotic chromosome-associated RNAs. Sci Data 2024; 11:43. [PMID: 38184632 PMCID: PMC10771512 DOI: 10.1038/s41597-023-02884-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
The faithful transmission of a cell's identity and functionality to its daughters during mitosis requires the proper assembly of mitotic chromosomes from interphase chromatin in a process that involves significant changes in the genome-bound material, including the RNA. However, our understanding of the RNA that is associated with the mitotic chromosome is presently limited. Here, we present complete and quantitative characterizations of the full-length mitotic chromosome-associated RNAs (mCARs) for 3 human cell lines, a monkey cell line, and a mouse cell line derived from high-depth RNA sequencing (3 replicates, 47 M mapped read pairs for each replicate). Overall, we identify, on average, more than 20,400 mCAR species per cell-type (including isoforms), more than 5,200 of which are enriched on the chromosome. Notably, overall, more than 2,700 of these mCARs were previously unknown, which thus also expands the annotated genome of these species. We anticipate that these datasets will provide an essential resource for future studies to better understand the functioning of mCARs on the mitotic chromosome and in the cell.
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Affiliation(s)
- Le Zhang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chuansheng Hu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zeqian Xu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hua Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Bishan Ye
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinhui Li
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Daniel M Czajkowsky
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Zhang L, Ye B, Xu Z, Li X, D M C, Shao Z. Genome-wide identification of mammalian cell-cycle invariant and mitotic-specific macroH2A1 domains. Biosci Trends 2023; 17:393-400. [PMID: 37778979 DOI: 10.5582/bst.2023.01214] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
The histone variant macroH2A has been found to play important regulatory roles in genomic processes, especially in regulating transcriptomes. However, whether macroH2A nucleosomes are retained on mitotic chromosomes to enable maintenance of cell-specific transcriptomes is not known. Here, examining mouse embryonic fibroblast cells (NIH-3T3) with native chromatin immunoprecipitation and sequencing (nChIP-seq), we show that the overwhelming majority (~90%) of macroH2A1 domains identified at the G1/S stage are indeed stably retained on mitotic chromosomes. Unexpectedly though, we also find that there are a number of macroH2A domains that are specific for either mitotic or G1/S cells. Notably, more than 7,000 interphase expressed genes flanked by macroH2A1 domains are loaded with macroH2A1 nucleosomes on the mitotic chromosome to form extended domains. Overall, these results reveal that, while the majority of macroH2A1 domains are indeed faithfully transmitted through the mitotic chromosomes, there is a previously unknown cell-cycle dependent exchange of macroH2A1 nucleosomes at numerous genomic loci, indicating the existence of molecular machineries for this dynamically regulated process. We anticipate that these findings will prove to be essential for the integrity of mitotic progression and the maintenance of cellular identity.
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Affiliation(s)
- Le Zhang
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University, Shanghai, China
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Bishan Ye
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zeqian Xu
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xinhui Li
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Czajkowsky D M
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhifeng Shao
- State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University, Shanghai, China
- Bio-ID Center, Shanghai Jiao Tong University, Shanghai, China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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3
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Schwenke J, Yusuf M, Shemilt LA, Wagner U, Sajid A, Morrison GR, Zhang F, Parsons A, Rau C, Robinson IK. Quantitative phase measurements of human cell nuclei using X-ray ptychography. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1166-1173. [PMID: 34212880 DOI: 10.1107/s1600577521004586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/29/2021] [Indexed: 06/13/2023]
Abstract
The human cell nucleus serves as an important organelle holding the genetic blueprint for life. In this work, X-ray ptychography was applied to assess the masses of human cell nuclei using its unique phase shift information. Measurements were carried out at the I13-1 beamline at the Diamond Light Source that has extremely large transverse coherence properties. The ptychographic diffractive imaging approach allowed imaging of large structures that gave quantitative measurements of the phase shift in 2D projections. In this paper a modified ptychography algorithm that improves the quality of the reconstruction for weak scattering samples is presented. The application of this approach to calculate the mass of several human nuclei is also demonstrated.
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Affiliation(s)
- Jorg Schwenke
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Mohammed Yusuf
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Laura A Shemilt
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Ulrich Wagner
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Atiqa Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi, Pakistan
| | - Graeme R Morrison
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Fucai Zhang
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
| | - Aaron Parsons
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Christoph Rau
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Ian K Robinson
- London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, United Kingdom
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4
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Sajid A, Lalani EN, Chen B, Hashimoto T, Griffin DK, Bhartiya A, Thompson G, Robinson IK, Yusuf M. Ultra-Structural Imaging Provides 3D Organization of 46 Chromosomes of a Human Lymphocyte Prophase Nucleus. Int J Mol Sci 2021; 22:ijms22115987. [PMID: 34206020 PMCID: PMC8198510 DOI: 10.3390/ijms22115987] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/18/2022] Open
Abstract
Three dimensional (3D) ultra-structural imaging is an important tool for unraveling the organizational structure of individual chromosomes at various stages of the cell cycle. Performing hitherto uninvestigated ultra-structural analysis of the human genome at prophase, we used serial block-face scanning electron microscopy (SBFSEM) to understand chromosomal architectural organization within 3D nuclear space. Acquired images allowed us to segment, reconstruct, and extract quantitative 3D structural information about the prophase nucleus and the preserved, intact individual chromosomes within it. Our data demonstrate that each chromosome can be identified with its homolog and classified into respective cytogenetic groups. Thereby, we present the first 3D karyotype built from the compact axial structure seen on the core of all prophase chromosomes. The chromosomes display parallel-aligned sister chromatids with familiar chromosome morphologies with no crossovers. Furthermore, the spatial positions of all 46 chromosomes revealed a pattern showing a gene density-based correlation and a neighborhood map of individual chromosomes based on their relative spatial positioning. A comprehensive picture of 3D chromosomal organization at the nanometer level in a single human lymphocyte cell is presented.
