Table 1.
List of primary antibodies used in the present study.
Figure 1.
Karyotyping of immunolabelled metaphase chromosomes.
(A-C) Original image of chromosomal distribution of H3K4me2 from a maize inbred line (chang7-2) (2D). (D-F) Enhancement of the contrast of the original image by three-dimensional reconstruction after deconvolution (3D). (A, D) 4, 6-diamidino-2-phenylindole (DAPI) staining signals in blue, (B, E) immunostaining signals in green and (C, F) merge of both. (G, H) FISH karyogram constructed from the same spread. Assignments of pseudo-colors to each probe: TAG as white, CentC as green, 45s rDNA as yellow and knob 180-bp as red. (G) Metaphase chromosome identification by combining the four probes and DAPI staining. (H) Ideogram of FISH karyotype indicating the position of the four probes. (I) Karyogram of the H3K4me2 profile constructed from the immunolabelled chromosomes by three-dimensional reconstruction after deconvolution. NOR: nucleolus organizing regions. Scale bar = 10 µm.
Figure 2.
Comparison of the chromosomal distribution of six histone modifications of five maize lines.
The 3D immunolabelled (H3K4me2, H3K4me3, H3K9ac, H4K5ac, H3K9me2, and H3K27me2) and DAPI stained chromosomes of four maize inbred lines (B73, Mo17, Chang7-2 and Zheng58) and a hybrid: ZD958 (Chang7-2×Zheng58)) in figure S1 to figure S6 were arranged in the order of the maize chromosome number (1−10). Immunostaining signals in green and DAPI staining signals in blue. Scale bar = 10 µm.
Figure 3.
Ideogram of FISH karyotype of four maize lines.
The four maize lines include B73, Mo17, Zheng58 and ZD958 (Chang7-2×Zheng58). Assignments of pseudo-colors to each probe: TAG as white, CentC as green, 45S rDNA as yellow and knob 180-bp as red.
Figure 4.
Characterization of chang7-2 metaphase chromosomes by FISH, immunostaining and DAPI signals.
(A) FISH karyogram. TAG as white, CentC as green, 45S rDNA as yellow and knob 180-bp as red. (B, D, F and H) Image of immunofluorescence signals (green) and DAPI staining signals (blue) after 3D deconvolution. (C, E. G and I) Immunostaining karyogram. Scale bar = 10 µm.
Figure 5.
Comparison of H3K4me3 and FISH signal distribution in Z. mays ssp. parviglumis and Z. nicaraguensis.
(A, E) 2D image of DAPI staining (blue) signals and H3K4me3 signals (green). (B, F) Image of DAPI staining (blue) signals and H3K4me3 signals (green) after 3D deconvolution. (C, G) Metaphase chromosome identification by combination of the four probes and DAPI staining; Assignments of pseudo-colors to each probe: TAG as white (pseudo-color), CentC as green, 45S rDNA as yellow (pseudo-color) and knob 180-bp as red. (D, H) H3K4me3 and FISH karyotypes in Z. mays ssp. parviglumis and Z. nicaraguensis. Scale bar = 10 µm.
Figure 6.
Comparison of H3K4me3 distribution of across interphase nuclei and metaphase chromosomes in B73.
Immunolabelled metaphase chromosomes (DAPI staining signals in blue and immunosignals in green) by H3K4me3 are aligned with the distribution of H3K4me3 and DNA methylation in the equivalent interphase nuclei assembled from ChIP-seq data [31]. Each chromosome was divided into 10 Mb intervals. The left vertical axis indicates the number of unique reads per 10 Mb of H3K4me3 (blue curve), and the right vertical axis indicates the number of unique reads per 10 Mb of DNA methylation (red curve).
Figure 7.
Comparison of the distribution of H3K9ac across interphase nuclei and metaphase chromosomes in B73.
Immunolabelled metaphase chromosomes (DAPI staining signals in blue and immunosignals in green) by H3K9ac are aligned with the distribution of H3K9ac and DNA methylation in the equivalent interphase nuclei assembled from ChIP-seq data [31]. Each chromosome was divided into 10 Mb intervals. The left vertical axis indicates the number of unique reads per 10 Mb of H3K9ac (blue curve), and the right vertical axis indicates the number of unique reads per 10 Mb of DNA methylation (red curve).
Figure 8.
Histone modifications at 180-bp knobs in chang7-2 root nuclei.
(A) 2D image. DAPI staining signals in blue, immunosignals in green and knob 180-bp signals in red. (B) Image after 3D deconvolution. (C) The intensity signals along the white line. The horizontal axis indicates the location of the selected chromatin, and the vertical axis indicates the grey level. Scale bar = 5 µm.