Applications of image analysis in plant chromosome and chromatin structure study

Abstract

Background: The use of image analysis to understand the structure of chromosome and chromatin is critical to the study of genetic evolution and diversification. Furthermore, a detailed chromosome map and the structure of chromatin in the nucleus may contribute to the plant breeding and the study of fundamental biology and genetics in organisms.

Results: In plants with a fully annotated genome project, such as the Leguminosae species, the integration of genetic information, including DNA sequence data, a linkage map, and the cytological quantitative chromosome map could further improve their genetic value. The numerical parameters of chromocenters in 3D can provide useful genetic information for phylogenetic studies of plant diversity and heterochromatic markers whose epigenetic changes may explain the developmental and environmental changes in the plant genome. Extended DNA fibers combined with fluorescence in situ hybridization revealed the highest spatial resolution of the obtained genome structure. Moreover, image analysis at the nano-scale level using a helium ion microscope revealed the surface structure of chromatin, which consists of chromatin fibers compacted into plant chromosomes.

Conclusions: The studies described in this review sought to measure and evaluate chromosome and chromatin using the image analysis method, which may reduce measurement time and improve resolution. Further, we discussed the development of an effective image analysis to evaluate the structure of chromosome and chromatin. An effective application study of cell biology and the genetics of plants using image analysis methods is expected to be a major propeller in the development of new applications.

Author summary

This review focuses on the development of imaging analysis for the integration chromosome map using chromosome image analyzing system (CHIAS) and fluorescence in situ hybridization (FISH) in important crops, e.g., rice and beans. 3D chromatin structures of chromocenters (CCs) in nuclei and extended DNA fibers (EDFs) for the measurement of DNA repeats and gene sizes are informative for plant genetics. Nano scale imaging using the helium ion microscope (HIM) represents new information about chromatin condensation. We demonstrated how imaging applications subjected to plant chromosomes and chromatin are effective in fundamental biology and genetics in plants.

Graphical abstract

Keywords

CHIAS / chromosome / chromatin / extended DNA fiber / helium ion microscopy / nucleus / plants

References

[1] Sumner,A. T., Evans,H. J. Buckland,R. ( 1971). New technique for distinguishing between human chromosomes. Nat. New Biol., 232 : 31– 32

[2] Caspersson,T., Lomakka,G. ( 1972). Computerized chromosome identification by aid of the quinacrine mustard fluorescence technique. Hereditas, 67 : 103– 110

[3] Zahed,L., Murer-Orlando,M. ( 1989). The application of automated metaphase scanning to direct preparations of chorionic villi. Prenat. Diagn., 9 : 7– 17

[4] Pellicer,J. Leitch,I. ( 2020). The Plant DNA C-values database (release 7. 1): an updated online repository of plant genome size data for comparative studies. New Phytol., 226 : 301– 305

[5] Fukui,K. ( 1986). Standardization of karyotyping plant chromosomes by a newly developed chromosome image analyzing system (CHIAS). Theor. Appl. Genet., 72 : 27– 32

[6] Kakeda,K., Fukui,K. ( 1991). Heterochromatic differentiation in barley chromosomes revealed by C- and N-banding techniques. Theor. Appl. Genet., 81 : 144– 150

[7] KatoS., HiroseT., AkiyamaY., neillC. M.. ( 1997) Manual on the chromosome image analyzing system III, CHIAS III. Res. Report Hokuriku Natl. Agr. Exp. Stn., 1– 76

[8] Nakayama,S. ( 1997). Quantitative chromosome mapping of small plant chromosomes by improved imaging on CHIAS II. Genes Genet. Syst., 72 : 35– 40

[9] Iijima,K., Kakeda,K. ( 1991). Identification and characterization of somatic rice chromosomes by imaging methods. Theor. Appl. Genet., 81 : 597– 605

[10] Fukui,K., Nakayama,S., Ohmido,N., Yoshiaki,H. ( 1998). Quantitative karyotyping of three diploid Brassica species by imaging methods and localization of 45s rDNA loci on the identified chromosomes. Theor. Appl. Genet., 96 : 325– 330

[11] Fukui,K. ( 1991). Somatic chromosome map of rice by imaging methods. Theor. Appl. Genet., 81 : 589– 596

[12] Ito,M., Ohmido,N., Akiyama,Y. ( 2000). Quantitative chromosome map of Arabidopsis thaliana L. by imaging methods. Cytologia (Tokyo), 65 : 325– 331

[13] Langer,P. R., Waldrop,A. A. Ward,D. ( 1981). Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc. Natl. Acad. Sci. USA, 78 : 6633– 6637

