SMC complexes orchestrate the mitotic chromatin interaction landscape
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Chromatin is a very long DNA–protein complex that controls the expression and inheritance of the genetic information. Chromatin is stored within the nucleus in interphase and further compacted into chromosomes during mitosis. This process, known as chromosome condensation, is essential for faithful segregation of genomic DNA into daughter cells. Condensin and cohesin, members of the structural maintenance of chromosomes (SMC) family, are fundamental for chromosome architecture, both for establishment of chromatin structure in the interphase nucleus and for the formation of condensed chromosomes in mitosis. These ring-shaped SMC complexes are thought to regulate the interactions between DNA strands by topologically entrapping DNA. How this activity shapes chromosomes is not yet understood. Recent high throughput chromosome conformation capture studies revealed how chromatin is reorganized during the cell cycle and have started to explore the role of SMC complexes in mitotic chromatin architecture. Here, we summarize these findings and discuss the conserved nature of chromosome condensation in eukaryotes. We highlight the unexpected finding that condensin-dependent intra-chromosomal interactions in mitosis increase within a distinctive distance range that is characteristic for an organism, while longer and shorter-range interactions are suppressed. This reveals important molecular insight into chromosome architecture.
KeywordsChromosome condensation SMC complex Chromatin Cell cycle Hi-C
How chromatin is spatially organized within the cell nucleus and within chromosomes is a fundamental question in cell biology. Centimeter-long DNA molecules change their spatial chromatin organization within micrometer-sized cells during cell cycle progression. In interphase, chromatin is distributed throughout the nucleus to express the genetic information. When cells enter mitosis, chromatin becomes compacted to form mitotic chromosomes. Chromosome condensation, the gross morphological change of spatial chromatin organization in mitosis, is indispensable for the faithful inheritance of genetic information. Structural maintenance of chromosomes (SMC) complexes are large proteinaceous rings that control spatial chromatin organization at various stages during cell growth and differentiation. By topologically entrapping more than one DNA strand within its ring, SMC complexes are thought to mediate interactions between DNA strands for the establishment of chromatin architecture (Uhlmann 2016). Two members of the SMC complex family, cohesin and condensin, play distinct yet overlapping roles in shaping mitotic chromosomes: cohesin holds sister chromatids together (Peters and Nishiyama 2012), while condensin compacts chromatin (Hirano 2016). A third member of SMC family, the Smc5/6 complex is involved in DNA recombination. Its contribution to chromosome architecture is less well understood (Jeppsson et al. 2014). Condensin plays a key role in chromosome condensation, since mitotic chromosome-like structures can be reconstituted by condensin in vitro even in the absence of histones, which form the nucleosome units of chromatin (Shintomi et al. 2017). How condensin promotes mitotic chromosome formation is a topic of great current interest.
Chromosome conformation capture is a powerful technique to investigate spatial chromatin organization (Dekker et al. 2013). Using this technique, spatial information of chromatin interactions is obtained from crosslinked chromatin followed by DNA fragmentation and ligation. High throughout sequencing-based chromosome conformation capture, Hi-C, is able to capture spatial proximities of chromatin in a genome-wide manner (Lieberman-Aiden et al. 2009). Recent Hi-C studies have revealed that chromatin within the interphase nucleus forms domain structures at different size ranges, such as topologically associating domains (TADs) as well as A and B compartments in higher eukaryotes (Dixon et al. 2012; Lieberman-Aiden et al. 2009). These domain structures are controlled by cohesin together with CTCF, the sequence-specific CCCTC-binding factor, to regulate gene expression (Rao et al. 2014; Sofueva et al. 2013). Similarly, cohesin-mediated smaller chromatin domains, called globules, can be seen in fission yeast interphase nucleus (Mizuguchi et al. 2014). In this review, we summarize recent findings on mitotic chromatin architecture in different eukaryotes and discuss how SMC complexes contribute to chromosome condensation.
Chromatin interactions that convert interphase nuclei into mitotic chromosomes
A notable feature of mitotic chromosomes is a steep drop of contact probabilities at very large genomic distances, over 10 Mb in human cells (Naumova et al. 2013). Mitotic reduction of the longest-range interactions can also be seen in both fission yeast and budding yeast (Kakui et al. 2017; Schalbetter et al. 2017). It is probably a reflection of mitotic chromosome arm stiffening, which is expected to disfavor longest-range interactions. An important point to keep in mind, when comparing interaction frequencies in interphase and mitosis, is that Hi-C reports on relative interaction frequencies, not on absolute contact frequencies. To calibrate interaction changes, we have quantitatively analyzed chromatin contact frequency changes by 3C followed by quantitative real-time PCR. Cytological observations served as an additional means to validate interaction frequency changes. This confirmed an absolute increase of mitotic interactions in the range between 90 and 900 kb in fission yeast, while local interactions are indeed reduced (Kakui et al. 2017). This portrays mitotic chromosome formation as the consequence of increased interactions in a specific size range, accompanied by a quantitative reduction of short- and longest-range interactions.
The mitotic reduction of local chromatin contacts comes as a surprise, as one would expect that all DNA sequences come closer together in a condensed chromosome. However, new interactions at longer distances will restrict the freedom of movement of the chromatin chain, thereby reducing the probability of local interactions. Consistently, local chromatin motility becomes constrained in mitosis (Kakui et al. 2017). It will be important to investigate whether a quantitative reduction of short-range chromatin interactions occurs in organisms other than fission yeast. If confinement of local chromatin motility is a general feature of mitotic chromosomes, its consequences for maintenance and reprogramming of the gene expression program during mitosis will be important to examine.
The contribution of SMC complexes to chromosome condensation
The recent Hi-C experiments unveiled that SMC complexes drive a dramatic reorganization of chromatin contacts as cells enter mitosis. They did not elucidate the mechanism of how SMC complexes mediate chromatin interactions. Two proposed models how SMC rings modulate chromatin contacts are the stabilization of stochastic pairwise interactions and loop extrusion, two models that need not be mutually exclusive (Cheng et al. 2015; Fudenberg et al. 2016). Higher resolution Hi-C datasets, coupled with computational modeling, should shed light on the mechanism of how SMC complexes control chromosome formation. A molecular understanding of how chromosomes take shape might soon be in sight.
This work was supported by the European Research Council and by The Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001198), the UK Medical Research Council (FC001198), and the Wellcome Trust (FC001198). Y.K. acknowledges support from the Japan Society for the Promotion of Science.
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