Toshiyuki Wako

Cell cycle-dependent and lysine residue-specific dynamic changes of histone H4 acetylation in barley.

Histone acetylation affects chromatin conformation and regulates various cellular functions, such as transcription and cell cycle progression. Although mitosis dependent transcriptional silencing and large-scale chromatin structural changes are well established, acetylation of histone H4 during the mitosis is poorly understood in plants. Here, the dynamics of acetylation of histone H4 in defined genome regions has been examined in the fixed barley cells throughout the mitosis by three-dimensional microscopy. Patterns of strong acetylation of the two lysine residues K5 and K16 of histone H4 in the barley genomes were found to be different. In interphase nuclei, H4 acetylated at K16 was associated with the gene-rich, telomere-associated hemispheres, whereas K5 acetylation was detected in centromeric regions where the heterochromatin is distributed. Regions of strong K5 acetylation changed dynamically as the cell cycle proceeded. At prometaphase, centromeric acetylation at K5 decreased suddenly, with accompanying rapid increases of acetylation in the nucleolar organizing regions (NORs). Reverse changes occurred at telophase. On the other hand, the strongly acetylated regions of the K16 showed changes compatible with transcriptional activities and chromosome condensation throughout the cell cycle. Telomeric acetylation at K16 was detected throughout the cell cycle, although it was reduced at metaphase which corresponds to the most condensed stage of the chromosomes. It is concluded that dynamic changes in H4 acetylation occur in a lysine residue-, stage-, and region-specific manner and that they correlate with changes in the chromosome structure through the cell cycle.

Flow karyotypes and chromosomal DNA contents of genus Triticum species and rye (Secale cereale)

The flow cytometry and chromosome imaging method were jointly used for analyzing genome content and chromosomal DNA content of hexaploid wheat (AABBDD), hexaploid triticale (AABBRR), tetraploid wheat (AABB), and AA, BB, DD genome donors and RR genome rye. Their genome sizes were 34.4 pg, 40.9 pg, 26.2 pg, 12.1 pg, 13.7 pg, 10.5 pg, and 16.9 pg, respectively. The 2C nuclear DNA content of BB genome donor with 13.7 pg was the highest value among the other genome donors, AA or DD. The genome content of tetraploid wheat, unlike hexaploid wheat or hexaploid triticale, was larger than the sum of the genomes of AA and BB genome donors. The DNA content of each chromosome ranged from 1.22 pg in DD genome donor to 2.61 pg in rye. Each chromosome peak was divided into three to four groups. Only one chromosome was included in the highest chromosomal DNA peak in hexaploid wheat, tetraploid wheat, DD genome donor and rye but two chromosomes in AA, BB genome donors, and hexaploid triticale. Correlation between 2C nuclear DNA content and chromosome density volume was the highest value compared with the other chromosomal parameters of chromosome area, or chromosome length.

Comparative analysis of topographic distribution of acetylated histone H4 by using confocal microscopy and a deconvolution system

Recent data demonstrate the close links between histone acetylation and basic cell processes. The spatial distribution of acetylated histone H4 was studied using two three-dimensional microscopical systems, confocal microscopy and a deconvolution system. Both systems provide satisfactory three-dimensional digital images. Acetylation of histone H4 at lysine 5 occurred throughout the whole nucleus except for the nucleolus, and highly acetylated regions clustered close to the surface of the nucleus. Internal details of these regions, invisible by confocal microscopy, were revealed by the deconvolution system. On the other hand, the deconvolution system failed to detect scattered nuclear signals which were clearly observed by the confocal microscopy. Deconvolution of the images obtained by confocal microscopy made the image a little clearer, but was not particularly useful.