[14] Kato,S., Ohmido,N. ( 2009). Image analysis of small plant chromosomes by using an improved system, CHIAS IV. Chromosome Sci., 12 : 43– 50

[15] Choi,H. K., Mun,J. H., Kim,D. J., Zhu,H., Baek,J. M., Mudge,J., Roe,B., Ellis,N., Doyle,J., Kiss,G. B. . ( 2004). Estimating genome conservation between crop and model legume species. Proc. Natl. Acad. Sci. USA., 101 : 15289– 15294

[16] Doyle,J. J. Luckow,M. ( 2003). The rest of the iceberg. Legume diversity and evolution in a phylogenetic context. Plant Physiol., 131 : 900– 910

[17] Jiang,Q. Gresshoff,P. ( 1997). Classical and molecular genetics of the model legume Lotus japonicus. Mol. Plant Microbe Interact., 10 : 59– 68

[18] Udvardi,M. K., Tabata,S., Parniske,M. ( 2005). Lotus japonicus: legume research in the fast lane. Trends Plant Sci., 10 : 222– 228

[19] Sato,S., Nakamura,Y., Kaneko,T., Asamizu,E., Kato,T., Nakao,M., Sasamoto,S., Watanabe,A., Ono,A., Kawashima,K. . ( 2008). Genome structure of the legume, Lotus japonicus. DNA Res., 15 : 227– 239

[20] Ohmido,N., Ishimaru,A., Kato,S., Sato,S., Tabata,S. ( 2010). Integration of cytogenetic and genetic linkage maps of Lotus japonicus, a model plant for legumes. Chromosome Res., 18 : 287– 299

[21] Kataoka,R., Hara,M., Kato,S., Isobe,S., Sato,S., Tabata,S. ( 2012). Integration of linkage and chromosome maps of red clover (Trifolium pratense L. ). Cytogenet. Genome Res., 137 : 60– 69

[22] Sato,S., Isobe,S., Asamizu,E., Ohmido,N., Kataoka,R., Nakamura,Y., Kaneko,T., Sakurai,N., Okumura,K., Klimenko,I. . ( 2005). Comprehensive structural analysis of the genome of red clover (Trifolium pratense L. ). DNA Res., 12 : 301– 364

[23] Dolezel,J. ( 2005). Plant DNA flow cytometry and estimation of nuclear genome size. Ann. Bot., 95 : 99– 110

[24] Avivi,L. ( 1980). Arrangement of chromosomes in the interphase nucleus of plants. Hum. Genet., 55 : 281– 295

[25] Wako,T. ( 2003). Quantitative analysis of nuclear chromocenter in Spiranthes sinensis (Pers. ) Ames. Bioimages, 11 : 97– 103

[26] Ohmido,N. ( 1997). Visual verification of close disposition between a rice A genome-specific DNA sequence (TrsA) and the telomere sequence. Plant Mol. Biol., 35 : 963– 968

[27] Dong,F. ( 1998). Non-Rabl patterns of centromere and telomere distribution in the interphase nuclei of plant cells. Chromosome Res., 6 : 551– 558

[28] Shaw,P. J., Abranches,R., Paula Santos,A., Beven,A. F., Stoger,E., Wegel,E. ( 2002). The architecture of interphase chromosomes and nucleolar transcription sites in plants. J. Struct. Biol., 140 : 31– 38

[29] Prieto,P., Shaw,P. ( 2004). Homologue recognition during meiosis is associated with a change in chromatin conformation. Nat. Cell Biol., 6 : 906– 908

[30] Fujimoto,S., Ito,M., Matsunaga,S. ( 2005). An upper limit of the ratio of DNA volume to nuclear volume exists in plants. Genes Genet. Syst., 80 : 345– 350

[31] Schubert,I. ( 2011). Organization and dynamics of plant interphase chromosomes. Trends Plant Sci., 16 : 273– 281

[32] Nagl,W. ( 1979). Ultrastructure; condensed chromatin in plants is species-specific (karyotypical) but not tissue-specific (functional). Protoplasma, 100 : 53– 71

[33] Tanaka,R. ( 1971). Types of resting nuclei in Orchidaceae. Not. Mag., 84 : 118– 122

[34] IshidaM., FrankP., DoiK.. ( 1983) High quality digital radiographic images: improved detection of low-contrast objects and preliminary clinical studies. Radiographics, 3, 325– 328

[35] FukuiK., TsujimotoH.. ( 1988) Imaging techniques for wheat karyotyping. In: Proc. 7th. Intl. Wheat Genet. Symp., pp. 275– 280

