Selective loss of ribosomal RNA genes during the aging of post-mitotic tissues

Relationship between ribosomal RNA gene transcription activity and motoneuron death: Observations of avulsion and axotomy of the facial nerve in rats

Motoneuron number and expression of cytoplasmic RNA and ribosomal RNA (rRNA) gene transcription activity in the facial nucleus were examined quantitatively and chronologically for up to 4 weeks in rats after facial nerve axotomy and avulsion in order to elucidate interrelationships in axonal changes. The right facial nerves of adult Fischer rats were avulsed at a portion of the outlet or axotomized at a portion of the foramen stylomastoideus. The number of large motoneurons in the facial nucleus was reduced by 40% 2 weeks after avulsion and by 70% 4 weeks after avulsion but displayed a 19% loss even 4 weeks after axotomy. The amount of cytoplasmic RNA decreased significantly and progressively from 1 day after avulsion. rRNA gene transcription activity in the large motoneurons of the facial nucleus decreased significantly beginning 30 min after both axotomy and avulsion, but the severity of the decrease was far more marked in the avulsion group, showing a 59% loss from the control value 4 weeks after avulsion. These findings indicate that rRNA gene transcription activity, expression of cytoplasmic RNA, and the number of motoneurons that survive are interrelated and that the decrease in rRNA gene transcription activity is a very early event in the phenomena observed in the axonal reactions of motoneurons.

Klotho insufficiency causes decrease of ribosomal RNA gene transcription activity, cytoplasmic RNA and rough ER in the spinal anterior horn cells

The klotho gene was identified in 1997 as the gene whose severe insufficiency (kl/kl) causes a syndrome resembling human aging, such as osteoporosis, arteriosclerosis, gonadal atrophy, emphysema, and short life span in a mouse strain. Regarding the gait disturbance reported in kl/kl mice, the present study examined the spinal cord of kl/kl mice, and revealed decreases in the number of large anterior horn cells (AHCs), the amount of cytoplasmic RNA, the number of ribosomes and rough endoplasmic reticulum (rER), and the activity of ribosomal (r) RNA gene transcription without significant loss of the total number of neurons in the ventral gray matter. Increased immunostaining of phosphorylated neurofilament in the AHCs and of glial fibrillary acidic protein in reactive astrocytes in the anterior horn of kl/kl mice were also observed. On the other hand, the posterior horn was quite well preserved. The results suggest that the kl/kl insufficiency causes atrophy and dysfunction of the spinal AHCs through decreased activity of rRNA gene transcription, which may reduce the amount of cytoplasmic RNA and the number of ribosomes and rER. These findings resemble those found in the spinal cord of patients with classic amyotrophic lateral sclerosis (ALS). The results show that klotho gene insufficiency causes dysfunction of the protein synthesizing system in the AHCs, and might indicate the klotho gene is involved in the pathological mechanism of classic ALS. The kl/kl is a new animal model of AHC degeneration, and may provide clues to understanding the etiology of classic ALS.

Extrachromosomal circular DNAs and genomic sequence plasticity in eukaryotic cells

The ability of eukaryotic organisms of the same genotype to vary in developmental pattern or in phenotype according to varying environmental conditions is frequently associated with changes in extrachromosomal circular DNA (eccDNA) sequences. Although variable in size, sequence complexity, and copy number, the best characterized of these eccDNAs contain sequences homologous to chromosomal DNA which indicates that they might arise from genetic rearrangements, such as homologous recombination. The abundance of repetitive sequence families in eccDNAs is consistent with the notion that tandem repeats and dispersed repetitive elements participate in intrachromosomal recombination events. There is also evidence that a fraction of this DNA has characteristics similar to retrotransposons. It has been suggested that eccDNAs could reflect altered patterns of gene expression or an instability of chromosomal sequences during development and aging. This article reviews some of the findings and concepts regarding eccDNAs and sequence plasticity in eukaryotic genomes.

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.

Age-related RNA polymerase I activity in isolated nuclei of PHA stimulated human lymphocytes

In order to extend to the immune system previous findings that there is an age-related loss of hybridizability of the genes for ribosomal RNA (rRNA) in several tissues of mice, dogs and humans, we have investigated the function of the genes for rRNA in human T lymphocytes. These cells were chosen because they show a substantial decline in function with age, greater than that of other components of the immune system. rRNA synthesis was determined by measuring tritiated-UTP incorporation into acid precipitable counts as a result of the action of RNA polymerase I in nuclei isolated from phytohemagglutinin (PHA) stimulated peripheral-blood lymphocytes from 24 young adult and old human donors. The number of PHA-responsive cells from each donor was determined by counting grains in autoradiographs after a pulse of tritiated-uridine had been administered to them. The aggregate PHA induced synthesis of rRNA in the cultures decreased as a function of the age of the donor. However, the number of PHA-responsive cells also dropped with age. When the data are normalized for the number of PHA-responsive cells in each culture, it appears that rRNA synthesis per PHA-responding cell does not significantly decline with age, even though there is a suggestion of a decrease after corrections are made. On the average, differences between individuals of the same age group were as great or greater than age-related differences.

