FISH analysis at regions of low to moderate gene density (Fig. 3) showed that in three of the four CdLS cell lines, there was no significant change (P > 0.05, Table 3) in regional chromatin compaction compared with wild-type cells.
Because of the reported binding of NIPBL at gene promoters in association with Rpol II and Mediator (36), we selected two regions of low gene and CpG island (CGI) density, 11p12 and 18q22.2 (Fig. 2A and B), one of moderate gene density, 18p11.3 (Fig. 2C), and two regions, 11q13.3 and 19q13.3, of high gene and CGI density (Fig. 2D and E).
In contrast, several probes in a region of moderate gene density on human chromosome 11p13 showed a rather interior position in Hypo-MAA-fixed lymphoblast nuclei, while in BF-fixed nuclei, they were closer to the territory edge (Mahy et al. 2002b).
In the genome, fragments with the highest gene densities are in subgenome LF, fragments with moderate gene densities are in subgenome MF1, and the fragments with the least genes are in subgenome MF2 [ 37, 42].
These subgenomes have been reconstructed by grouping the 24 conserved blocks: the least fractionated subgenome (LF), with the highest gene densities; the medium fractionated subgenome (MF1), with moderate gene densities; and the most fractionated subgenome (MF2), with the lowest gene densities [ 3, 4].
The level of gene loss among the three subgenomes of B. rapa is biased: fragments with the highest gene densities comprise subgenome LF, fragments with moderate gene densities comprise subgenome MF1, and those with the least genes comprise subgenome MF2 [ 41, 42].
In agreement with this, gene expression data from human LCLs show transcripts originating from the high and moderate gene-density regions, while no transcripts are detected in the regions of low gene density (49).
The observed DNA methylation changes were detected predominantly in regions of moderate or high gene density, probably due to the enrichment of probe sets specific to those regions on the BeadChip that was used for this study.
As we found that 87% of the genes were mapped on the 81% most distal parts of chromosome 3B, our result is in agreement with the moderate gradient of gene density along wheat chromosomes suggested by Munkvold et al. [ 13], Devos et al. [ 15], Charles et al. [ 14] and more recently, Choulet et al. [ 16].
Moreover, for CdL223P cells, the extent of decompaction measured at these loci relative to wild-type cells was greater (2.4-fold for 11q13.3 and 3.7-fold for 19q13.3) than that at the regions of moderate to low gene density (<2-fold; Table 3).
As stated in Cutter et al. [ 23], chromosome arms have moderate to high rates of crossover recombination and low gene density and cores have strikingly little recombination despite comprising nearly half of each autosome.
