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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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Related in: MedlinePlus

Amounts of 2-Kb sequences <35% GC as present in 50-Kb stretches of chromosome 21 are plotted against the GC levels of the 50-Kb stretches.Vertical red lines indicate the borders of isochore families.
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pone.0143739.g006: Amounts of 2-Kb sequences <35% GC as present in 50-Kb stretches of chromosome 21 are plotted against the GC levels of the 50-Kb stretches.Vertical red lines indicate the borders of isochore families.

Mentions: Recent investigations have shown, however, the existence of two problems with this model: 1) the complete disintegration of metaphase chromosomes upon the action of micrococcal nuclease shows that metaphase chromosomes do not have a continuous protein scaffold [81]. 2) AT-rich (<35% GC) regions of 0.7 to several Kilobases practically do not exist in the isochores of the H1, H2, H3 families that form the R bands (see Fig 6). In chromosome 1, only one R band out of fourteen (0.7% of all R bands) is below 41%GC, the border between L2 and H1 isochores (see Fig 5B). The latter point raises an insoluble problem for the model [81], because the regular existence of AT-rich queues in R bands of chromosomes is not supported.


Chromosome Architecture and Genome Organization.

Bernardi G - PLoS ONE (2015)

Amounts of 2-Kb sequences <35% GC as present in 50-Kb stretches of chromosome 21 are plotted against the GC levels of the 50-Kb stretches.Vertical red lines indicate the borders of isochore families.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143739.g006: Amounts of 2-Kb sequences <35% GC as present in 50-Kb stretches of chromosome 21 are plotted against the GC levels of the 50-Kb stretches.Vertical red lines indicate the borders of isochore families.
Mentions: Recent investigations have shown, however, the existence of two problems with this model: 1) the complete disintegration of metaphase chromosomes upon the action of micrococcal nuclease shows that metaphase chromosomes do not have a continuous protein scaffold [81]. 2) AT-rich (<35% GC) regions of 0.7 to several Kilobases practically do not exist in the isochores of the H1, H2, H3 families that form the R bands (see Fig 6). In chromosome 1, only one R band out of fourteen (0.7% of all R bands) is below 41%GC, the border between L2 and H1 isochores (see Fig 5B). The latter point raises an insoluble problem for the model [81], because the regular existence of AT-rich queues in R bands of chromosomes is not supported.

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
Related in: MedlinePlus