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Affiliation(s)
- Atiqa Sajid
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - El-Nasir Lalani
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
| | - Bo Chen
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- School of Materials Science and Engineering, Tongji University, Shanghai 201804, China
- Key Laboratory of Performance Evolution and Control for Engineering Structures of the Ministry of Education, Tongji University, Shanghai 200092, China
| | - Teruo Hashimoto
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | | | - Archana Bhartiya
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
| | - George Thompson
- Department of Materials, University of Manchester, Oxford Road, Manchester M13 9PL, UK; (T.H.); (G.T.)
| | - Ian K. Robinson
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mohammed Yusuf
- Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi 74800, Pakistan; (A.S.); (E.-N.L.)
- London Centre for Nanotechnology, University College London, London WC1H 0AH, UK; (B.C.); (A.B.); (I.K.R.)
- Correspondence:
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5
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Bhartiya A, Batey D, Cipiccia S, Shi X, Rau C, Botchway S, Yusuf M, Robinson IK. X-ray Ptychography Imaging of Human Chromosomes After Low-dose Irradiation. Chromosome Res 2021; 29:107-126. [PMID: 33786705 PMCID: PMC8328905 DOI: 10.1007/s10577-021-09660-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/15/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022]
Abstract
Studies of the structural and functional role of chromosomes in cytogenetics have spanned more than 10 decades. In this work, we take advantage of the coherent X-rays available at the latest synchrotron sources to extract the individual masses of all 46 chromosomes of metaphase human B and T cells using hard X-ray ptychography. We have produced ‘X-ray karyotypes’ of both heavy metal–stained and unstained spreads to determine the gain or loss of genetic material upon low-level X-ray irradiation doses due to radiation damage. The experiments were performed at the I-13 beamline, Diamond Light Source, Didcot, UK, using the phase-sensitive X-ray ptychography method.
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Affiliation(s)
- Archana Bhartiya
- London Centre for Nanotechnology, University College, London, UK.,Department of Chemistry, University College, London, UK.,Research Complex at Harwell, Harwell Campus, Didcot, UK
| | - Darren Batey
- Diamond Light Source, Harwell Campus, Didcot, UK
| | | | - Xiaowen Shi
- Diamond Light Source, Harwell Campus, Didcot, UK.,Department of Physics, New Mexico State University, Las Cruces, NM, 88003, USA
| | | | | | - Mohammed Yusuf
- London Centre for Nanotechnology, University College, London, UK.,Research Complex at Harwell, Harwell Campus, Didcot, UK.,Centre for Regenerative Medicine and Stem Cell Research, Aga Khan University, Karachi, Pakistan
| | - Ian K Robinson
- London Centre for Nanotechnology, University College, London, UK. .,Research Complex at Harwell, Harwell Campus, Didcot, UK. .,Condensed Matter Physics and Materials Science Division, Brookhaven National Lab, Upton, NY, 11973, USA.
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6
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Feng H, Hockin M, Capecchi M, Gale B, Sant H. Size and shape based chromosome separation in the inertial focusing device. BIOMICROFLUIDICS 2020; 14:064109. [PMID: 33312330 PMCID: PMC7714521 DOI: 10.1063/5.0026281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
In this paper, we use a spiral channel inertial focusing device for isolation and purification of chromosomes, which are highly asymmetric. The method developed is proposed as a sample preparation process for transchromosomic research. The proposed microfluidics-based chromosome separation approach enables rapid, label-free isolation of bioactive chromosomes and is compatible with chromosome buffer. As part of this work, particle force analysis during the separation process is performed utilizing mathematic models to estimate the expected behavior of chromosomes in the channel and the model validated with experiments employing fluorescent beads. The chromosome sample is further divided into subtypes utilizing fluorescent activated cell sorting , including small condensed chromosomes, single chromosomes, and groups of two chromosomes (four sister chromatids). The separation of chromosome subtypes is realized based on their shape differences in the spiral channel device under high flow rate conditions. When chromosomes become aligned in the shear flow, the balance between the inertial focusing force and the Dean flow drag force is determined by the chromosome projection area and aspect ratio, or shape difference, leading to different focusing locations in the channel. The achieved results indicate a new separation regime in inertial microfluidics that can be used for the separation of non-spherical particles based on particle aspect ratios, which could potentially be applied in fields such as bacteria subtype separation and chromosome karyotyping.