[36] Kikuchi,S., Tanaka,H., Wako,T. ( 2007). Centromere separation and association in the nuclei of an interspecific hybrid between Torenia fournieri and T. baillonii (Scrophulariaceae) during mitosis and meiosis. Genes Genet. Syst., 82 : 369– 375

[37] Poulet,A., Arganda-Carreras,I., Legland,D., Probst,A. V., Andrey,P. ( 2015). NucleusJ: an ImageJ plugin for quantifying 3D images of interphase nuclei. Bioinformatics, 31 : 1144– 1146

[38] Dubos,T., Poulet,A., Gonthier-Gueret,C., Mougeot,G., Vanrobays,E., Li,Y., Tutois,S., Pery,E., Chausse,F., Probst,A. V. . ( 2020). Automated 3D bio-imaging analysis of nuclear organization by NucleusJ 2. 0. Nucleus, 11 : 315– 329

[39] Fransz,P., De Jong,J. H., Lysak,M., Castiglione,M. R. ( 2002). Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc. Natl. Acad. Sci. USA, 99 : 14584– 14589

[40] Yan,S., Zhang,Q., Li,Y., Huang,Y., Zhao,L., Tan,J., He,S. ( 2014). Comparison of chromatin epigenetic modification patterns among root meristem, elongation and maturation zones in maize (Zea mays L. ). Cytogenet. Genome Res., 143 : 179– 188

[41] MatsunagaS., NobukoO.. ( 2006) Tabacco NY-2 cells: from cellular dynamics to omics. In: Biotechnology in Agriculture and Forestry, Nagata, T., Matsuoka, K. and Inze, D. (eds.). Springer-Verlag Berlin Heidelberg, Vol. 8, pp. 51– 63

[42] Kurihara,D., Matsunaga,S., Omura,T., Higashiyama,T. ( 2011). Identification and characterization of plant Haspin kinase as a histone H3 threonine kinase. BMC Plant Biol., 11 : 73

[43] Soppe,W. J., Jasencakova,Z., Houben,A., Kakutani,T., Meister,A., Huang,M. S., Jacobsen,S. E., Schubert,I. Fransz,P. ( 2002). DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J., 21 : 6549– 6559

[44] van Zanten,M., Koini,M. A., Geyer,R., Liu,Y., Brambilla,V., Bartels,D., Koornneef,M., Fransz,P. Soppe,W. ( 2011). Seed maturation in Arabidopsis thaliana is characterized by nuclear size reduction and increased chromatin condensation. Proc. Natl. Acad. Sci. USA, 108 : 20219– 20224

[45] Braszewska-Zalewska,A. ( 2013). Epigenetic modifications of nuclei differ between root meristematic tissues of Hordeum vulgare. Plant Signal Behav., 8

[46] Braszewska-Zalewska,A. J., Wolny,E. A., Smialek,L. ( 2013). Tissue-specific epigenetic modifications in root apical meristem cells of Hordeum vulgare. PLoS One, 8 : e69204

[47] Tessadori,F., van Zanten,M., Pavlova,P., Clifton,R., Pontvianne,F., Snoek,L. B., Millenaar,F. F., Schulkes,R. K., van Driel,R., Voesenek,L. A. . ( 2009). Phytochrome B and histone deacetylase 6 control light-induced chromatin compaction in Arabidopsis thaliana. PLoS Genet., 5 : e1000638

[48] Polosoro,A., Enggarini,W. ( 2019). Global epigenetic changes of histone modification under environmental stresses in rice root. Chromosome Res., 27 : 287– 298

[49] Pooley,A. S., Pardon,J. F. Richards,B. ( 1974). The relation between the unit thread of chromosomes and isolated nucleohistone. J. Mol. Biol., 85 : 533– 549

[50] Skinner,L. G. Ockey,C. ( 1971). Isolation, fractionation and biochemical analysis of the metaphase chromosomes of Microtus agrestis. Chromosoma, 35 : 125– 142

[51] Huberman,J. A. ( 1966). Isolation of metaphase chromosomes from HeLa cells. J. Cell Biol., 31 : 95– 105

[52] Segal,E., Fondufe-Mittendorf,Y., Chen,L., Field,Y., Moore,I. K., Wang,J. P. ( 2006). A genomic code for nucleosome positioning. Nature, 442 : 772– 778

[53] Baldi,S., Korber,P. Becker,P. ( 2020). Beads on a string-nucleosome array arrangements and folding of the chromatin fiber. Nat. Struct. Mol. Biol., 27 : 109– 118

