Large-scale Fragmentation of Mammalian DNA in the Course of Apoptosis Proceeds via Excision of Chromosomal DNA Loops and Their Oligomers

Lagarkova, Maria A.; Iarovaia, Olga V.; Razin, Sergey V.

doi:10.1074/jbc.270.35.20239

Cited by 126 publications

(86 citation statements)

References 17 publications

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“…34 There have been a number of reports in the literature suggesting that initiation of apoptotic DNA cleavage occurs at matrix attachment regions. 6,7,[35][36][37] The first supporting evidence came from studies that establish that high molecular weight DNA fragments of 50 and 300 kb, produced in early stages of apoptosis, represent structural domains of chromatin, loops and rosettes, respectively. 1,7 It was then suggested that topoisomerase II, located at matrix attachment sites, is responsible for this cleavage since inhibition of its activity generated the same pattern of DNA fragments.…”

Section: Discussionmentioning

confidence: 99%

“…1,7 It was then suggested that topoisomerase II, located at matrix attachment sites, is responsible for this cleavage since inhibition of its activity generated the same pattern of DNA fragments. 6,38 However, others have shown that the activation of endogenous and several exogenous nucleases also results in DNA digestion in the proximity of MARs and produces similar sets of high molecular weight 50 and 300 kb fragments as those generated by topoisomerase II inhibitors. 7,36 More direct evidence that MARs are specific targets for early DNA cleavage came recently from the study of Khodarev et al 39 These authors performed a directional cloning of DNA ends corresponding to high molecular weight chromatin fragments produced during radiation-induced apoptosis, and found them to contain ATrich MAR-like sequences.…”

Section: Discussionmentioning

confidence: 99%

“…1,2 The large DNA fragments are thought to arise from the cleavage of DNA domains at matrix attachment regions (MARs) and may result from the accumulation of single-strand (ss) breaks introduced in the vulnerable DNA regions in contact with the nuclear matrix. [3][4][5][6][7] Many chromatinassociated proteins, such as DNA topoisomerase II, PARP, NuMA, lamin B, SAF-A and SATB1, have been shown to undergo site-specific proteolysis during apoptosis. [8][9][10][11][12][13] This process can be temporally linked to the initiation of DNA cleavage, suggesting that the latter may be a consequence of the loss of a protective protein coating.…”

Section: Introductionmentioning

confidence: 99%

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Mapping the initial DNA breaks in apoptotic Jurkat cells using ligation-mediated PCR

et al. 2003

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Apoptotic DNA degradation could be initiated by the accumulation of single-strand (ss) breaks in vulnerable chromatin regions, such as base unpairing regions (BURs), which might be preferentially targeted for degradation by both proteases and nucleases. We tested this hypothesis in antiFas-treated apoptotic Jurkat cells. Several nuclear proteins known for their association with both MARs and the nuclear matrix, that is, PARP, NuMA, lamin B and SATB1, were degraded, but the morphological rearrangement of the BURbinding SATB1 protein was one of the earliest detected changes. Subsequently, we have identified several genes containing sequences homologous to the 25 bp BUR element of the IgH gene, a known SATB1-binding site, and examined the integrity of genomic DNA in their vicinity. Multiple ss breaks were found in close proximity to these sites relative to adjacent regions of DNA. Consistent with our prediction, the results indicated that the initiation of DNA cleavage in antiFas-treated Jurkat cells occurred within the BUR sites, which likely became accessible to endonucleases due to the degradation of BUR-binding proteins.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Mapping the initial DNA breaks in apoptotic Jurkat cells using ligation-mediated PCR

et al. 2003

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“…This event has been considered essential for apoptosis and it is, most likely, catalysed by an endonuclease that resides at the matrix attachment regions (MARs) where DNA binds to the nuclear scaffold. 1,2 The second stage of nuclear destruction involves more extensive DNA degradation and usually produces oligonucleosomal DNA ladders. Some authors consider this stage as a housekeeping process, since blocking it does not prevent apoptosis; 3 however, there are also reports arguing that the inhibition of the internucleosomal ladder formation may reduce, or at least delay apoptosis.…”

Section: Introductionmentioning

confidence: 99%

Regulation of DNaseY activity by actinin-α4 during apoptosis

et al. 2004

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DNaseY, a Ca 2 þ -and Mg 2 þ -dependent endonuclease, has been implicated in apoptotic DNA degradation; however, the molecular mechanisms controlling its involvement in this process have not been fully elucidated. We have obtained evidence from yeast two-hybrid screening and coimmunoprecipitation experiments that DNaseY interacted physically with actinin-a4 and this interaction significantly enhanced its endonuclease activity. Accordingly, simultaneous overexpression of both proteins in PC12 cells dramatically increased the rate of apoptosis in response to teniposide' VM26. However, overexpression of DNaseY alone neither triggered apoptosis nor facilitated cell death in response to VM26 or serum deprivation. Instead, the overexpression of DNaseY increased the production of single-strand DNA breaks and evoked a profound upregulation of DNA repair pathways. Taken together, our results point to a novel regulatory mechanism of DNaseY activity and offer an explanation for why cells must first cleave key DNA repair and replication proteins before the successful execution of apoptosis.

