Molliex, A. | bioRxiv Science

bioRxiv2023

Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture

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, whereas mouse embryonic stem cells (mESC) display prominent binding at a subset of CTCF sites in mitosis. Here, we perform parallel footprint ATAC-seq data analyses of mESCs and somatic mouse and human cells to further explore these differences. We then 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 (200-350 kb), compared to human (500-750 kb) and mouse (1-2 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.

genomics↗

bioRxiv2022

Mitotic bookmarking redundancy by nuclear receptors mediates robust post-mitotic reactivation of the pluripotency network.

Mitotic bookmarking transcription factors (TFs) are thought to mediate rapid and accurate post-mitotic gene reactivation. However, the loss of individual bookmarking TFs often leads to the deregulation of only a small proportion of their mitotic targets, raising doubts on the significance and importance of their bookmarking function. Here, we used targeted proteomics of the mitotic bookmarking TF ESRRB, an orphan nuclear receptor, to discover an unexpected redundancy among members of the protein superfamily of nuclear receptors. Focusing on the nuclear receptor NR5A2, which together with ES-RRB is essential for mouse pluripotency, we demonstrate conjoint bookmarking activity of both factors on promoters and enhancers of a large fraction of active genes, particularly the most rapidly and strongly reactivated ones. Upon fast and simultaneous degradation of both factors during mitotic exit, hundreds of mitotic targets of ESRRB/NR5A2, including key players of the pluripotency network, display attenuated transcriptional reactivation. We propose that redundancy in mitotic bookmarking TFs, especially by nuclear receptors, confers robustness to the reestablishment of gene regulatory networks after mitosis.

molecular biology↗