Mitotic chromosomes harbor cell type and species specific architectural features

The architecture of mammalian mitotic chromosomes is considered to be universal across species and cell types. However, some studies suggest that features of mitotic chromosomes might be cell type or species specific. We previously reported that CTCF binding in human differentiated cell lines is lost in mitosis. Seemingly in contrast to this finding, other studies showed that in mouse stem cells and progenitor cells CTCF remains bound to a subset of sites during mitosis. Here, we confirm these findings by performing CTCF footprint analysis of ATAC-seq data in mitotic mESCs. Additionally, we investigate roles of mitotically bound
(bookmarked) CTCF in prometaphase chromosome organization by Hi-C. We do not find any remaining interphase structures such as TADs or CTCF loops at mitotically bookmarked CTCF sites in mESCs. This suggests that mitotic loop extruders condensin I and II are not blocked by bound CTCF, and thus that any remaining CTCF binding does not alter mitotic chromosome folding. Lastly, we compare mitotic Hi-C data generated in this study in mouse with publicly available data from human and chicken cell lines. We do not find any cell type specific differences; however, we do find a difference between species. The average genomic size of mitotic loops is much smaller in chicken (350 kb), compared to human (750 kb) and mouse (2 Mb). Interestingly, we find that this difference in loop size
is correlated with the average genomic length of the q-arm in these species, a finding we confirm by microscopy measurements of chromosome compaction. This suggests that the dimensions of mitotic chromosomes can be modulated through control of sizes of loops generated by condensins to facilitate species-appropriate shortening of chromosome arms.