Chen, B

Estandarte, AK

Hashimoto, T

Lu, JA

Robinson, I

Robinson, IK

Thompson, G

Yusuf, M

UCL Discovery

3D Structure of A Nucleus and ChromosomesFine Structure Investigation of a Human Nucleus with ChromosomesBo Chen1,2, JiaWei Lu2, Teruo Hashimoto3, George Thompson3, Ian Robinson1,2,4As lack of high-resolution tools for direct ac-cesses, our understanding still remains contro-versial on the higher-order structure of human chromosomes between a few tens and hun-dreds of nanometers. In this work, the three-dimensional (3D) spatial structure of a human prophase nucleus and chromosomes was re-vealed by using a powerful 3D imaging tool, serial block-face scanning electron microscopy (SBFSEM). The acquired 3D image provided rich spatial structure information of the human pro-phase nucleus and chromosomes at a resolu-tion of around 50 nm for quantitative analysis in three dimensions.IntroductionWhen we are talking about chromo-somes, the familiar images with X-shape would easily flash into our minds. Did you ever think that the chromosomes could be in other shapes, not the X-shape, with organized structure?A team of researchers from the Lon-don Centre for Nanotechnology, UCL and Tongji University used serial block-face scanning electron microscopy (SB-FSEM) to quantitatively reveal the spa-tial structure of human chromosomes and nucleus. SBFSEM uses a scanning electron microscope (SEM) with a built-in ultra-microtome to do automatic se-rial sectioning for three-dimensional (3D) imaging [1-3]. The work revealed the spatial structure of chromosomes in a human nucleus [4] by the 3D high-resolution microscopy method without flattening samples [5, 6]. The obtained 3D image provided us some unique and vital information which can determine the relative positions of the chromo-somes within the nuclear inner space, and can also make us rather accurately identify the chromosomes by the statis-tic of their 3D structural information such as volumes/sizes, shape and cen-tromere positions.Results and DiscussionsThe original 2D backscattered electron (BSE) micrographs of the human nucleus sample were acquired by SBFSEM mea-surement. After stacking all the obtained Fig. 1: 3D structure of the human nucleus with chromosomes in, with its envelope in light blue and the chromosomes in color.2 • G.I.T. Imaging & Microscopy 4/2017ELECTRON MICROSCOPY2D BSE micrograph slices together, the 3D image of the observed human nu-cleus, with 36 chromosomes out of the whole set of 46 chromosomes, was seg-mented and rendered. The chromosomes were classified into the individual intact ones (shown as yellow and green ones in fig. 1) and the broken ones (shown as red in fig. 1). The research found out that the chro-mosomes are also S-shaped and C- shaped, not only X-shaped, and the larger chromosomes were more likely to be in S shape or C shape, whereas the smaller chromosomes tend to be the familiar X-shape. It also found out that chromo-somes are nonrandomly positioning in the prophase nucleus with the gene-rich chromosomes near the nuclear center and gene-poor ones near the periphery. This nonrandom positioning of the chro-mosomes in prophase also resembles the chromosome territory positioning pat-tern found in interphase: the smaller chromosomes are closer to the center of the nucleus, whereas the larger ones are nearer the periphery. The research team deduced that the chromatin condenses locally into “visible” chromosomes dur-ing the cell cycle. Furthermore, during the chromatin condensation, the sister chromatid pairs were found are not iden-tical in morphology, but kept the volumes similar. From the quantitative analysis of the obtained 3D structure of chromosomes, the volume of base pair was calculated to be 6.69 nm3, and the sister chroma-tids have a well-conserved diameter of about 765nm in cylindrical shape re-gardless of their sizes (see fig. 2 as one of the examples). The research team also proposed a potential new method for identifying human chromosomes, in three dimensions, based on the analysis of their 3D morphology and sizes, but not conducting the multicolor fluorescence in situ hybridization (M-FISH) measure-ments as traditionally done. The method can be used in the future to identify hu-man chromosomes through 3D imaging approaches.ConclusionsThe work has applied a powerful and persuasive method to the biological and biomaterials area and is able to go further in the investigation of the con-densation process of the chromatin by comparing the 3D structure of chromo-somes and nuclei at the different stages of cell cycle using the newly established SBFSEM facility at the Tongji University, Shanghai, China.AcknowledgementThis work was supported by the Biotech-nology and Biological Sciences Research Council (UK), the Engineering and Physi-cal Sciences Research Council (UK) and partially by Tongji University (China).Other InformationText and data are partially courtesy of the London Centre for Nanotechnology. This report is based on the original publica-tion “Three-dimensional positioning and structure of chromosomes in a human prophase nucleus” in Science Advances by Bo Chen, Mohammed Yusuf, Teruo Hashimoto, Ana Katrina Estandarte, George Thompson, Ian Robinson. Link to publication is presented as below: http://advances.sciencemag.org/content/3/7/e1602231 For the “Materials and Methods”, please refer to the above original publication.Affiliation1London Centre for Nanotechnology, Uni-versity College London, UK2School of Materials Science and En-gineering, Tongji University, Shanghai, China3School of Materials, The University of Manchester, UK4Condensed Matter Physics and Materi-als Science Department, Brookhaven Na-tional Laboratory, Upton, NY, USAContact Bo ChenSchool of Materials Science and EngineeringTongji UniversityShanghai, Chinabo.chen@tongji.edu.cnMore information on 3D imaging:  http://bit.ly/IM3DIM More about serial block-face  scanning electron microscopy:  http://bit.ly/SBF-IMAll references: http://bit.ly/IM-Chen[1]Fig. 2: 3D structure of a human  chromosome with sister chromatids  separated by Avizo.G.I.T. Imaging & Microscopy 4/2017 • 3 ELECTRON MICROSCOPY

3D Structure of A Nucleus and Chromosomes: Fine Structure Investigation of a Human Nucleus with Chromosomes

http://discovery.ucl.ac.uk/10049760/1/BoChen_SIM0417.pdf

3D Structure of A Nucleus and Chromosomes: Fine Structure Investigation of a Human Nucleus with Chromosomes

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