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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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A. Compositional profile of human chromosome 21 (from the hg19 release) as seen through non-overlapping 100-Kb windows, using the IsoSegmenter program [15]. DNA stretches from isochore families L1 to H3 are represented here in different colors, deep blue, light blue, yellow, orange, red, respectively. The ordinate values are the minima GC values (valleys) between isochore families (see S1 Table). The red horizontal line at 41% GC separates the two (GC-poor and GC-rich) genome compartments. B. Isochore families. The histogram displays the isochores from the human genome as pooled in bins of 1% GC (modified from ref. [16]). The Gaussian profile shows the distribution of isochore families, which are represented in different colors as in Fig 1A. Gene densities (and all other structural and functional properties tested; see Table 1) define a genome desert, isochore families L1, L2, H1, and a genome core, isochore families H2, H3 (separated by a vertical broken red line). C. The scheme compares isochores belonging to the genome desert and to the genome core with chromatin domains and chromatin boundaries.
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pone.0143739.g001: A. Compositional profile of human chromosome 21 (from the hg19 release) as seen through non-overlapping 100-Kb windows, using the IsoSegmenter program [15]. DNA stretches from isochore families L1 to H3 are represented here in different colors, deep blue, light blue, yellow, orange, red, respectively. The ordinate values are the minima GC values (valleys) between isochore families (see S1 Table). The red horizontal line at 41% GC separates the two (GC-poor and GC-rich) genome compartments. B. Isochore families. The histogram displays the isochores from the human genome as pooled in bins of 1% GC (modified from ref. [16]). The Gaussian profile shows the distribution of isochore families, which are represented in different colors as in Fig 1A. Gene densities (and all other structural and functional properties tested; see Table 1) define a genome desert, isochore families L1, L2, H1, and a genome core, isochore families H2, H3 (separated by a vertical broken red line). C. The scheme compares isochores belonging to the genome desert and to the genome core with chromatin domains and chromatin boundaries.

Mentions: The 10–20 Kb DNA molecules mentioned above derived, in fact, by degradation during preparation from much larger DNA stretches, fairly homogeneous in base composition [14], that were called “isochores” for (compositionally) equal landscapes. Isochores can be visualized by looking at the GC profiles of chromosomal sequences by using a 100-Kb fixed window (see Fig 1A for chromosome 21, the smallest human chromosome, which comprises, however, isochores from all families).


Chromosome Architecture and Genome Organization.

Bernardi G - PLoS ONE (2015)

A. Compositional profile of human chromosome 21 (from the hg19 release) as seen through non-overlapping 100-Kb windows, using the IsoSegmenter program [15]. DNA stretches from isochore families L1 to H3 are represented here in different colors, deep blue, light blue, yellow, orange, red, respectively. The ordinate values are the minima GC values (valleys) between isochore families (see S1 Table). The red horizontal line at 41% GC separates the two (GC-poor and GC-rich) genome compartments. B. Isochore families. The histogram displays the isochores from the human genome as pooled in bins of 1% GC (modified from ref. [16]). The Gaussian profile shows the distribution of isochore families, which are represented in different colors as in Fig 1A. Gene densities (and all other structural and functional properties tested; see Table 1) define a genome desert, isochore families L1, L2, H1, and a genome core, isochore families H2, H3 (separated by a vertical broken red line). C. The scheme compares isochores belonging to the genome desert and to the genome core with chromatin domains and chromatin boundaries.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4664426&req=5

pone.0143739.g001: A. Compositional profile of human chromosome 21 (from the hg19 release) as seen through non-overlapping 100-Kb windows, using the IsoSegmenter program [15]. DNA stretches from isochore families L1 to H3 are represented here in different colors, deep blue, light blue, yellow, orange, red, respectively. The ordinate values are the minima GC values (valleys) between isochore families (see S1 Table). The red horizontal line at 41% GC separates the two (GC-poor and GC-rich) genome compartments. B. Isochore families. The histogram displays the isochores from the human genome as pooled in bins of 1% GC (modified from ref. [16]). The Gaussian profile shows the distribution of isochore families, which are represented in different colors as in Fig 1A. Gene densities (and all other structural and functional properties tested; see Table 1) define a genome desert, isochore families L1, L2, H1, and a genome core, isochore families H2, H3 (separated by a vertical broken red line). C. The scheme compares isochores belonging to the genome desert and to the genome core with chromatin domains and chromatin boundaries.
Mentions: The 10–20 Kb DNA molecules mentioned above derived, in fact, by degradation during preparation from much larger DNA stretches, fairly homogeneous in base composition [14], that were called “isochores” for (compositionally) equal landscapes. Isochores can be visualized by looking at the GC profiles of chromosomal sequences by using a 100-Kb fixed window (see Fig 1A for chromosome 21, the smallest human chromosome, which comprises, however, isochores from all families).

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