Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix

Iarovaia, Olga V.; Akopov, S. B.; Николаев, Л. Г.; Razin, Sergey V.

doi:10.1093/nar/gki733

Cited by 31 publications

(34 citation statements)

References 32 publications

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“…This result is similar to that obtained previously in experiments with a human genomic domain containing actively transcribed genes [Iarovaia et al, 2005]. Also, according to the previous data, the same 250 Kb DNA fragment was partially looped out from the nuclear matrix in DT40 cells where the central area of this fragment (including the domain of alphaglobin genes) is either not transcribed at all or transcribed at a very low level.…”

Section: Discussionsupporting

confidence: 91%

“…This finding correlates well with previous observations demonstrating that active genes are associated with the nuclear matrix [Ciejek et al, 1983;Robinson et al, 1983]. In our recent study we have demonstrated that activation of transcription of several tissue-specific genes within a large DNA loop domain induces an association with the nuclear matrix of the whole looped DNA fragment [Iarovaia et al, 2005]. In the same study it was observed that genes transcribed at a very low level were not necessarily associated with the nuclear matrix [Iarovaia et al, 2005].…”

supporting

confidence: 93%

“…In the present study we have characterized the spatial organization in erythroid and non-erythroid cells of a large (250 Kb) region of chicken chromosome 14 which includes a cluster of erythroid cellspecific alpha globin genes and a number of other open reading frames that are transcribed and believed to represent essential house-keeping genes [Flint et al, 2001;Tufarelli et al, 2004]. Using in situ hybridization with nuclear halos [Iarovaia et al, 2004[Iarovaia et al, , 2005, we have demonstrated that in lymphoid cells the region under study was partially associated with the nuclear matrix. In AEVtransformed cultured erythroid cells derived from bone marrow of anemic chickens this region was fully associated with the nuclear matrix both before and after induction of alpha-globin gene transcription.…”

mentioning

confidence: 88%

“…The 250 Kb insertion of this clone includes the whole DNA region presented in Figure 1A. Nuclear halos representing the crown of extended DNA loops fixed at the nuclear matrix were prepared by 2 M NaCl extraction of cells cytospun on microscopic slides [Iarovaia et al, 2004[Iarovaia et al, , 2005. In the first set of experiments nuclear halos were prepared from DT40 cells.…”

Section: Analysis Of the Spatial Organization Of The Genomic Region Umentioning

confidence: 99%

“…In our recent study we have demonstrated that activation of transcription of several tissue-specific genes within a large DNA loop domain induces an association with the nuclear matrix of the whole looped DNA fragment [Iarovaia et al, 2005]. In the same study it was observed that genes transcribed at a very low level were not necessarily associated with the nuclear matrix [Iarovaia et al, 2005]. In connection with these results, it was interesting to study the pattern of association with the nuclear matrix of a large genomic area containing both tissue-specific and house-keeping genes.…”

mentioning

confidence: 99%

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In embryonic chicken erythrocytes actively transcribed alpha globin genes are not associated with the nuclear matrix

Iarovaia

Borounova

Philonenko

et al. 2008

J of Cellular Biochemistry

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The spatial organization of a 250 Kb region of chicken chromosome 14, which includes the alpha globin gene cluster, was studied using in situ hybridization of a corresponding BAC probe with nuclear halos. It was found that in non-erythroid cells (DT40) and cultured erythroid cells of definite lineage (HD3) the genomic region under study was partially (DT40 cells) or fully (HD3 cells) associated with the nuclear matrix. In contrast, in embryonic red blood cells (10-day RBC) the same area was located in the crown of DNA loops surrounding the nuclear matrix, although both globin genes and surrounding house-keeping genes were actively transcribed in these cells. This spatial organization was associated with the virtual absence of RNA polymerase II in nuclear matrices prepared from 10-day RBC. In contrast, in HD3 cells a significant portion of RNA polymerase II was present in nuclear matrices. Taken together, these observations suggest that in embryonic erythroid cells transcription does not occur in association with the nuclear matrix.