Genetic instability as the primary cause of human aging

The origins of aging of higher forms of life, particularly humans, is presented as the consequence of an evolved balance between 4 specific kinds of dysfunction-producing events and 4 kinds of evolved counteracting effects in long-lived forms. Among the deleterious events, particular importance is assigned to damage to DNA, but damage of a different kind than classical mutations. The evolution in man's ancestors of means to counteract the kinds of events that limit the life-spans of short lived mammals is postulated to be the indirect consequence of the prior evolution of superior mental capacities. Further, it is shown that the human species rapidly evolved its life-extending mutations because of the special circumstances afforded by the subdivision of the species into small semi-isolated (genetically) tribes of 10-100 individuals in which polygamy was the key factor in rapid incorporation of life- and well-being-extending new features. These conditions permit at least one or two orders of magnitude more of such beneficial genes to have been incorporated into our genomes during the 100,000 years or so of extremely rapid human evolution that evidently occurred about 100,000 to 200,000 years age than has been posited by other workers. The sources of damage to DNA are then considered, with special emphasis on free-radical derivatives of molecular oxygen and evidence is presented that longer lived forms of mammals have peroxide lysing enzymes that produce a lower steady state of damaging radicals derived from this compound. Evidence that so-called "classical" mutations cannot be the source of aging is then reviewed. A different kind of mutation, one that is not increased in proportion to point mutations by mutagens, namely deletion of tandemly duplicated copies of genes, is discussed and the evidence that such damage (gene loss) occurs in an amount sufficient to account for the major losses in function during aging is presented. The most likely mechanisms of such loss plus the prospects for evolving and bio-engineering means to counteract these losses together with some implications regarding the documented loss of NORs with age (as regards rDNA loss) together with key areas for intensive present and future research on aging are presented.

Appearance of extrachromosomal circular DNAs during in vivo and in vitro ageing of mammalian cells

Appearance of extrachromosomal circular DNAs with in vivo and in vitro cellular ageing was examined by using a new technique of mica-press-adsorption for electron microscopy. The size distribution and the copy number of circular DNA complexes varied, depending on the cellular age. Extrachromosomal circular DNA complexes of variable length of more than 0.5 microns or 1.5 kilobase (kb) appeared during in vivo ageing of rat lymphocytes and in vitro ageing of cultured human lung fibroblasts. A restricted size class of circular forms of less than 0.5 microns in contour length was amplified in human skin fibroblasts from aged normal or Werner's syndrome subjects. These circular DNA molecules are suggested to be products of DNA rearrangements or gene amplification occurring in the chromosome.

Amplification of extrachromosomal small circular DNAs in a murine model of accelerated senescence. A brief note

Extrachromosomal circular DNA complexes from peripheral blood lymphocytes from inbred mice of accelerated senescence, were detected by mica-press-adsorption method. In senescence-resistant series (SAM-R), polydisperse circular DNAs were observed at 7 weeks of age and a restricted size class of small circular forms of 0.4-0.8 microns in contour length was amplified several-fold at 26 months of age. In senescence-prone series (SAM-P), a similar amplification of small circular DNAs was observed at young age of 10 weeks and more progressive at 17 months of age.

Age changes of chromatin. A review

The age-related studies of chromatin and DNA has attracted significant interest in recent years. However, individual works describe only some and a few of the many changes of chromatin. It is often difficult to decide whether these changes have secondary or primary nature. The overview of these studies makes it possible to realize how many very complex and interdependent changes occur in chromatin during ageing. Chromatin is the most complex among self-reproducible parts of the cell. A very sophisticated structure of chromatin makes possible the differential transcription of a genetic programme which supports the accurate specialized functions of each cell in interphase and also provides a mechanism for perfect reproduction of this complex machinery of genetic information during cell division. It is known that chromatin proteins, more than chromatin DNA show tissue specificity and developmental changes. There are many theories of cellular ageing which select some special types of DNA, RNA or protein changes and to promote them as the main or primary causes of cellular senescence. However, if these changes are considered within the more comprehensive picture of functional structure of chromatin the results show the interdependence of individual alterations and their proper place in the complex, multichannel, species and tissue-specific character of actual ageing. An attempt to summarize the basic facts and theories about age changes of the two main parts of chromatin structure, proteins and DNA is being made in this review. At the same time the author tried to develop a concept of non-random distribution of the age changes in chromatin and a possible higher rate of accumulation of different alteration and lesions in the transcribed and functionally active parts of chromatin.

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.

Constancy of ribosomal RNA genes during aging of mouse heart cells and during serial passage of WI-38 cells

The DNA content and ribosomal RNA gene copy number in heart of the inbred mouse strain C57BL/6 were determined at different ages. The DNA content of mouse heart remained constant, at about 150 micrograms DNA per heart, from 1 to 30 mth of age. The number of rRNA genes, as estimated by 28S rRNA . DNA hybridization, was not found to change significantly as a function of age. Likewise, the extent of rRNA hybridization to DNA from cultured human WI-38 cells at early and late passage levels was the same. These data support the notion that genomic rDNA sequences are not lost during in vivo and in vitro aging. However, the rDNA sequences are quite large and numerous small deletions or base pair substitutions would not have been detected in these studies.