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“…In addition, another type of DNA cleavage during apoptosis has been reported to yield a set of the high molecular weight (HMW) 1 DNA fragments of about 50 -100 kb (7). The formation of HMW DNA fragments is widely thought to result from the excision of DNA loop domains at the positions of their attachment to the nuclear matrix (8,9) and is considered to be an initial step in DNA disintegration during apoptosis (7, 10 -12).…”

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confidence: 99%

The Role of Topoisomerase II in the Excision of DNA Loop Domains during Apoptosis

Solovyan¹,

Bezvenyuk²,

Salminen³

et al. 2002

Journal of Biological Chemistry

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Disintegration of nuclear DNA into high molecular weight (HMW) and oligonucleosomal DNA fragments represents two major periodicities of DNA fragmentation during apoptosis. These are thought to originate from the excision of DNA loop domains and from the cleavage of nuclear DNA at the internucleosomal positions, respectively. In this report, we demonstrate that different apoptotic insults induced apoptosis in NB-2a neuroblastoma cells that was invariably accompanied by the formation of HMW DNA fragments of about 50 -100 kb but proceeded either with or without oligonucleosomal DNA cleavage, depending on the type of apoptotic inducer. We demonstrate that differences in the pattern of DNA fragmentation were reproducible in a cell-free apoptotic system and develop conditions that allow in vitro separation of the HMW and oligonucleosomal DNA fragmentation activities. In contrast to apoptosis associated with oligonucleosomal DNA fragmentation, the HMW DNA cleavage in apoptotic cells was accompanied by down-regulation of caspase-activated DNase (CAD) and was not affected by z-VAD-fmk, suggesting that the caspase/CAD pathway is not involved in the excision of DNA loop domains. We further demonstrate that nonapoptotic NB-2a cells contain a constitutively present nuclease activity located in the nuclear matrix fraction that possessed the properties of topoisomerase (topo) II and was capable of reproducing the pattern of HMW DNA cleavage that occurred in apoptotic cells. We demonstrate that the early stages of apoptosis induced by different stimuli were accompanied by activation of topo II-mediated HMW DNA cleavage that was reversible after removal of apoptotic inducers, and we present evidence of the involvement of topo II in the formation of HMW DNA fragments at the advanced stages of apoptosis. The results suggest that topo II is involved in caspase-independent excision of DNA loop domains during apoptosis, and this represents an alternative pathway of apoptotic DNA disintegration from CAD-driven caspase-dependent oligonucleosomal DNA cleavage.At the higher level of chromatin compaction, nuclear DNA is arranged into loop domains by periodical attachment of the chromatin fiber to the nuclear matrix (1, 2). The domain level of chromatin organization is supported by the interaction of specific DNA sequences, matrix/scaffold attachment regions, with nuclear matrix proteins (3). The chromatin loops represent the basic structural components of higher-order chromatin folding, which is maintained during the cell cycle and in differentiated cells (3-5).Disintegration of nuclear DNA into nucleosome-sized fragments represents a classical manifestation of apoptosis (6). In addition, another type of DNA cleavage during apoptosis has been reported to yield a set of the high molecular weight (HMW) 1 DNA fragments of about 50 -100 kb (7). The formation of HMW DNA fragments is widely thought to result from the excision of DNA loop domains at the positions of their attachment to the nuclear matrix (8, 9) and is considered to be an initial...

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Large-scale Fragmentation of Mammalian DNA in the Course of Apoptosis Proceeds via Excision of Chromosomal DNA Loops and Their Oligomers

Cited by 126 publications

References 17 publications

Mapping the initial DNA breaks in apoptotic Jurkat cells using ligation-mediated PCR

Mapping the initial DNA breaks in apoptotic Jurkat cells using ligation-mediated PCR

Regulation of DNaseY activity by actinin-α4 during apoptosis

The Role of Topoisomerase II in the Excision of DNA Loop Domains during Apoptosis

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