Regulation of the mitotic chromosome folding machines

Abstract

Over the last several years enormous progress has been made in identifying the molecular machines, including condensins and topoisomerases that fold mitotic chromosomes. The discovery that condensins generate chromatin loops through loop extrusion has revolutionized, and energized, the field of chromosome folding. To understand how these machines fold chromosomes with the appropriate dimensions, while disentangling sister chromatids, it needs to be determined how they are regulated and deployed. Here, we outline the current understanding of how these machines and factors are regulated through cell cycle dependent expression, chromatin localization, activation and inactivation through post-translational modifications, and through associations with each other, with other factors and with the chromatin template itself. There are still many open questions about how condensins and topoisomerases are regulated but given the pace of progress in the chromosome folding field, it seems likely that many of these will be answered in the years ahead.

Visualization of the three-dimensional structure of the human centromere in mitotic chromosomes by superresolution microscopy

“…The sinusoidal patch model also allows for H3-containing nucleosomes to be present on the surface of the centromeric chromatin to interact with kinetochore proteins (Verdaasdonk and Bloom, 2011). Here, we try to reconcile the mitotic ring-like centromere structure that we observed with Cen-CO-FISH and 3D SIM with information from the previous models, taking into consideration the recent advances in understanding mitotic chromosomes folding through chromatin loops (Gibcus, Samejima, Goloborodko, et al, 2018;Dekker and Dekker, 2022), the interposition of CENP-A-containing nucleosomes with H3-containing nucleosomes (Blower, Sullivan, et al, 2002;Sullivan and Karpen, 2004), the latest genomic data including the information that CENP-A is highly enriched in the CDR (centromeric dip region, where "dip" refers to a region with lower DNA methylation often concomitant with CENP-A chromatin enrichment; Altemose, Logsdon, Bzikadze, Sidhwani, Langley, Caldas, et al, 2022a) with respect to the rest of the active HOR array (Bodor et al, 2014;Altemose, Logsdon, Bzikadze, Sidhwani, Langley, Caldas, et al, 2022a;Gershman et al, 2022), and the concept that the mammalian kinetochore is based on the repetition of the budding yeast single structure (Yeh, Haase, et al, 2008). We propose a model where centromeric mitotic chromatin is looped in a ring structure and layered with the flanking pericentromere.…”

“…Here, we try to reconcile the mitotic ring-like centromere structure that we observed with Cen-CO-FISH and 3D SIM with information from the previous models, taking into consideration the recent advances in understanding mitotic chromosomes folding through chromatin loops ( Gibcus, Samejima, Goloborodko, et al. , 2018 ; Dekker and Dekker, 2022 ), the interposition of CENP-A-containing nucleosomes with H3-containing nucleosomes ( Blower, Sullivan, et al. , 2002 ; Sullivan and Karpen, 2004 ), the latest genomic data including the information that CENP-A is highly enriched in the CDR (centromeric dip region, where “dip” refers to a region with lower DNA methylation often concomitant with CENP-A chromatin enrichment; Altemose, Logsdon, Bzikadze, Sidhwani, Langley, Caldas, et al.…”

Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions

“…We now test the applicability of the “B-Z TopoII” mechanism to rationalize aspects of cellular mitosis, the autopoietic [ 103 ] process underlying cell division in which the expression of topoII peaks (at G2-M, there are ~10 6 molecules/cell [ 104 ]) as it executes the essential functions of chromosomal DNA condensation and then segregation [ 46 , 105 , 106 ], distinct from its contributions to genome stability and organization in interphase [ 3 ]. The sequential progressive stages of the mitotic cell cycle (G2-interphase → prophase → prometaphase → metaphase → anaphase + telophase → cytokinesis) are precisely choreographed [ 105 , 106 , 107 , 108 , 109 , 110 , 111 , 112 ] and are accessible to high-resolution microscopy [ 105 ]. In prophase, the topologically associated domains (TADs) of interphase are disrupted, and the 6.3 Gbps (human diploid) DNA is organized by condensin II in a process of loop extrusion (LE) into ~4·10 4 loops of ~450 kb.…”

“…TopoII is bound to the chromosome axes and centromeres and is a key and indispensable participant in the processes outlined in the preceding paragraph [ 46 , 115 , 116 ]. Particular emphasis has been placed on the interplay between the respective roles of topoII and condensin II/KIF4 [ 112 ]. This focus arises because the fundamental activities of the two components (LE/compaction vs. topological simplification) are seemingly antagonistic in the coordination of DNA condensation with the equally requisite and concurrent elimination of spurious knots, tangles and sister chromatid interlinks [ 115 ].…”

“…Lateral chromosomal compaction has been attributed to condensin and KIF4 and axial compression to topoII [ 117 ]. Adding to the complexity of the system are: a dual driver–damper role of two condensin ATPases [ 108 ]; the intervention of other topoisomerases, chromokinesins, cohesin, and cyclins; and extensive temporally synchronized protein modifications [ 118 ], notably (de)phosphorylation and sumoylation, such as of the DNA-gate and the C-terminal domain (CTD) of topoII [ 41 , 112 ]. The mitosis literature abounds with conundrums, assertions, and still open questions, including the following: What are the ultrastable topoII-DNA complexes that play a structural role in chromosome architecture?…”