Smallness: gain and loss in plant chromosome research

Once, a good microscope was the pride of a laboratory in the field of cytology and cytogenetics. Now the situation seems to have completely changed. Biochemical and molecular biological equipment replace the position of microscopes even in the laboratories of cytology and cytogenetics. In this paper, the importance of the visual sense to the study of small plant chromosomes is again demonstrated through typical examples. New methodologies related to visual approaches in chromosome research are also reviewed based on the results obtained mainly in our research group. Smallness is, thus, no longer disadvantageous for chromosome research.

The Effect of Magnesium Ions on Chromosome Structure as Observed by Helium Ion Microscopy

One of the few conclusions known about chromosome structure is that Mg2+ is required for the organization of chromosomes. Scanning electron microscopy is a powerful tool for studying chromosome morphology, but being nonconductive, chromosomes require metal/carbon coating that may conceal information about the detailed surface structure of the sample. Helium ion microscopy (HIM), which has recently been developed, does not require sample coating due to its charge compensation system. Here we investigated the structure of isolated human chromosomes under different Mg2+ concentrations by HIM. High-contrast and resolution images from uncoated samples obtained by HIM enabled investigation on the effects of Mg2+ on chromosome structure. Chromatin fiber information was obtained more clearly with uncoated than coated chromosomes. Our results suggest that both overall features and detailed structure of chromatin are significantly affected by different Mg2+ concentrations. Chromosomes were more condensed and a globular structure of chromatin with 30 nm diameter was visualized with 5 mM Mg2+ treatment, while 0 mM Mg2+ resulted in a less compact and more fibrous structure 11 nm in diameter. We conclude that HIM is a powerful tool for investigating chromosomes and other biological samples without requiring metal/carbon coating.

Development of a quantitative pachytene chromosome map and its unification with somatic chromosome and linkage maps of rice (Oryza sativa L.)

A quantitative pachytene chromosome map of rice (Oryza sativa L.) was developed using imaging methods. The map depicts not only distribution patterns of chromomeres specific to pachytene chromosomes, but also the higher order information of chromosomal structures, such as heterochromatin (condensed regions), euchromatin (decondensed regions), the primary constrictions (centromeres), and the secondary constriction (nucleolar organizing regions, NOR). These features were image analyzed and quantitatively mapped onto the map by Chromosome Image Analyzing System ver. 4.0 (CHIAS IV). Correlation between H3K9me2, an epigenetic marker and formation and/or maintenance of heterochromatin, thus was, clearly visualized. Then the pachytene chromosome map was unified with the existing somatic chromosome and linkage maps by physically mapping common DNA markers among them, such as a rice A genome specific tandem repeat sequence (TrsA), 5S and 45S ribosomal RNA genes, five bacterial artificial chromosome (BAC) clones, four P1 bacteriophage artificial chromosome (PAC) clones using multicolor fluorescence in situ hybridization (FISH). Detailed comparison between the locations of the DNA probes on the pachytene chromosomes using multicolor FISH, and the linkage map enabled determination of the chromosome number and short/long arms of individual pachytene chromosomes using the chromosome number and arm assignment designated for the linkage map. As a result, the quantitative pachytene chromosome map was unified with two other major rice chromosome maps representing somatic prometaphase chromosomes and genetic linkages. In conclusion, the unification of the three rice maps serves as an indispensable basic information, not only for an in-depth comparison between genetic and chromosomal data, but also for practical breeding programs.

Image Analysis of DNA Fiber and Nucleus in Plants.

Advances in cytology have led to the application of a wide range of visualization methods in plant genome studies. Image analysis methods are indispensable tools where morphology, density, and color play important roles in the biological systems. Visualization and image analysis methods are useful techniques in the analyses of the detailed structure and function of extended DNA fibers (EDFs) and interphase nuclei. The EDF is the highest in the spatial resolving power to reveal genome structure and it can be used for physical mapping, especially for closely located genes and tandemly repeated sequences. One the other hand, analyzing nuclear DNA and proteins would reveal nuclear structure and functions. In this chapter, we describe the image analysis protocol for quantitatively analyzing different types of plant genome, EDFs and interphase nuclei.