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Chromosome Architecture and Genome Organization.

Bernardi G - PLoS ONE (2015)

Bottom Line: This is a critical range that encompasses isochores, interphase chromatin domains and boundaries, and chromosomal bands.The solution rests on the following key points: 1) the transition from the looped domains and sub-domains of interphase chromatin to the 30-nm fiber loops of early prophase chromosomes goes through the unfolding into an extended chromatin structure (probably a 10-nm "beads-on-a-string" structure); 2) the architectural proteins of interphase chromatin, such as CTCF and cohesin sub-units, are retained in mitosis and are part of the discontinuous protein scaffold of mitotic chromosomes; 3) the conservation of the link between architectural proteins and their binding sites on DNA through the cell cycle explains the "mitotic memory" of interphase architecture and the reversibility of the interphase to mitosis process.The results presented here also lead to a general conclusion which concerns the existence of correlations between the isochore organization of the genome and the architecture of chromosomes from interphase to metaphase.

View Article: PubMed Central - PubMed

Affiliation: Science Department, Roma Tre University, Marconi, Rome, Italy.

ABSTRACT
How the same DNA sequences can function in the three-dimensional architecture of interphase nucleus, fold in the very compact structure of metaphase chromosomes and go precisely back to the original interphase architecture in the following cell cycle remains an unresolved question to this day. The strategy used to address this issue was to analyze the correlations between chromosome architecture and the compositional patterns of DNA sequences spanning a size range from a few hundreds to a few thousands Kilobases. This is a critical range that encompasses isochores, interphase chromatin domains and boundaries, and chromosomal bands. The solution rests on the following key points: 1) the transition from the looped domains and sub-domains of interphase chromatin to the 30-nm fiber loops of early prophase chromosomes goes through the unfolding into an extended chromatin structure (probably a 10-nm "beads-on-a-string" structure); 2) the architectural proteins of interphase chromatin, such as CTCF and cohesin sub-units, are retained in mitosis and are part of the discontinuous protein scaffold of mitotic chromosomes; 3) the conservation of the link between architectural proteins and their binding sites on DNA through the cell cycle explains the "mitotic memory" of interphase architecture and the reversibility of the interphase to mitosis process. The results presented here also lead to a general conclusion which concerns the existence of correlations between the isochore organization of the genome and the architecture of chromosomes from interphase to metaphase.

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The percentages of single-isochore bands are plotted against the total number of bands at metaphase (400 bands), prometaphase (850 bands) and mid-prophase (1,700 bands) and extrapolated to 100% single-isochore bands.
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pone.0143739.g003: The percentages of single-isochore bands are plotted against the total number of bands at metaphase (400 bands), prometaphase (850 bands) and mid-prophase (1,700 bands) and extrapolated to 100% single-isochore bands.

Mentions: At the beginning of mitosis the three-dimensional organization of interphase chromatin disappears [64], as expected, and is replaced in early prophase of human chromosomes by over 3,000 bands [77]. This number approximately matches the number of isochores, ~3,200. This preliminary indication that early prophase bands may correspond to individual isochores [16] is now definitely supported by the observation (Fig 3) that single-isochore bands represent ~8% of metaphase bands, ~25% of prometaphase bands and ~50% of mid-prophase bands (in chromosome 1, for example, the 122 bands of mid-prophase [77] correspond to 233 isochores; ratio = 0.52). Indeed, the three relative amounts just quoted indicate, by extrapolation, that single-isochore bands represent the totality of early prophase bands when the number of the latter is ~3,400, a value close to the total number of isochores (see Fig 3).


Chromosome Architecture and Genome Organization.

Bernardi G - PLoS ONE (2015)

The percentages of single-isochore bands are plotted against the total number of bands at metaphase (400 bands), prometaphase (850 bands) and mid-prophase (1,700 bands) and extrapolated to 100% single-isochore bands.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664426&req=5

pone.0143739.g003: The percentages of single-isochore bands are plotted against the total number of bands at metaphase (400 bands), prometaphase (850 bands) and mid-prophase (1,700 bands) and extrapolated to 100% single-isochore bands.
Mentions: At the beginning of mitosis the three-dimensional organization of interphase chromatin disappears [64], as expected, and is replaced in early prophase of human chromosomes by over 3,000 bands [77]. This number approximately matches the number of isochores, ~3,200. This preliminary indication that early prophase bands may correspond to individual isochores [16] is now definitely supported by the observation (Fig 3) that single-isochore bands represent ~8% of metaphase bands, ~25% of prometaphase bands and ~50% of mid-prophase bands (in chromosome 1, for example, the 122 bands of mid-prophase [77] correspond to 233 isochores; ratio = 0.52). Indeed, the three relative amounts just quoted indicate, by extrapolation, that single-isochore bands represent the totality of early prophase bands when the number of the latter is ~3,400, a value close to the total number of isochores (see Fig 3).

Bottom Line: This is a critical range that encompasses isochores, interphase chromatin domains and boundaries, and chromosomal bands.The solution rests on the following key points: 1) the transition from the looped domains and sub-domains of interphase chromatin to the 30-nm fiber loops of early prophase chromosomes goes through the unfolding into an extended chromatin structure (probably a 10-nm "beads-on-a-string" structure); 2) the architectural proteins of interphase chromatin, such as CTCF and cohesin sub-units, are retained in mitosis and are part of the discontinuous protein scaffold of mitotic chromosomes; 3) the conservation of the link between architectural proteins and their binding sites on DNA through the cell cycle explains the "mitotic memory" of interphase architecture and the reversibility of the interphase to mitosis process.The results presented here also lead to a general conclusion which concerns the existence of correlations between the isochore organization of the genome and the architecture of chromosomes from interphase to metaphase.

View Article: PubMed Central - PubMed

Affiliation: Science Department, Roma Tre University, Marconi, Rome, Italy.

ABSTRACT
How the same DNA sequences can function in the three-dimensional architecture of interphase nucleus, fold in the very compact structure of metaphase chromosomes and go precisely back to the original interphase architecture in the following cell cycle remains an unresolved question to this day. The strategy used to address this issue was to analyze the correlations between chromosome architecture and the compositional patterns of DNA sequences spanning a size range from a few hundreds to a few thousands Kilobases. This is a critical range that encompasses isochores, interphase chromatin domains and boundaries, and chromosomal bands. The solution rests on the following key points: 1) the transition from the looped domains and sub-domains of interphase chromatin to the 30-nm fiber loops of early prophase chromosomes goes through the unfolding into an extended chromatin structure (probably a 10-nm "beads-on-a-string" structure); 2) the architectural proteins of interphase chromatin, such as CTCF and cohesin sub-units, are retained in mitosis and are part of the discontinuous protein scaffold of mitotic chromosomes; 3) the conservation of the link between architectural proteins and their binding sites on DNA through the cell cycle explains the "mitotic memory" of interphase architecture and the reversibility of the interphase to mitosis process. The results presented here also lead to a general conclusion which concerns the existence of correlations between the isochore organization of the genome and the architecture of chromosomes from interphase to metaphase.

Show MeSH