Limits...
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.

Show MeSH

Related in: MedlinePlus

GC levels of prometaphase (A) and metaphase (B) bands of chromosome 1.Black arrows indicate p/q arms intervals, blue and red points indicates G and R bands, arrows single-isochore bands. Horizontal broken lines indicate the GC boundaries of isochore families. C. Scheme of the coalescence of prometaphase into metaphase bands.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4664426&req=5

pone.0143739.g005: GC levels of prometaphase (A) and metaphase (B) bands of chromosome 1.Black arrows indicate p/q arms intervals, blue and red points indicates G and R bands, arrows single-isochore bands. Horizontal broken lines indicate the GC boundaries of isochore families. C. Scheme of the coalescence of prometaphase into metaphase bands.

Mentions: An important feature of prometaphase bands is that not only their isochores and macroisochores alternate between higher and lower GC levels, but also that these levels are different in different sub-chromosomal regions, the compositional compartments. For example, the first two R bands on the centromeric side of chromosome 21 are lower in GC than the last two G bands on the telomeric side (see Fig 4D; see also Fig 5A for chromosome 1). These results lead to three conclusions: 1) GC contrasts and not absolute GC values are responsible for banding; 2) contrasts may be stronger or weaker (see Fig 4D), in agreement with the different degrees of staining intensity (G1 to G4) already noted for G bands [78]; 3) compositional compartments correspond to several prometaphase (and metaphase) bands. In fact, GC-rich and GC-poor compartments also alternate and tend to be located in telomeric and centromeric regions; interestingly, they show some profile similarity to the A and B compartments [64], respectively.


Chromosome Architecture and Genome Organization.

Bernardi G - PLoS ONE (2015)

GC levels of prometaphase (A) and metaphase (B) bands of chromosome 1.Black arrows indicate p/q arms intervals, blue and red points indicates G and R bands, arrows single-isochore bands. Horizontal broken lines indicate the GC boundaries of isochore families. C. Scheme of the coalescence of prometaphase into metaphase bands.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0143739.g005: GC levels of prometaphase (A) and metaphase (B) bands of chromosome 1.Black arrows indicate p/q arms intervals, blue and red points indicates G and R bands, arrows single-isochore bands. Horizontal broken lines indicate the GC boundaries of isochore families. C. Scheme of the coalescence of prometaphase into metaphase bands.
Mentions: An important feature of prometaphase bands is that not only their isochores and macroisochores alternate between higher and lower GC levels, but also that these levels are different in different sub-chromosomal regions, the compositional compartments. For example, the first two R bands on the centromeric side of chromosome 21 are lower in GC than the last two G bands on the telomeric side (see Fig 4D; see also Fig 5A for chromosome 1). These results lead to three conclusions: 1) GC contrasts and not absolute GC values are responsible for banding; 2) contrasts may be stronger or weaker (see Fig 4D), in agreement with the different degrees of staining intensity (G1 to G4) already noted for G bands [78]; 3) compositional compartments correspond to several prometaphase (and metaphase) bands. In fact, GC-rich and GC-poor compartments also alternate and tend to be located in telomeric and centromeric regions; interestingly, they show some profile similarity to the A and B compartments [64], respectively.

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