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Affiliation(s)
- Haidong Feng
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, USA
| | - Matthew Hockin
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Mario Capecchi
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Bruce Gale
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, USA
| | - Himanshu Sant
- Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, USA
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7
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Brandariz-Nuñez A, Robinson SJ, Evilevitch A. Pressurized DNA state inside herpes capsids-A novel antiviral target. PLoS Pathog 2020; 16:e1008604. [PMID: 32702029 PMCID: PMC7377361 DOI: 10.1371/journal.ppat.1008604] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/05/2020] [Indexed: 01/25/2023] Open
Abstract
Drug resistance in viruses represents one of the major challenges of healthcare. As part of an effort to provide a treatment that avoids the possibility of drug resistance, we discovered a novel mechanism of action (MOA) and specific compounds to treat all nine human herpesviruses and animal herpesviruses. The novel MOA targets the pressurized genome state in a viral capsid, "turns off" capsid pressure, and blocks viral genome ejection into a cell nucleus, preventing viral replication. This work serves as a proof-of-concept to demonstrate the feasibility of a new antiviral target-suppressing pressure-driven viral genome ejection-that is likely impervious to developing drug resistance. This pivotal finding presents a platform for discovery of a new class of broad-spectrum treatments for herpesviruses and other viral infections with genome-pressure-dependent replication. A biophysical approach to antiviral treatment such as this is also a vital strategy to prevent the spread of emerging viruses where vaccine development is challenged by high mutation rates or other evasion mechanisms.
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Affiliation(s)
- Alberto Brandariz-Nuñez
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Scott J. Robinson
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Alex Evilevitch
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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8
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Use of 3D imaging for providing insights into high-order structure of mitotic chromosomes. Chromosoma 2018; 128:7-13. [PMID: 30175387 PMCID: PMC6394650 DOI: 10.1007/s00412-018-0678-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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9
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Robinson I, Yang Y, Zhang F, Lynch C, Yusuf M, Cloetens P. Nuclear incorporation of iron during the eukaryotic cell cycle. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:1490-1497. [PMID: 27787255 PMCID: PMC5082466 DOI: 10.1107/s1600577516012807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 08/08/2016] [Indexed: 05/31/2023]
Abstract
Scanning X-ray fluorescence microscopy has been used to probe the distribution of S, P and Fe within cell nuclei. Nuclei, which may have originated at different phases of the cell cycle, are found to show very different levels of Fe present with a strongly inhomogeneous distribution. P and S signals, presumably from DNA and associated nucleosomes, are high and relatively uniform across all the nuclei; these agree with X-ray phase contrast projection microscopy images of the same samples. Possible reasons for the Fe incorporation are discussed.
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Affiliation(s)
- Ian Robinson
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
- London Centre for Nanotechnology, University College London, London WC1E 6BT, UK
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Yang Yang
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Fucai Zhang
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
- London Centre for Nanotechnology, University College London, London WC1E 6BT, UK
| | - Christophe Lynch
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
- London Centre for Nanotechnology, University College London, London WC1E 6BT, UK
| | - Mohammed Yusuf
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, Oxon OX11 0FA, UK
- London Centre for Nanotechnology, University College London, London WC1E 6BT, UK
| | - Peter Cloetens
- ESRF – The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble, France
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10
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Xiao W, Wu L, Yavas G, Simonyan V, Ning B, Hong H. Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine. Pharmaceutics 2016; 8:E15. [PMID: 27110816 PMCID: PMC4932478 DOI: 10.3390/pharmaceutics8020015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/11/2016] [Accepted: 04/06/2016] [Indexed: 01/15/2023] Open
Abstract
Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics of appearance or responsiveness to medical treatments. Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. However, the public reference genome was derived with the DNA from multiple individuals. As a result of this, the reference genome is incomplete and may misrepresent the sequence variants of the general population. The more reliable solution is to compare sequences of diseased tissue with its own genome sequence derived from tissue in a normal state. As the price to sequence the human genome has dropped dramatically to around $1000, it shows a promising future of documenting the personal genome for every individual. However, de novo assembly of individual genomes at an affordable cost is still challenging. Thus, till now, only a few human genomes have been fully assembled. In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging "third generation sequencing" technologies. We present the currently available de novo assembly and post-assembly software packages for human genome assembly and their requirements for computational infrastructures. We recommend that a combined hybrid assembly with long and short reads would be a promising way to generate good quality human genome assemblies and specify parameters for the quality assessment of assembly outcomes. We provide a perspective view of the benefit of using personal genomes as references and suggestions for obtaining a quality personal genome. Finally, we discuss the usage of the personal genome in aiding vaccine design and development, monitoring host immune-response, tailoring drug therapy and detecting tumors. We believe the precision medicine would largely benefit from bioinformatics solutions, particularly for personal genome assembly.
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Affiliation(s)
- Wenming Xiao
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Leihong Wu
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Gokhan Yavas
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
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11
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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] [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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