Subchromatid structure of chromosomes in the living state

Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields

Nucleosomes package genomic DNA into chromatin. By regulating DNA access for transcription, replication, DNA repair, and epigenetic modification, chromatin forms the nexus of most nuclear processes. In addition, dynamic organization of chromatin underlies both regulation of gene expression and evolution of chromosomes into individualized sister objects, which can segregate cleanly to different daughter cells at anaphase. This collaborative review shines a spotlight on technologies that will be crucial to interrogate key questions in chromatin and chromosome biology including state-of-the-art microscopy techniques, tools to physically manipulate chromatin, single-cell methods to measure chromatin accessibility, computational imaging with neural networks and analytical tools to interpret chromatin structure and dynamics. In addition, this review provides perspectives on how these tools can be applied to specific research fields such as genome stability and developmental biology and to test concepts such as phase separation of chromatin.

The 3D Topography of Mitotic Chromosomes

A long-standing conundrum is how mitotic chromosomes can compact, as required for clean separation to daughter cells, while maintaining close parallel alignment of sister chromatids. Pursuit of this question, by high resolution 3D fluorescence imaging of living and fixed mammalian cells, has led to three discoveries. First, we show that the structural axes of separated sister chromatids are linked by evenly spaced "mini-axis" bridges. Second, when chromosomes first emerge as discrete units, at prophase, they are organized as co-oriented sister linear loop arrays emanating from a conjoined axis. We show that this same basic organization persists throughout mitosis, without helical coiling. Third, from prophase onward, chromosomes are deformed into sequential arrays of half-helical segments of alternating handedness (perversions), accompanied by correlated kinks. These arrays fluctuate dynamically over <15 s timescales. Together these discoveries redefine the foundation for thinking about the evolution of mitotic chromosomes as they prepare for anaphase segregation.

Visualization of chromosome condensation in plants with large chromosomes

BACKGROUND

Most data concerning chromosome organization have been acquired from studies of a small number of model organisms, the majority of which are mammals. In plants with large genomes, the chromosomes are significantly larger than the animal chromosomes that have been studied to date, and it is possible that chromosome condensation in such plants was modified during evolution. Here, we analyzed chromosome condensation and decondensation processes in order to find structural mechanisms that allowed for an increase in chromosome size.

RESULTS

We found that anaphase and telophase chromosomes of plants with large chromosomes (average 2C DNA content exceeded 0.8 pg per chromosome) contained chromatin-free cavities in their axial regions in contrast to well-characterized animal chromosomes, which have high chromatin density in the axial regions. Similar to animal chromosomes, two intermediates of chromatin folding were visible inside condensing (during prophase) and decondensing (during telophase) chromosomes of Nigella damascena: approximately 150 nm chromonemata and approximately 300 nm fibers. The spatial folding of the latter fibers occurs in a fundamentally different way than in animal chromosomes, which leads to the formation of chromosomes with axial chromatin-free cavities.

CONCLUSION

Different compaction topology, but not the number of compaction levels, allowed for the evolution of increased chromosome size in plants.

Structural-functional model of the mitotic chromosome

In the present review the structural role of noncoding DNA, mechanisms of differential staining of mitotic chromosomes, and structural organization of different levels of DNA compactization are discussed. A structural-functional model of the mitotic chromosome is proposed based on the principle of discreteness of structural levels of DNA compactization.

ASYNCHRONY OF DNA REPLICATION IN THE CHROMATIDS OF PEONY

The presence in some cells of Paeonia japonica of two satellites on each chromatid of the satellited chromosomes, indicates the chromatids are subdivided into at least two subunits and thus contain at least two DNA double helixes. Pulse labeling with3H thymidine reveals an asynchromous DNA replication pattern within the chromosomes. In some cases a region of one chromatid was labeled and the corresponding region in the sister chromatid was unlabeled. The most plausible explanation for this unichromatid labeling appears to be asynchronous DNA replication in a bineme model.

The strandedness of chromosomes: evidence from chromosomal aberrations

If cells are irradiated late in the mitotic cycle (late G2or early prophase), at the following anaphase they frequently exhibit characteristic chromosomal configurations known as sidearm bridges. These are often interpreted as sub-chromatid aberrations and are taken as evidence that chromosomes are multi-stranded. This interpretation, although recently challenged, is supported by experiments based upon the normal replication that converts chromatids to full chromosomes. The rationale is that aberrations involving only one chromatid of a chromosome are converted by replication to chromosome aberrations involving both chromatids. After replication, therefore, there should be no chromatid aberrations remaining unless the initial aberration involved less than a full chromatid. The results show that chromatid aberrations do appear after chromosomal replication: at the second mitosis after irradiation. Another experiment shows that most such chromatid aberrations are not the result of errors in the replication of previous chromatid aberrations.

Ultrastructural studies of radiation-induced chromosome damage

The fine structure of radiation-induced chromosomal aberrations in Potorous tridactylis (rat kangaroo) cells was examined in situ by electron microscopy. The observations on the structure of terminal deletions (acentric fragments), anaphase bridges and "gaps," sidearm bridges, and specialized regions, such as the nucleolus organizer, are discussed in detail. Conclusions based on these observations are the following: (a) damage is physically expressed only at anaphase; (b) a gap region is composed of two subunits, each of which is about 800-1000 A in diameter and may correspond to a half-chromatid structure; (c) the ends of acentric fragments are structurally similar to normal chromosome ends, except where the break occurs in a specific region such as the secondary constriction; (d) at metaphase the fragment and the main portion of the chromosome move as a single unit to the equator, and the two units are disconnected only at the onset of anaphase; (e) sidearm bridges appear to be exchanges, involving a subchromatid unit. The interpretation of this evidence is consistent with the hypothesis that the chromosome is a multistranded structure.

Chromosome structure--a model based on DNA replication

A model of chromosome structure is proposed which assumes: (i) that DNA replication is accomplished via right-hand (RH) rotation; and (ii), that where replicating DNA segments arc very long RH-rotation will not proceed with absolute freedom. It is expected that inhibition of rotation in daughter molecules will lead to the formation of left-hand-individual (LH-I) coiling systems in the two daughter molecules. It is also expected that inhibition of rotation in the parental molecule will cause the LH-I coiled daughters to be held together in a right-hand-relational (RH-R) association. The interaction between LH-I and RH-R coiling is expected to cause separation of the daughter molecules. Multistranded DNA-containing structures are expected to show, in addition to the LH-I coiling heirarchies formed within individual strands, an RH-R coiling heirarchy formed by the complex as a whole. An LH-I coiling heirarchy was looked for, and found, in Cleveland's drawings of flagellate chromosomes. Evidence for the existence of RH-R coiling was also found. Results of electron-microscope studies on chromosome structure were briefly examined, as were the structures of lampbrush chromosomes, salivary chromosomes and "normal" chromosomes. These studies provided additional, though less direct, evidence in favor of the replication hypothesis and the predictions developed from it.