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DNA moves sequentially towards the nuclear matrix during DNA replication in vivo.

Rivera-Mulia JC, Hernández-Muñoz R, Martínez F, Aranda-Anzaldo A - BMC Cell Biol. (2011)

Bottom Line: We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops.Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated.These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, CP 50000 Toluca, Edo Méx, México.

ABSTRACT

Background: In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). There is varied evidence indicating that DNA replication occurs in replication factories organized upon the NM and that DNA loops may correspond to the actual replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but they synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration in vivo. We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops.

Results: In the present work we tracked down the movement relative to the NM of DNA sequences located at different points within such five structural DNA loops during the S phase and after the return to cellular quiescence during liver regeneration. Our results indicate that looped DNA moves sequentially towards the NM during replication and then returns to its original position in newly quiescent cells, once the liver regeneration has been achieved.

Conclusions: Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated. These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.

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Changes in the configuration of the structural DNA loops as a function of DNA replication. A) Structural DNA loop organization of the 162 kbp region containing the rat albumin locus in undisturbed, control G0 hepatocytes. The letters (a-o) indicate the position of the corresponding target sequences relative to the NM. Color lines indicate the position of the corresponding named gene. The small dashed lines indicate projected loop regions outside of the region studied. The black ovals within the NM correspond to putative LARs. B) Average configuration of the structural DNA loops in the same region at the peak of DNA synthesis (24 h after partial hepatectomy) deduced from the results in Tables 2 and 3. Dashed lines indicate the segment of the corresponding gene possibly awaiting replication. Bold-color lines indicate the daughter duplexes containing one parental strand and one newly made strand, that are extruded in loops as the parental duplex slides through the fixed replication sites on the NM (parental loops shrink whereas daughter loops grow). Letters (b...) indicate target sequences to be replicated. Letters with apostrophe (a'...) indicate target sequences that have been replicated already. The double-headed arrows in the NM correspond to active replication forks derived from putative origins of replication located close to the LARs. In this representation the early-replicating LARs (black ovals) become attached to the NM immediately after replication, thus producing tiny but transient duplicate daughter loops that should disappear once the whole region has been duplicated.
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Figure 5: Changes in the configuration of the structural DNA loops as a function of DNA replication. A) Structural DNA loop organization of the 162 kbp region containing the rat albumin locus in undisturbed, control G0 hepatocytes. The letters (a-o) indicate the position of the corresponding target sequences relative to the NM. Color lines indicate the position of the corresponding named gene. The small dashed lines indicate projected loop regions outside of the region studied. The black ovals within the NM correspond to putative LARs. B) Average configuration of the structural DNA loops in the same region at the peak of DNA synthesis (24 h after partial hepatectomy) deduced from the results in Tables 2 and 3. Dashed lines indicate the segment of the corresponding gene possibly awaiting replication. Bold-color lines indicate the daughter duplexes containing one parental strand and one newly made strand, that are extruded in loops as the parental duplex slides through the fixed replication sites on the NM (parental loops shrink whereas daughter loops grow). Letters (b...) indicate target sequences to be replicated. Letters with apostrophe (a'...) indicate target sequences that have been replicated already. The double-headed arrows in the NM correspond to active replication forks derived from putative origins of replication located close to the LARs. In this representation the early-replicating LARs (black ovals) become attached to the NM immediately after replication, thus producing tiny but transient duplicate daughter loops that should disappear once the whole region has been duplicated.

Mentions: Since the target sequences correspond to sites located at different points along the five structural loops comprising the region studied (Figure 5A), these results suggest that at 24 h after partial hepatectomy the DNA loops are somehow reeled or pulled progressively towards the NM where the replication factories are assembled (Figure 5B), recovering later on their original configuration. This is confirmed by the fact that the positions of most target sequences relative to the NM in rat hepatocytes obtained 7 days after partial hepatectomy (when liver regeneration is complete) are basically the same as those in undisturbed G0 controls (Table 2 and 3).


DNA moves sequentially towards the nuclear matrix during DNA replication in vivo.

