Comparative analysis of DNA loop length in nontransformed and transformed hamster cells

Linskens, Maarten H.K.; Eijsermans, Anneline; Dijkwel, Pieter A.

doi:10.1016/0027-5107(87)90275-2

Cited by 14 publications

(10 citation statements)

References 35 publications

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“…The occurrence of MARs at 70-to 120-kb intervals within the DHFR locus agrees well with estimates for the average size of DNA loops in mammalian cells (6,21,34). In several studies, it has been suggested that chromosomal loops correspond to replicons on the basis of their similar average sizes and proposed mechanisms for DNA replication (e.g., 6, 34).…”

Section: Discussionsupporting

confidence: 78%

“…DNA concentrations were additionally determined by a fluorimetric assay based on Hoechst staining (20). In a typical matrix preparation digested with an enzyme such as EcoRI, 4% of the total DNA remains attached to the matrix, which is close to the figure one would expect if the enzyme cuts every 4 kb on average and if chromosomal loops are 80 to 100 kb in length (6,21,36). Incubation with the combination EcoRI-HindIII-BamHIPvuII reduced this proportion to 1 to 2%.…”

Section: Methodsmentioning

confidence: 88%

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Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells.

Dijkwel¹,

Hamlin²

1988

Mol. Cell. Biol.

174

102

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Genomic DNA in higher eucaryotic cells is organized into a series of loops, each of which may be affixed at its base to the nuclear matrix via a specific matrix attachment region (MAR). In this report, we describe the distribution of MARs within the amplified dihydrofolate reductase (DHFR) domain (amplicon) in the methotrexate-resistant CHO cell line CHOC 400. In one experimental protocol, matrix-attached and loop DNA fractions were prepared from matrix-halo structures by restriction digestion and were analyzed for the distribution of amplicon sequences between the two fractions. A second, in vitro method involved the specific binding to the matrix of cloned DNA fragments from the amplicon. Both methods of analysis detected a MAR in the replication initiation locus that we have previously defined in the DHFR amplicon, as well as in the 5'-flanking region of the DHFR gene. The first of these methods also suggests the presence of a MAR in a region mapping -120 kilobases upstream from the DHFR gene. Each of these MARs was detected regardless of whether the matrix-halo structures were prepared by the high-salt or the lithium 3,5-diiodosalicylate extraction protocols, arguing against their artifactual association with the proteinaceous scaffolding of the nucleus during isolation procedures. However, the in vitro binding assay did not detect the MAR located 120 kilobases upstream from the DHFR gene but did detect specific matrix attachment of a sequence near the junction between amplicons. The results of these experiments suggest that (i) MARs can occur next to different functional elements in the genome, with the result that a DNA loop formed between two MARs can be smaller than a replicon; and (ii) different methods of analysis detect a somewhat different spectrum of matrix-attached DNA fragments.In the eucaryotic genome, the chromatin loop represents a basic structural unit. The loops are generated by periodic attachment of the chromatin fiber to a nonhistone chromosomal protein scaffolding in the nucleus, which has been referred to as the nuclear matrix (3,8,9,36). During mitosis, part of this matrix probably rearranges to become the metaphase chromosomal scaffold (2,19). Although neither the interphase nuclear matrix nor the mitotic chromosomal scaffold has been fully characterized as yet, topoisomerase II has been identified as an integral component of both (5,14). This finding has led to the suggestion that the nuclear matrix may somehow poise individual chromatin domains for transcription by allowing torsional stress to be introduced into defined regions (7). Nonrandom organization of the chromatin is further suggested by the presence at the base of the loops of specific DNA sequences that associate with the nuclear matrix. In Drosophila cells, specific matrix attachment regions (MARs) have been found in the 5'-flanking regions of several active genes (12,26,33), and these MARs coincide with enhancerlike elements (12). However, in the murine K light-chain gene, an attachment site is found at an intragenic site...

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Section: Discussionsupporting

confidence: 78%

Section: Methodsmentioning

confidence: 88%

Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells.

Dijkwel¹,

Hamlin²

1988

Mol. Cell. Biol.

174

102

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“…In Figure 5, we propose a model of chromatin organization of the studied 167 kb genomic region containing p53 and neighboring genes. Our results are quite surprising, since the average loop size is believed to be smaller in cancer cells as compared to that in normal controls [Linskens et al, 1987;Oberhammer et al, 1993]. Considering the importance of the TP53 tumor suppressor, it is possible that the studied region is contextually dependent on the state of the cell.…”

Section: Discussionmentioning

confidence: 47%

“…Rearrangement of DNA loops occurs during development when the loop size increases in somatic cells [Buongiorno-Nardelli et al, 1982;Vassetzky et al, 2000a]. Conversely, the average loop size decreases in transformed cells [Linskens et al, 1987] and in several human cancer cell lines in which it was found to be smaller than in their non-transformed counterparts [Oberhammer et al, 1993]. This may reflect a reversal in the differentiated state of the normal cells.…”

mentioning

confidence: 89%

Loop domain organization of the p53 locus in normal and breast cancer cells correlates with the transcriptional status of the TP53 and the neighboring genes

Góes¹,

Cappellen²,

Santos³

et al. 2011

J. Cell. Biochem.

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P53 is a tumor suppressor protein critical for genome integrity. Although its control at the protein level is well known, the transcriptional regulation of the TP53 gene is still unclear. We have analyzed the organization of the TP53 gene domain using DNA arrays in several breast cancer and control cell lines. We have found that in the control breast epithelial cell line, HB2, the TP53 gene is positioned within a relatively small DNA domain, encompassing 50 kb, delimited by two nuclear matrix attachment sites. Interestingly, this domain structure was found to be radically different in the studied breast cancer cell lines, MCF7, T47D, MDA-MB-231, and BT474, in which the domain size was increased and TP53 transcription was decreased. We propose a model in which the organization of the TP53 gene domain correlates with the transcriptional status of TP53 and neighboring genes.

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“…Rearrangement of DNA loops was also found in transformed BHK21 cells where the average size of loops was found to decrease [Linskens et al, 1987]. Additionally, the loop size in several human cancer cell lines was found to be ca.…”

Section: Loop Modification During Development and Cancermentioning

confidence: 74%

Rearrangement of chromatin domains in cancer and development

2000

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Both the accomplishment of developmental programs and neoplastic transformation are linked to changes in the long-range organization of chromatin, in particular, DNA loop domains. The development of new methods that allow the study of interactions between the bases of DNA loops and the proteins of the nuclear matrix will help our understanding of the molecular mechanisms in such changes. These methods should also allow the establishment of a ®ngerprint``signature'' for many cancers that may serve for diagnostic purposes.

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Comparative analysis of DNA loop length in nontransformed and transformed hamster cells

Abstract: Comparative analysis of DNA loop length in nontransformed and transformed hamster cells Linskens, Maarten; Eijsermans, Anneline; Dijkwel, Peter A.

Cited by 14 publications

References 35 publications

Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells.

Matrix attachment regions are positioned near replication initiation sites, genes, and an interamplicon junction in the amplified dihydrofolate reductase domain of Chinese hamster ovary cells.

Loop domain organization of the p53 locus in normal and breast cancer cells correlates with the transcriptional status of the TP53 and the neighboring genes

Rearrangement of chromatin domains in cancer and development

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