A proposed unified mitotic chromosome architecture

Abstract

A molecular architecture is proposed for a representative mitotic chromosome, human chromosome 10. This architecture is built on an interphase chromosome structure based on cryo-electron microscopy (cryo-EM) cellular tomography [J. Sedat et al., Proc. Natl. Acad. Sci. U.S.A., in press], thus unifying chromosome structure throughout the complete mitotic cycle. The basic organizational principle for mitotic chromosomes is specific coiling of the 11-nm nucleosome fiber into large scale, ∼200-nm interphase structures, a Slinky [https://en.wikipedia.org/wiki/Slinky; motif cited in S. Bowerman et al., eLife 10, e65587 (2021)], then further modified with subsequent additional coiling for the final mitotic chromosome structure. The final mitotic chromosome architecture accounts for the dimensional values as well as the well-known cytological configurations. In addition, proof is experimentally provided by digital PCR technology that G1 T cell nuclei are diploid with one DNA molecule per chromosome. Many nucleosome linker DNA sequences, the promotors and enhancers, are suggestive of optimal exposure on the surfaces of the large-scale coils.

Keywords: biophysics and computational structure analysis; cell biology; chromosome structure; computational structure analysis.

Fig. 1.

This figure documents human chromosome 10 from DNA level to Slinky nucleosome coil. (A) Depicts human chromosome 10 DNA, properly scaled. (B) Shows the nucleosomes (red disks, scaled) with the green linker DNA extended while it is possible the nucleosome chain can be compressed with the linker DNA more compactly as green hairpins. The histone tails are black wavy lines. Blue dash denotes continuation of the structure. (C) Shows human chromosome 10 nucleosome coiling to form a Slinky with variable diameter, compaction, and Slinky length. The extended nucleosome length is 669k nucleosomes (11 nm [the nucleosome size]) + 669k nucleosomes (18.4 nm [linker DNA size]), while compact nucleosome fiber is 669k nucleosomes (11 nm) + 669k nucleosomes (2 × 2 nm [DNA size for linker]). The number of Slinky and race track Slinky gyri can be calculated assuming 669k nucleosomes/66 nucleosomes/gyrus = 10,136 gyri. The compaction is Slinky length/DNA length, where the Slinky length is 10 mm [the compressed nucleosome fiber length]/Slinky gyrus circumference [to give the number of Slinky gyri] × 11 nm [nucleosome size; the gyrus size assuming maximal Slinky packing].

Fig. 2.

Copy number per cell (dark gray symbols) of two different genes that appeared once per haploid genome, Albumin (Alb; Left) and Prdm15 (Right), as assessed by droplet digital PCR in murine CD4⁺CD8⁺ thymocytes. Ten separate samples of 1 million CD4⁺/CD8⁺/CD3^lo/CD5^lo thymocytes were sorted from two different C57BL/6 mice, and their genomic DNA was prepared with radioisotope-based recovery tracking as described in Materials and Methods. A precisely known number of input cell equivalents was then amplified using primers and TaqMan probes specific for the indicated genes, and copies per cell were calculated based on the counts of positive droplets. Bold red and lighter pink lines represent the means and 95% confidence intervals of the measurements, respectively.

Fig. 3.

The race track Slinky coil is a modified Slinky helix of the nucleosome fiber. (A) Depicts a single race track Slinky gyrus accurately to scale, with a Condensin I (11) for scale. (B) Shows a race track Slinky helical coiled region with coils more compressed. The minor axis of the race track is 50 nm, with the major axis about 285 nm. (C) Shows a folded race track Slinky with short axis and long axis dimensioned. (D) Shows a folded race track Slinky as a short coiled structure. The green lines are the chromosomes and the red structures are the nucleosomes.

Fig. 4.

Folded race track Slinky coils can be further helically coiled to form a final mitotic coil helix, the final coil of the mitotic chromosome. (A) One-half helical turn of the final mitotic coil using the folded race track Slinky, drawn to scale, is shown. The width of the folded race track Slinky coil (the minor axis of the folded race track) is ∼60 nm, and the final mitotic coil of coils is the width of the mitotic chromosome, ∼0.6 μm. (B) Shows two and a half helical turns of final mitotic coil. Nucleosomes of the folded race track Slinky coils are visible. The green lines are the chromosomes and the red structures are the nucleosomes.

Fig. 5.

Human chromosome 10 mitotic chromosome structure. Left: Shows 97 final mitotic coil helix coils that build the human chromosome 10 mitotic chromosome for a length of about 6 μm and a diameter of about 0.6 μm. The centromere constriction separates the two unequal arms (scaled) of human chromosome 10, a metacentric mitotic chromosome. Lower: Depicts the banding cytology map for human chromosome 10 (7), as accurately aligned with the structure as possible. See (7, 15) for spread mitotic chromosome structures. Right: A cross-section of human chromosome 10 mitotic chromosome, properly dimensioned.

Fig. 6.

Faces of the final mitotic coil winds highlight optimally exposed nucleosome linker DNA. (A) Shows the enlarged inside surface of the final mitotic coil half-coil. See Fig. 4 for orientation. The enlarged back face of the final mitotic coil is shown in (B). The green lines are the chromosomes and the red structures are the nucleosomes.

Fig. 7.

A summary of the unified architecture changes, using the helical multiple coiling motif taking place throughout the cell cycle, interphase through mitosis, a complete cell cycle for human chromosome 10. (A) Shows the DNA level, and (B) shows the nucleosome 11-nm organization with extended linker DNA (green). (C) Depicts the Slinky level with the coiled nucleosomes tightly packed with 66 nucleosomes/gyrus, while (D) depicts indents/folds of the Slinky structure to a folded race track. (E) Shows the final level of organization, a mitotic chromosome based on the final mitotic coiling. The structures are drawn to scale. See Fig. 1 legend. The 6,897 nucleosomes/final mitotic coil gyrus is given by 668,987 nucleosomes/97 final mitotic coil gyri. The green lines are the chromosomes; the black squiggly lines are the histones tails; and the red structures are the nucleosomes.