Micrococcal nuclease and DNase I digestion of DNA from aging human diploid cells

Gene Expression, Epigenetics and Ageing

As the popular adage goes, all diseases run into old age and almost all physiological changes are associated with alterations in gene expression, irrespective of whether they are causal or consequential. Therefore, the quest for mechanisms that delay ageing and decrease age-associated diseases has propelled researchers to unravel regulatory factors that lead to changes in chromatin structure and function, which ultimately results in deregulated gene expression. It is therefore essential to bring together literature, which until recently has investigated gene expression and chromatin independently. With advances in biomedical research and the emergence of epigenetic regulators as potential therapeutic targets, enhancing our understanding of mechanisms that 'derail' transcription and identification of causal genes/pathways during ageing will have a significant impact. In this context, this chapter aims to not only summarize the key features of age-associated changes in epigenetics and transcription, but also identifies gaps in the field and proposes aspects that need to be investigated in the future.

Image analysis-based measurement of DNA supercoiling changes in transformed and nontransformed human cell lines

An image analysis system was used to visualize and measure the changes in nucleoid diameter (nuclear matrix core plus extruded DNA loops) which occur when increasing concentrations of propidium iodide are used to titrate the DNA supercoiling response. Parallel core size measurements allow estimates of the changes in apparent DNA loop size. Unlike sedimentation assays, DNA loop size estimates are not influenced by particle mass, require no prior cell labeling, and can be performed on a per cell basis. This technique was used to examine changes in DNA loop characteristics which may occur when cells are transformed or undergo changes in their proliferative state. SV40-transformation of human diploid fibroblast lines resulted in a significant increase in both the nucleoid core and average DNA loop size. Lymphoblast cell lines also had larger nucleoid dimensions than normal lymphocytes. The response of several established human tumor cell lines indicated slightly increased loop but not core sizes as compared to normal human diploid fibroblasts. Changes in proliferative state also resulted in changes in DNA loop characteristics as measured in this assay. Both quiescent fibroblasts and unstimulated lymphocytes appeared to have smaller or more condensed DNA loop structures than their proliferating counterparts. These results demonstrate the utility of this assay in detecting changes in DNA loop structure which occur in association with changes in the proliferative activity of cells in culture.

Chromatin reorganization during senescence of proliferating cells

It was previously proposed (Macieira-Coelho, 1979) that aging of proliferating cells is the result of genome reorganization taking place during the division cycle. This hypothesis was investigated and a reorganization could indeed be ascertained in the different hierarchical orders of DNA structure; a correlation was found between changes in chromatin organization and the impairment of cell cycle-related events. Indeed, like the latter, the reorganization of chromatin structure is characterized by a succession of subtle changes through the cell population life span, and a final short stage with abrupt events. The final events seem to concern mainly the organization of heterochromatin. The reorganization in the genome is accompanied by structural changes in the cellular scaffold and an evolution of cell morphology. The remodeling occurring in the cell through serial divisions seems to take place in such a way as to decrease the probability of further reorganizations, tending to a limit. The decline of the proliferative activity seems to be the result of the tendency to reach this limit.

Organization of DNA in cerebellar neurons of ageing unirradiated and irradiated rats

Male Fischer 344 rats were either unirradiated or whole-brain irradiated with single doses of 10.83 or 17.16 Gy of X-rays at 4 months of age, and the organization of the DNA in permanently non-dividing cerebellar neurons examined as a function of age, dose and time after irradiation. In unirradiated rats and rats receiving a whole-brain dose of 10.83 Gy, there were no statistically significant changes in the organization of the bulk DNA and its association with the nuclear matrix as determined by: (a) the sensitivity of the DNA to digestion by micrococcal nuclease, (b) the sensitivity of the nuclear matrix-associated DNA to digestion by DNase I, (c) the relative DNA and protein content of undigested neuronal nuclei, and (d) the relative amount of DNA and protein that is tightly associated with the nuclear matrix after digestion with DNase I. In rats that were irradiated with 17.16 Gy at 4 months of age, there was a gradual decrease in the amount of nuclear proteins as a function of age (P less than 0.003). The amount of protein associated with the nuclear matrix in these irradiated aging rats was also consistently lower than that of their unirradiated counterparts (P less than 0.03). This decrease in the nuclear protein content of the cerebellar neurons in aging rats irradiated with 17.16 Gy may have caused a change in the overall organization of their neuronal DNA. Such a change in the organization of their neuronal DNA was indicated by a higher stainability of their bulk DNA by propidium iodide (P less than 0.03) and a higher sensitivity of the bulk DNA to digestion by m. nuclease (P = 0.087). Although these organizational changes in the neuronal DNA of aging rats irradiated with 17.16 Gy at 4 months of age are subtle, they might alter DNA repair processes or other neuronal functions that may be associated with the "natural" process of aging.

Changes in chromatin structure during aging of human skin fibroblasts

Human skin fibroblasts from embryo, 16-, 30- and 60-year-old adults were cultivated and passaged in vitro. Their chromatin structures were examined by the sensitivity to micrococcal nuclease and by electron microscopy. When the mode of DNA degradation by the nuclease was analysed during in vitro aging of the embryo skin fibroblasts, the discrete ladder of nucleosomal DNA became obscure in old cells. Analogous change of chromatin structure was also observed even in young cells as their donor ages increased. From the observation with electron microscopy, it became clear that chromatin of fibroblasts from 30-year-old adults does not have regularly spaced nucleosomes, compared with chromatin from embryo. These results suggest that the length of the linker DNA which connects core particles becomes to be heterogeneous by aging, both in vivo and in vitro in human skin fibroblasts.

