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Imaging approaches for chromosome structures

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Abstract

This review describes image analyses for chromosome visible structures, focusing on the chromosome imaging system CHIAS (Chromosome Image Analyzing System). CHIAS is the first comprehensive imaging system for the analysis and characterization of plant chromosomes. A simulation method for human vision for capturing band positive regions was developed and used for the image analysis of large plant chromosomes with bands. Applying this method to C-banded Crepis chromosomes enabled recognition of band positive regions as seen by human vision. Furthermore, a new image parameter, condensation pattern was developed and successfully applied to identify small plant chromosomes such as rice and brassicas. Condensation profile (CP) derived from condensation pattern was also effective in developing quantitative chromosome maps. The result was quantitative chromosomal maps of several plants with small chromosomes, including Arabidopsis, diploid brassicas, rapeseed, rice, spinach, and sugarcane. In the final chapter, various applications of imaging techniques to the analysis of pachytene chromosomes, improved visibility of multicolor FISH images, 3D reconstruction of a human chromosome based on cross-section images obtained by a FIB/SEM, automatic extraction of chromosomal regions by machine learning, etc. are described.

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Abbreviations

BAC:

bacterial artificial chromosome

CCD:

charge-coupled device

CEN:

centromere

CHIAS:

Chromosome Image Analyzing System

CP:

condensation profile (density profile at the mid-rib of chromatid)

DAPI:

4,6-diamidino-2-phenylindole

DRWID:

drawing idiogram

EDF:

extended DNA fiber

FIB/SEM:

focused ion beam/scanning electron microscope

FISH:

fluorescence in situ hybridization

Idiogram:

quantitative chromosome map

IRGSP:

International Rice Genome Sequencing Project

LUT:

lookup table

NOR:

nucleolar organizing region

OpenCV:

Open Source Computer Vision Library

PAC:

P1-derived artificial chromosome

PI:

propidium iodide

rDNA:

ribosomal DNA

SDK:

software development kit

Trs-A:

tandem repeat sequence

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Acknowledgements

We thank the members of the Chromosome Link for helpful comments and discussion.

Funding

This work was supported by the grant to K.F. from The Japan Science and Technology Agency (JST) (Strategic International Collaborative Research Program JPMJSC17E2).

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Authors and Affiliations

  1. Graduate School of Pharmaceutical Sciences, Osaka University, Yamada-oka, Suita, Osaka, 565-0871, Japan

    Kiichi Fukui

  2. Kobe Active Aging Research Hub (KAARb), Graduate School of Human Development and Environment, Kobe University, Tsurukabuto, Kobe, 657-8501, Japan

    Seiji Kato

Authors
  1. Kiichi Fukui
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  2. Seiji Kato
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Contributions

KF and SK devised and designed the study. They also performed survey and analysis data. Both authors read and approved the manuscript.

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Correspondence to Kiichi Fukui.

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Supplementary information

ESM 1

Suppl. Video1a. Movie for a reconstructed human chromosome based on 224 cross-sectioned images obtained by FIB/SEM (Wako et al. 2020). For the observation of the surface of a human chromosome, the 3D chromosome image can be rotated in any direction. (MP4 1913 kb)

ESM 2

Suppl. Video1b. Movie for the observation of the chromosome interior by virtual cuts of the 3D chromosome image with a plane at any position and any angle. (MP4 597 kb)

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Fukui, K., Kato, S. Imaging approaches for chromosome structures. Chromosome Res 29, 5–17 (2021). https://doi.org/10.1007/s10577-021-09648-3

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