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Chromosome condensation

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Figure 1 Interphase nucleus and mitotic chromosomes in human cells. Bar, 10 μm

Chromosome condensation refers to the process by which dispersed interphase chromatin is transformed into a set of compact, rod-shaped structures during mitosis and meiosis (Figure 1).[1][2][3][4][5]

The term "chromosome condensation" has long been used in biology. However, it is now increasingly recognized that mitotic chromosome condensation proceeds through mechanisms distinct from those governing "condensation" in physical chemistry (e.g., gas-to-liquid phase transitions) or the formation of "biomolecular condensates" in cell biology. Consequently, some researchers have argued that the term "chromosome condensation" may be misleading in this context. For this reason, alternative terms such as "chromosome assembly" or "chromosome formation" are also commonly used.

Processes of chromosome condensation

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From DNA to chromosomes

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A diploid human cell contains 46 chromosomes: 22 pairs of autosomes (22 × 2) and one pair of sex chromosomes (XX or XY). The total length of DNA within a single nucleus reaches ~2 m. These DNA molecules are initially wrapped around histones to form nucleosomes, which are further compacted into chromatin fibers, commonly referred to as 30-nm fibers. During interphase, these fibers are confined within the nucleus, which has a diameter of only ~10–20 um. During mitosis, chromatin is reorganized into a set of rod-shaped structures (i.e., mitotic chromosomes) that can be individually distinguished under a microscope.

This transformation was first described meticulously in the late 19th century by the German cytologist Walther Flemming. Originally, the term "chromosome" referred specifically to these highly condensed mitotic structures, although its meaning has since broadened (see chromosome).

In mitotic chromosomes of higher eukaryotes, DNA is compacted lengthwise by a factor of ~10,000. For example, human chromosome 8 contains a DNA molecule about 50 mm long, yet it is folded into a metaphase chromosome only ~5 um in length. This degree of compaction is comparable to folding a 600-meter-long thread (the height of the Tokyo Skytree) into the size of an AA battery.

Physiological significance of chromosome condensation

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As described above, although DNA in interphase is already organized into chromatin, it is dispersed throughout the nucleus and therefore not observed as individual chromosomes. Upon entry into prophase, condensation begins near the nuclear periphery, and fibrous structures gradually become visible. After nuclear envelope breakdown in prometaphase, condensation proceeds further. By metaphase, when condensation is apparently complete, the two sister chromatids of each chromosome can be clearly distinguished. This entire sequence of processes is often collectively referred to as chromosome condensation; however, due to our currently limited understanding of the higher-order structure of chromosomes, the precise definition of this term remains ambiguous.

Figure 2. Steps of chromosome condensation
Figure 3. Eukaryotic chromosome segregation

In principle, the process of chromosome condensation can be divided into three sequential but overlapping steps (Figure 2):[6]

1. Individualization – Disentanglement of chromatin fibers dispersed throughout the nucleus into discrete chromosome units.

2. Shaping/Compaction – Organization of each chromosome into a compact, rod-like structure.

3. Resolution – Resolution of replicated DNA strands within each chromosome into two distinct sister chromatids.

Although conceptually distinct, these steps occur concurrently and synergistically during mitosis. For this reason, the entire process is often collectively referred to as chromosome condensation. Importantly, chromosome condensation is not merely a reduction in chromatin length. Rather, it involves the organized folding of chromatin, initially in a random-coil–like state, into a highly structured rod-shaped form. This structural transformation is critical for ensuring the proper separation of sister chromatids during anaphase and provides the mechanical stiffness necessary for their faithful segregation (Figure 3).[7] Defects in chromosome condensation can impair chromosome segregation and ultimately lead to genome instability.

Protein factors essential for chromosome condensation

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Eukaryotic chromosome condensation has long been regarded as a highly complex process involving numerous proteins. However, recent studies have shown that single chromatids can be reconstituted in vitro by mixing sperm nuclei with only six purified proteins: core histones, three histone chaperones, topoisomerase II, and condensin I.[8][9] The three histone chaperones serve distinct roles in this reconstitution assay: (1) Npm2 (Nucleoplasmin 2) removes basic sperm-specific proteins from sperm chromatin; (2) Nap1 (Nucleosome assembly protein 1) deposits core histones H2A-H2B onto DNA to form nucleosomes; (3) FACT (Facilitates Chromatin Transcription) dynamically remodels nucleosomes, thereby aiding the actions of topoisomerase II and condensin I. These chaperones do not remain associated with the final product of mitotic chromatids. In other words, the core reactions of mitotic chromosome condensation can be recapitulated using only three structural proteins, core histones, topoisomerase II, and condensin I, provided that their actions are aided by appropriate chaperone-mediated regulation.

Independent lines of previous evidence support this simple picture of chromosome condensation. For example, it has long been known that histones account for approximately half of the total protein mass in mitotic chromosomes. Both topoisomerase II and condensin I have been identified as major structural components of mitotic chromosomes [10][11] as well as of the so-called chromosome scaffold.[12] Functional assays using Xenopus egg extracts [10][11] and genetic analyses in fission yeast [13][14] have demonstrated that both proteins are essential for properly assembling mitotic chromosomes.

Surprisingly, it has been shown that chromosome-like structures can be assembled in Xenopus egg extracts even under conditions in which nucleosome assembly is suppressed, in a manner dependent on condensins and topoisomerase II.[15][9] These “nucleosome-depleted" chromosomes consist of a central condensin-enriched axis and extended DNA loops emanating from it. This observation indicates that condensins are essential for the shaping of chromosome architecture, whereas histones contribute to the compaction of DNA loops.