Histone gene stability during cellular senescence

The extent to which human histone gene organization is conserved during the in vitro lifespan of human diploid fibroblast-like cells was determined by comparing the restriction patterns of a human H4 and an H3 histone gene from cells of various in vitro ages. No age related change in the organization of these two genes was detected.

Nuclease digestion of DNA and RNA in nuclei from young adult and senescent Caenorhabditis elegans (Nematoda)

Nuclei prepared from young adult and senescent Caenorhabditis elegans (Nematoda) were subjected to digestion by micrococcal nuclease and DNaseI. The kinetics of digestion of nuclei by micrococcal nuclease showed no change with age. There was, however, an age-related increase of acid-soluble deoxyribonucleotides released by DNaseI, suggesting that subtle alterations of chromatin conformation occur in aged nematodes. The ratio of nuclear RNA to DNA decreased and the nuclear RNA became more susceptible to enzymatic degradation as the worms grew old. These findings appear to indicate that nuclear RNA is less protected by protein in old nematodes. The decline of the nuclear RNA/DNA ratio with age is in good agreement with the generally accepted idea that there is a reduced level of RNA and protein synthesis in old animals.

Genome reorganization during aging of dividing cells

The study of the effect of low dose rate ionizing radiation on the long-term proliferation of fibroblasts led to the observation that radiation accentuated the growth potential of the cells, favoring events which normally take place during division. These events could be related to the genome reorganization taking place during division. Hence, it was hypothesized (Macieira-Coelho, 1979; Macieira-Coelho, 1980; Macieira-Coelho, 1981) that the long-term proliferation of fibroblasts depends upon the potential for reorganization of the genome, the latter being a self-limiting process. At each division residual quantitative and qualitative changes would accumulate in chromatin, limiting the long-term potential for further rearrangements. The hypothesis was checked looking for quantitative and qualitative changes in DNA through the in vitro lifespan of human fibroblast populations. It was found that at each population doubling in 20% of the cells there is unequal distribution of DNA between sister cells. Results show that this could be due to errors in chromosome assembly and segregation, to loss of DNA, to errors during semiconservative DNA synthesis and to multiple rounds of DNA replication at a single origin. An increased alkali- and thermo-lability of chromatin was found during in vitro aging. At the ultrastructural level after mild decondensation, chromatin fibers were spaced and shorter. After Miller's spreading, most of the chromatin of old cells had lost the nucleosome organization and was fragmented. These chromatin changes became apparent only towards the end of the life span of human embryonic fibroblasts but were already present in a significant fraction of low population doubling level (PDL) fibroblasts from human adults. Almost all cells of low-PDL fibroblasts from the Werner syndrome presented these chromatin changes. In addition, short, unbeaded DNA fragments could be seen in these fibroblasts, occasionally forming circles; they could correspond to transposable elements which detach during the division cycle and fail to reintegrate into chromosomes because of the age-related chromatin structural changes.

Age-related changes in the structure and function of chromatin: a review

Due to rapid advancement in biochemical and biophysical techniques during the last decade, extensive studies have been undertaken to understand the structure and function of chromatin. Several interesting results have been reported regarding the changes in basic organization and function of chromatin during the life time of a eukaryotic cell. The data accumulated so far have been obtained with different organs and organisms and widely differing methods, and the conclusions drawn from them are sometimes contradictory. In this paper, therefore, the available data on the age-associated alterations in the composition, structure and function of chromatin have been discussed, and an attempt has been made to correlate the structural changes in chromatin with alteration in gene expression during aging.

Genome reorganization during cellular senescence

It was previously suggested that aging of dividing cells depends on the reorganization of the cell genome during the division cycle and is determined by chance, intrinsic properties of the genome and environmental factors. A considerable amount of evidence has accumulated supporting the hypothesis. This is reviewed in terms of the reorganization taking place at the different orders of DNA structure.

Chromatin organization and transcriptional activity in human embryonic lung fibroblasts aged in vitro

Chromatin organization was examined in confluent cultures of embryonic lung fibroblasts in the middle and at the end of their replicative lifespan. Age-related modifications resulted in an unusually wide spacing of the chromatin threads induced by a mild loosening treatment and an increased sensitivity of the nucleosomes to the Joy-containing hypotonic medium used in Miller's spreads. The profound changes in chromatin response to various hypotonic solutions were not associated with the disappearance of RNA synthesis in old type nuclei as demonstrated by high-resolution autoradiographical studies.

The effects of histones, in vitro age, and culture state on the digestion of DNA by micrococcal nuclease and deoxyribonuclease I

Nuclei from confluent and mitotically arrested populations of human diploid fibroblast-like cells were subjected to digestion by micrococcal nuclease and deoxyribonuclease (DNase I) following the removal of various histone components by salt extraction. There was no age or culture state variation in the susceptibility of DNA to micrococcal nuclease digestion. There was an age related inhibition of DNA digestion by DNase I in nuclei from older confluent cells before and after the removal of H1 histone but not after the removal of core particle histones. This inhibition was not detected in older arrested populations. These results indicate that an age-related masking by nucleosome core histones may limit the accessibility of DNA to enzymatic activities in older confluent cells. Since this inhibition was absent in older arrested populations, the importance of limited DNA accessibility as a primary cause of cellular senescence is questionable.