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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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Isochores, chromosomal bands and chromosome architecture.Interphase: See legends of Figs 1C and 2, for the top and bottom panels respectively. Prophase: See legend of Fig 2. The R band of prophase coalesces with two flanking G bands producing a G band. Prometaphase to Metaphase: The multiple-isochore prometaphase bands coalesce further into metaphase bands (see legend of Fig 5C). The central R band of prophase coalesces with two G bands giving rise to a larger G band. The 30-nm loops have different sizes and orientations (the figure is from ref. [64]); the protein scaffold is discontinuous (see Text).
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pone.0143739.g007: Isochores, chromosomal bands and chromosome architecture.Interphase: See legends of Figs 1C and 2, for the top and bottom panels respectively. Prophase: See legend of Fig 2. The R band of prophase coalesces with two flanking G bands producing a G band. Prometaphase to Metaphase: The multiple-isochore prometaphase bands coalesce further into metaphase bands (see legend of Fig 5C). The central R band of prophase coalesces with two G bands giving rise to a larger G band. The 30-nm loops have different sizes and orientations (the figure is from ref. [64]); the protein scaffold is discontinuous (see Text).

Mentions: As far as the results summarized the link between chromosome architecture and genome organization is concerned, we already knew that correlations existed between 1) the GC levels of coding and non-coding sequences within the large, compositionally fairly homogeneous DNA segments that were called isochores; and 2) the GC levels of isochores and all tested properties of the genome. These findings supported the idea that the genome is an integrated ensemble. A new, important point is now added to these correlations, that were called the genomic code, by finding that correlations also exist between the compositional properties of isochores and the structural properties of chromosomes through the cell cycle (see Figs 2 and 7). The most remarkable correlation is that between the architecture of interphase chromatin and the isochore organization of the genome (K. Jabbari and G. Bernardi, paper in preparation) because this new point considerably extends the significance of the genomic code and leads to a unifying view of genome organization and chromosome architecture.


Chromosome Architecture and Genome Organization.

Bernardi G - PLoS ONE (2015)

Isochores, chromosomal bands and chromosome architecture.Interphase: See legends of Figs 1C and 2, for the top and bottom panels respectively. Prophase: See legend of Fig 2. The R band of prophase coalesces with two flanking G bands producing a G band. Prometaphase to Metaphase: The multiple-isochore prometaphase bands coalesce further into metaphase bands (see legend of Fig 5C). The central R band of prophase coalesces with two G bands giving rise to a larger G band. The 30-nm loops have different sizes and orientations (the figure is from ref. [64]); the protein scaffold is discontinuous (see Text).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143739.g007: Isochores, chromosomal bands and chromosome architecture.Interphase: See legends of Figs 1C and 2, for the top and bottom panels respectively. Prophase: See legend of Fig 2. The R band of prophase coalesces with two flanking G bands producing a G band. Prometaphase to Metaphase: The multiple-isochore prometaphase bands coalesce further into metaphase bands (see legend of Fig 5C). The central R band of prophase coalesces with two G bands giving rise to a larger G band. The 30-nm loops have different sizes and orientations (the figure is from ref. [64]); the protein scaffold is discontinuous (see Text).
Mentions: As far as the results summarized the link between chromosome architecture and genome organization is concerned, we already knew that correlations existed between 1) the GC levels of coding and non-coding sequences within the large, compositionally fairly homogeneous DNA segments that were called isochores; and 2) the GC levels of isochores and all tested properties of the genome. These findings supported the idea that the genome is an integrated ensemble. A new, important point is now added to these correlations, that were called the genomic code, by finding that correlations also exist between the compositional properties of isochores and the structural properties of chromosomes through the cell cycle (see Figs 2 and 7). The most remarkable correlation is that between the architecture of interphase chromatin and the isochore organization of the genome (K. Jabbari and G. Bernardi, paper in preparation) because this new point considerably extends the significance of the genomic code and leads to a unifying view of genome organization and chromosome architecture.

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