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Section: Discussionsupporting

confidence: 91%

supporting

confidence: 93%

mentioning

confidence: 88%

Section: Analysis Of the Spatial Organization Of The Genomic Region Umentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

In embryonic chicken erythrocytes actively transcribed alpha globin genes are not associated with the nuclear matrix

Iarovaia

Borounova

Philonenko

et al. 2008

J of Cellular Biochemistry

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Measurement of Drug‐Stabilized Topoisomerase II Cleavage Complexes by Flow Cytometry

2017

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The poisoning of Topoisomerase II (Top2) has been found to be useful as a therapeutic strategy for the treatment of several tumors. The mechanism of Top2 poisons involves a drug-mediated stabilization of a Top2-DNA complex, termed Top2 cleavage complex (Top2cc), which maintains a 5' end of DNA covalently bound to a tyrosine from Top2 through a phosphodiester group. Drug-stabilized Top2cc leads to Top2-linked-DNA breaks, which are believed to mediate their cytotoxicity. Several time-consuming or cell type-limiting assays have been used in the past to study drug-stabilized Top2cc. Here, we describe a flow cytometry-based method that allows a rapid assessment of drug-induced Top2cc, which is suitable for high throughput analysis in almost any kind of human cell. The analyses of the drug-induced Top2cc in the cell cycle context and the possibility to track its removal are additional benefits from this methodology. © 2017 by John Wiley & Sons, Inc.

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A flow cytometry‐based method for a high‐throughput analysis of drug‐stabilized topoisomerase II cleavage complexes in human cells

2016

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Topoisomerase II (Top2) is an important target for anticancer therapy. A variety of drugs that poison Top2, including several epipodophyllotoxins, anthracyclines, and anthracenediones, are widely used in the clinic for both hematologic and solid tumors. The poisoning of Top2 involves the formation of a reaction intermediate Top2-DNA, termed Top2 cleavage complex (Top2cc), which is persistent in the presence of the drug and involves a 5 0 end of DNA covalently bound to a tyrosine from the enzyme through a phosphodiester group. Drug-induced Top2cc leads to Top2 linked-DNA breaks which are the major responsible for their cytotoxicity. While biochemical detection is very laborious, quantification of drug-induced Top2cc by immunofluorescence-based microscopy techniques is time consuming and requires extensive image segmentation for the analysis of a small population of cells. Here, we developed a flow cytometry-based method for the analysis of drug-induced Top2cc. This method allows a rapid analysis of a high number of cells in their cell cycle phase context. Moreover, it can be applied to almost any human cell type, including clinical samples. The methodology is useful for a high-throughput analysis of drugs that poison Top2, allowing not just the discrimination of the Top2 isoform that is targeted but also to track its removal. Key terms flow cytometry; topoisomerase II; Top2 poison; high throughput analysis TOPOISOMERASE II (Top2) is a dimeric enzyme that catalyzes topological changes in the DNA, thus being essential in several metabolic processes of the genome of eukaryotic cells (1,2). In mammals, there have been characterized two variants of Top2, a and b isoforms, showing different activities and regulation of their expression. While Top2a expression and activity increase throughout the cell cycle, Top2b remains at similar levels (3,4). Top2a is essential for cell proliferation, participating in several processes such as replication, transcription, and chromosome condensation and segregation (5). In contrast, Top2b is dispensable for cell proliferation, but contributes to transcription and is required during development (6,7). Top2 acts by nicking both strands of the DNA to allow the passage through it of other doublestranded segment of DNA from the same or a different molecule. Following the breakage of the double-stranded DNA, each monomer of Top2 remains covalently linked to each 5 0 terminus of DNA by a transient phosphotyrosyl linkage, a reaction intermediate termed cleavage complex (Top2cc) (8,9). Certain natural compounds, spontaneous DNA lesions and several chemotherapeutic agents can stabilize the Top2cc increasing their half-life (10-12). These agents interfere with the breakagereunion reaction that leads to a reversible DNA damage, which becomes irreversible

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Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix

Cited by 31 publications

References 32 publications

In embryonic chicken erythrocytes actively transcribed alpha globin genes are not associated with the nuclear matrix

In embryonic chicken erythrocytes actively transcribed alpha globin genes are not associated with the nuclear matrix

Measurement of Drug‐Stabilized Topoisomerase II Cleavage Complexes by Flow Cytometry

A flow cytometry‐based method for a high‐throughput analysis of drug‐stabilized topoisomerase II cleavage complexes in human cells

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