[54] Hans de Jong,J., Fransz,P. ( 1999). High resolution FISH in plants−techniques and applications. Trends Plant Sci., 4 : 258– 263

[55] Schubert,V. ( 2017). Super-resolution microscopy−applications in plant cell research. Front Plant Sci, 8 : 531

[56] Weisshart,K., Houben,A. ( 2020). Prospects and limitations of expansion microscopy in chromatin ultrastructure determination. Chromosome Res., 28 : 355– 368

[57] Fransz,P. F., Alonso-Blanco,C., Liharska,T. B., Peeters,A. J. M., Zabel,P. Jong,J. ( 1996). High-resolution physical mapping in Arabidopsis thaliana and tomato by fluorescence in situ hybridization to extended DNA fibres. Plant J., 9 : 421– 430

[58] Ohmido,N., Kijima,K., Ashikawa,I., de Jong,J. H. ( 2001). Visualization of the terminal structure of rice chromosomes 6 and 12 with multicolor FISH to chromosomes and extended DNA fibers. Plant Mol. Biol., 47 : 413– 421

[59] Szinay,D., Chang,S. B., Khrustaleva,L., Peters,S., Schijlen,E., Bai,Y., Stiekema,W. J., van Ham,R. C., de Jong,H. Klein Lankhorst,R. ( 2008). High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. Plant J., 56 : 627– 637

[60] Dechyeva,D. ( 2006). Molecular organization of terminal repetitive DNA in Beta species. Chromosome Res., 14 : 881– 897

[61] Jackson,S. A., Wang,M. L., Goodman,H. M. ( 1998). Application of fiber-FISH in physical mapping of Arabidopsis thaliana. Genome, 41 : 566– 572

[62] Jiang,J. Gill,B. ( 2006). Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research. Genome, 49 : 1057– 1068

[63] Ohmido,N., Wako,T., Kato,S. ( 2016). Image analysis of DNA fiber and nucleus in plants. Methods Mol. Biol., 1469 : 171– 180

[64] Abramhoff,M. D., Magelhaes,P. J. Ram,S. ( 2004). Image processing with ImageJ. Biophoton. Int., 11 : 36– 42

[65] Stupar,R. M., Lilly,J. W., Town,C. D., Cheng,Z., Kaul,S., Buell,C. R. ( 2001). Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc. Natl. Acad. Sci. USA, 98 : 5099– 5103

[66] Koo,D. H., Singh,B., Jiang,J., Friebe,B., Gill,B. S., Chastain,P. D., Manne,U., Tiwari,H. K. Singh,K. ( 2018). Single molecule mtDNA fiber FISH for analyzing numtogenesis. Anal. Biochem., 552 : 45– 49

[67] McGhee,J. D., Nickol,J. M., Felsenfeld,G. Rau,D. ( 1983). Higher order structure of chromatin: orientation of nucleosomes within the 30 nm chromatin solenoid is independent of species and spacer length. Cell, 33 : 831– 841

[68] Joens,M. S., Huynh,C., Kasuboski,J. M., Ferranti,D., Sigal,Y. J., Zeitvogel,F., Obst,M., Burkhardt,C. J., Curran,K. P., Chalasani,S. H. . ( 2013). Helium Ion Microscopy (HIM) for the imaging of biological samples at sub-nanometer resolution. Sci. Rep., 3 : 3514

[69] Dwiranti,A., Hamano,T., Takata,H., Nagano,S., Guo,H., Onishi,K., Wako,T., Uchiyama,S. ( 2014). The effect of magnesium ions on chromosome structure as observed by helium ion microscopy. Microsc. Microanal., 20 : 184– 188

[70] Sartsanga,C., Phengchat,R., Fukui,K., Wako,T. ( 2021). Surface structures consisting of chromatin fibers in isolated barley (Hordeum vulgare) chromosomes revealed by helium ion microscopy. Chromosome Res., 29 : 81– 94

[71] Wako,T., Yoshida,A., Kato,J., Otsuka,Y., Ogawa,S., Kaneyoshi,K., Takata,H. ( 2020). Human metaphase chromosome consists of randomly arranged chromatin fibres with up to 30-nm diameter. Sci. Rep., 10 : 8948

[72] Legland,D., Arganda-Carreras,I. ( 2016). MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. Bioinformatics, 32 : 3532– 3534

[73] Steger,C. ( 1998). An unbiased detector of curvilinear structures. IEEE PAMI, 20 : 113– 125