Regulation of chromosome condensation

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Chromosome condensation is a process unique to mitosis and meiosis, and thus, the proteins involved in this process are subject to cell cycle regulation, often mediated by post-translational modifications (PTMs).

Among these, the most intensively studied mechanism is the phosphorylation of condensin complexes. It has been shown that phosphorylation by Cdk1 is essential for both the DNA supercoiling activity [16] and chromosome assembly activity [8] of condensin I. Experiments using Xenopus egg extracts have led to a proposed mechanism in which phosphorylation of the N-terminal region of the CAP-H subunit relieves its self-suppression, thereby activating condensin I.[17] Similarly, in condensin II, Cdk1-dependent phosphorylation of the C-terminal region of the CAP-D3 subunit plays a role in releasing its inhibitory constraint.[18][19] However, phosphoregulation of condensins is complex and multilayered, and a full mechanistic understanding has not yet been achieved.

Topoisomerase II is also subject to numerous PTMs. However, it remains unclear whether any of these modifications specifically regulate its activity during mitosis.[20][21]

Mitotic phosphorylation of linker histone H1 and core histone H3 has been known for decades.[22] Nevertheless, there is currently no direct evidence that these modifications actively or directly regulate chromosome condensation. In contrast, histone deacetylation has recently been reported to play an important role in this process through a mechanism of phase transition.[23]

In addition to PTMs, external regulatory factors also contribute to the regulation of chromosome condensation. For example, KIF4A, a chromokinesin, acts as a positive regulator of condensin I,[24][25] whereas MCPH1, a microcephaly-associated protein, serves as a negative regulator of condensin II.[26][27] Ki-67, a nucleolar protein, plays a critical role in chromosome individualization during early mitosis by coating the surface of mitotic chromosomes.[28][29]

Models of mitotic chromosomes and emerging experimental approaches

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How chromatin fibers are folded within mitotic chromosomes remains an unsolved question in cell biology. Several models have been proposed to explain the higher-order architecture of condensed chromosomes. Classical models include the hierarchical folding model [30] and the radial loop model.[31] More recently, additional models such as the polymer model [32] and the hierarchical folding and axial glue model [33] have been introduced.

One of the major reasons for the slow progress in understanding the folding of chromatin fibers within mitotic chromosomes has been the limited availability of experimental tools for their structural analysis. Recently, however, the development of a variety of new technologies has enabled more detailed and multifaceted investigations.

  • Imaging-based approaches
    • Cryo-electron tomography (Cryo-ET) for high-resolution 3D structure [48][49]
    • Nano-scale 3D DNA tracing to map chromosome architecture [50]
    • FAST CHIMP (Facilitated Segmentation and Tracking of Chromosomes in Mitosis Pipeline) for mitotic chromosome tracking [51]
    • Single-nucleosome imaging to analyze nucleosome dynamics within mitotic chromosomes [52]
  • Theoretical modeling and computational simulation
    • Modeling mitotic chromosome assembly through a loop extrusion mechanism [57]
    • Modeling mitotic chromosome assembly through a loop capture mechanism [58]
    • Modeling mitotic chromosome assembly by incorporating condensin–condensin interactions [59]
    • Modeling mitotic chromosome assembly through a bridging-induced attraction mechanism [60]

Chromosome condensation in prokaryotes

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Figure 4. Bacterial chromosome segregation

Although bacteria lack histones, their genomic DNA associates with various nucleoid-associated proteins (NAPs) to form the nucleoid, a functional counterpart of the eukaryotic chromosome.

In bacteria, DNA compaction is facilitated by the introduction of negative supercoils (typically of the plectonemic type) by the enzyme DNA gyrase, a bacterial type II topoisomerase. In contrast, archaea possess histone-like proteins, and in some species, a nucleosome-like particle with ~60 base pair periodicity[61] or an extended polymeric structure[62] have been observed. Recent advances in metagenomics and structure prediction algorithms have led to the discovery and classification of numerous histone-like proteins across prokaryotes.[63]

Many bacterial and archaeal species also possess SMC protein complexes analogous to eukaryotic condensins, including SMC–ScpAB and MukBEF, which play direct roles in organizing the nucleoid structure.[64][65][66] Loss-of-function mutations in these complexes cause abnormal nucleoid morphology and defects in chromosome segregation. Thus, prokaryotes undergo a process functionally equivalent to chromosome condensation, which is critical for ensuring proper chromosome segregation within a spatially confined cell volume (Figure 4). Furthermore, Hi-C) technology has been applied to study the dynamics of nucleoid reorganization mediated by bacterial condensin in several model organisms, including Caulobacter crescentus,[67] Bacillus subtilis,[68] and Escherichia coli.[69]

The following table summarizes the similarities and differences in chromosome architecture between eukaryotes and prokaryotes. Such comparisons are crucial for redefining the process of chromosome condensation at the molecular level and for gaining insights into the evolutionary principles underlying higher-order chromosome organization.[70][71]

DNA binding protein local structure determinant of local structure determinant of global structure disentangling enzyme
eukaryotes histones left-handed toroidal 　nucleosome condensin topoisomerase II
prokaryotes NAPs negatively supercoiled 　DNA gyrase SMC-ScpAB/MukBEF topoisomerase IV

See also

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References

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