Rivera-Mulia JC, Hernández-Muñoz R, Martínez F, Aranda-Anzaldo A - BMC Cell Biol. (2011)

Changes in the configuration of the structural DNA loops as a function of DNA replication. A) Structural DNA loop organization of the 162 kbp region containing the rat albumin locus in undisturbed, control G0 hepatocytes. The letters (a-o) indicate the position of the corresponding target sequences relative to the NM. Color lines indicate the position of the corresponding named gene. The small dashed lines indicate projected loop regions outside of the region studied. The black ovals within the NM correspond to putative LARs. B) Average configuration of the structural DNA loops in the same region at the peak of DNA synthesis (24 h after partial hepatectomy) deduced from the results in Tables 2 and 3. Dashed lines indicate the segment of the corresponding gene possibly awaiting replication. Bold-color lines indicate the daughter duplexes containing one parental strand and one newly made strand, that are extruded in loops as the parental duplex slides through the fixed replication sites on the NM (parental loops shrink whereas daughter loops grow). Letters (b...) indicate target sequences to be replicated. Letters with apostrophe (a'...) indicate target sequences that have been replicated already. The double-headed arrows in the NM correspond to active replication forks derived from putative origins of replication located close to the LARs. In this representation the early-replicating LARs (black ovals) become attached to the NM immediately after replication, thus producing tiny but transient duplicate daughter loops that should disappear once the whole region has been duplicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037911&req=5

Figure 5: Changes in the configuration of the structural DNA loops as a function of DNA replication. A) Structural DNA loop organization of the 162 kbp region containing the rat albumin locus in undisturbed, control G0 hepatocytes. The letters (a-o) indicate the position of the corresponding target sequences relative to the NM. Color lines indicate the position of the corresponding named gene. The small dashed lines indicate projected loop regions outside of the region studied. The black ovals within the NM correspond to putative LARs. B) Average configuration of the structural DNA loops in the same region at the peak of DNA synthesis (24 h after partial hepatectomy) deduced from the results in Tables 2 and 3. Dashed lines indicate the segment of the corresponding gene possibly awaiting replication. Bold-color lines indicate the daughter duplexes containing one parental strand and one newly made strand, that are extruded in loops as the parental duplex slides through the fixed replication sites on the NM (parental loops shrink whereas daughter loops grow). Letters (b...) indicate target sequences to be replicated. Letters with apostrophe (a'...) indicate target sequences that have been replicated already. The double-headed arrows in the NM correspond to active replication forks derived from putative origins of replication located close to the LARs. In this representation the early-replicating LARs (black ovals) become attached to the NM immediately after replication, thus producing tiny but transient duplicate daughter loops that should disappear once the whole region has been duplicated.
Mentions: Since the target sequences correspond to sites located at different points along the five structural loops comprising the region studied (Figure 5A), these results suggest that at 24 h after partial hepatectomy the DNA loops are somehow reeled or pulled progressively towards the NM where the replication factories are assembled (Figure 5B), recovering later on their original configuration. This is confirmed by the fact that the positions of most target sequences relative to the NM in rat hepatocytes obtained 7 days after partial hepatectomy (when liver regeneration is complete) are basically the same as those in undisturbed G0 controls (Table 2 and 3).

Bottom Line: We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops.Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated.These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.

View Article: PubMed Central - HTML - PubMed

Affiliation: Laboratorio de Biología Molecular, Facultad de Medicina, Universidad Autónoma del Estado de México, Apartado Postal 428, CP 50000 Toluca, Edo Méx, México.

ABSTRACT

Background: In the interphase nucleus of metazoan cells DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). There is varied evidence indicating that DNA replication occurs in replication factories organized upon the NM and that DNA loops may correspond to the actual replicons in vivo. In normal rat liver the hepatocytes are arrested in G0 but they synchronously re-enter the cell cycle after partial-hepatectomy leading to liver regeneration in vivo. We have previously determined in quiescent rat hepatocytes that a 162 kbp genomic region containing members of the albumin gene family is organized into five structural DNA loops.

Results: In the present work we tracked down the movement relative to the NM of DNA sequences located at different points within such five structural DNA loops during the S phase and after the return to cellular quiescence during liver regeneration. Our results indicate that looped DNA moves sequentially towards the NM during replication and then returns to its original position in newly quiescent cells, once the liver regeneration has been achieved.

Conclusions: Looped DNA moves in a sequential fashion, as if reeled in, towards the NM during DNA replication in vivo thus supporting the notion that the DNA template is pulled progressively towards the replication factories on the NM so as to be replicated. These results provide further evidence that the structural DNA loops correspond to the actual replicons in vivo.

Show MeSH
Related in: MedlinePlus