[74] Poirier,M. G. Marko,J. ( 2002). Mitotic chromosomes are chromatin networks without a mechanically contiguous protein scaffold. Proc. Natl. Acad. Sci. USA, 99 : 15393– 15397

[75] Engelhardt,M. ( 2004). Condensation of chromatin in situ by cation-dependent charge shielding and aggregation. Biochem. Biophys. Res. Commun., 324 : 1210– 1214

[76] Strick,R., Strissel,P. L., Gavrilov,K. ( 2001). Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes. J. Cell Biol., 155 : 899– 910

[77] Dwiranti,A., Takata,H. ( 2019). Reversible changes of chromosome structure upon different concentrations of divalent cations. Microsc. Microanal., 25 : 817– 821

[78] Phengchat,R., Takata,H., Morii,K., Inada,N., Murakoshi,H., Uchiyama,S. ( 2016). Calcium ions function as a booster of chromosome condensation. Sci. Rep., 6 : 38281

[79] Dong,Y., Xie,M., Jiang,Y., Xiao,N., Du,X., Zhang,W., Tosser-Klopp,G., Wang,J., Yang,S., Liang,J. . ( 2013). Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat. Biotechnol., 31 : 135– 141

[80] Zhou,S., Bechner,M. C., Place,M., Churas,C. P., Pape,L., Leong,S. A., Runnheim,R., Forrest,D. K., Goldstein,S., Livny,M. . ( 2007). Validation of rice genome sequence by optical mapping. BMC Genomics, 8 : 278

[81] Young,N. D., Oldroyd,G. E., Geurts,R., Cannon,S. B., Udvardi,M. K., Benedito,V. A., Mayer,K. F., Gouzy,J., Schoof,H. . ( 2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 480 : 520– 524

[82] Zhou,S., Wei,F., Nguyen,J., Bechner,M., Potamousis,K., Goldstein,S., Pape,L., Mehan,M. R., Churas,C., Pasternak,S. . ( 2009). A single molecule scaffold for the maize genome. PLoS Genet., 5 : e1000711

[83] Shearer,L. A., Anderson,L. K., de Jong,H., Smit,S., Goicoechea,J. L., Roe,B. A., Hua,A., Giovannoni,J. J. Stack,S. ( 2014). Fluorescence in situ hybridization and optical mapping to correct scaffold arrangement in the tomato genome. G3 (Bethesda), 4 : 1395– 1405

[84] Lou,Q., Iovene,M., Spooner,D. M., Buell,C. R. ( 2010). Evolution of chromosome 6 of Solanum species revealed by comparative fluorescence in situ hybridization mapping. Chromosoma, 119 : 435– 442

[85] Jiang,J. ( 2019). Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res., 27 : 153– 165

[86] Ishii,T., Schubert,V., Khosravi,S., Dreissig,S., Metje-Sprink,J., Sprink,T., Fuchs,J., Meister,A. ( 2019). RNA-guided endonuclease−in situ labelling (RGEN-ISL): a fast CRISPR/Cas9-based method to label genomic sequences in various species. New Phytol., 222 : 1652– 1661

[87] Nagaki,K. ( 2020). Decrosslinking enables visualization of RNA-guided endonuclease—in situ labeling signals for DNA sequences in plant tissues. J. Exp. Bot., 71 : 1792– 1800

ABBREVIATIONS

FISH	Fluorescence in situ hybridization
CCs	Chromocenters
CHIAS	Chromosome image analyzing system
HIM	Helium ion microscopy
CP	Condensation pattern
EDFs	Extended DNA fibers
mtDNA	Mitochondrial DNA
SE	Secondary electrons

ACKNOWLEDGEMENTS

This work was supported by “e-ASIA Joint Research Program”, “Development of nano-visualization for structural analyses of genetic materials and early infection process for further innovation of functional bio-nanotechnology” from SICORP, and the Mobility Plus Project (No. JPJSBP 120203507) (to NO). This work was also supported by “The 51st Research Grants in the Natural Sciences” from The Mitsubishi Foundation and Nanotechnology Platform of MEXT (No. JPMXP09F20OS0004 (to NO). We thank the Nanotechnology Open Facilities Center in Osaka University for allowing us to conduct our HIM observation. Further, we would like to thank Dr. Kimihiro Norizawa from Osaka University for all his guidance regarding the HIM technique as well as Editage (www.editage.com) for English language editing.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Nobuko Ohmido, Astari Dwiranti, Seiji Kato and Kiichi Fukui declare that they have no conflict of interest or financial conflicts to disclose.

The article is a review article and does not contain any human or animal subjects performed by any of the authors.

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