Requirement of 2-mercaptoethanol for in vitro growth factor production by T cells and vulnerability of the response to age

The effects of 2-mercaptoethanol and age on spleen cells derived from young (3-4 months) and old (24-months) C57BL/6 mice were measured with respect to T cell growth factor or Interleukin 2 production. It was shown that: (A) 2-mercaptoethanol (or some homologue) is absolutely required for T cell growth factor production in vitro by murine cells (the optimum concentration is 5 X 10(-5) M for both young and old cells); (B) old cells are less responsive to suboptimum concentrations than young cells but their responses are not reduced to the same degree as young cells by supraoptimum toxic doses of 2-mercaptoethanol; and (C) at optimum 2-mercaptoethanol concentrations young and old cells have similar kinetic responses for T cell growth factor production and the accumulation of the T cell growth factor reaches a maximum between 18 and 24 hours. Considerations are presented of 2-mercaptoethanol (or some homologue) in its role as an important reactant in the production of T cell growth factor and in its susceptibility to aging.

Estimation of the single stranded region in the nuclear DNA of mouse tissues during aging with special reference to the brain

The proportion of single stranded DNA in various tissues of mouse during aging was examined by measuring sensitivity to a single-strand specific nuclease. Brain DNA from mice of more than 15 mth old contained 3% of the single stranded regions while that from younger animals contained 2%. The DNAs from liver, kidney, heart and spleen did not show significant age-associated changes.

The autoradiographic utilization and distribution of [1-3H]-galactose by the dental tissues of ageing mice

The uptake, turnover and distribution of [1-3H]-galactose by periodontal tissues associated with maxillary first molars of mice 5, 26 and 78 weeks of age showed that galactose was utilized by all oral tissues studied throughout the life-span. Uptake and turnover of the tracer revealed pulsed events. Synchrony of the pulsed events was noted. With increasing age, diminished utilization of galactose was evident, as well as a change in peak-time of the curves characteristic of ageing. The complex plots represent several metabolic events occurring simultaneously. The uptake of galactose by fibrogenic, osteogenic and cementogenic cells was low. Matrical output, on the other hand, remained high. Cementogenic cell output was the highest of all the tissues over the 30-day period. Despite decreased physiological activity with age and superimposed age changes, galactose utilization remained high throughout the study.

Cellular and molecular aspects of immune system aging

We begin with a brief discussion of the importance and advantages of immune studies to the problem of aging. This is followed by a short over-view of immune system aging at the systemic level. The major portion of the article is a review of observation, both at the cellular and molecular level, of changes in aging immune cells, with sections on intercellular communication, membrane phenomena, cyclic nucleotides, and molecular genetic changes.

Nucleolar changes in aging and autogamous Paramecium tetraurelia

A significant loss in nucleolar volume density (proportion of nuclear volume occupied by nucleoli) occurs in the macronucleus as clonal age increases, which suggests an age-correlated loss of ribosomal RNA synthesizing capacity. In the macronuclear fragments of cells undergoing autogamy, however, a significant gain in nucleolar volume density takes place.

Randomness, redundancy and repair: roles and relevance to biological aging

In this paper, some of the key findings of the last decade will briefly be surveyed and, where possible, be related to two separate computer simulation models which have been designed to determine the validity of certain widely accepted dogmas and to define the limits and restrictions imposed by attrition of or ambiguity of information retrieval from information storage systems. It is known: (1) that the idealized rectangular survival curve in an "ideal" environment is an extrapolation that is inconsistent with reasonable primary assumptions; (2) that loss of redundant copies of functional "housekeeping" genes may well be a dominant contributor to human senescence; and (3) that redundancy, particularly of informational storage, not only confers greater stability on an organism in dealing with stochastic or programmed age changes, but that it also provides a means through which a more optimized use of informational storage space may be attained.

Loss of gene repression activity: a theory of cellular senescence

Recent evidence bearing on cellular senescence has come from cell fusion and clonal lifespan studies. To date, no model has been developed that is consistent with the recent findings. The purpose of this paper is to present a mechanism for cell senescence that is qualitatively consistent with the experimental evidence.

Loss of hybridizable ribosomal DNA from human post-mitotic tissues during aging: I. Age-dependent loss in human myocardium

DNA obtained from 29 male humans at autopsy was hybridized in liquid phase with tritium-labelled 18 and 28S ribosomal RNA (rRNA) in order to determine whether a change in the dosage in rDNA, which codes for rRNA, occurs during human aging. The individuals ranged in age from 3 months to 76 years. It was found that the amount of rDNA hybridizable per 260 nm absorption unit by DNA decreases by about 0.5% per year with a regression coefficient of about -0.83. These findings confirm earlier ones from this laboratory and indicate either a loss of these key genes during aging of humans or decreased hybridizability due to some other factor or factors. In any event, this degree of loss or inactivation of genes involving an all protein synthesis would seem to impair function of post-mitotic cells in response to maximal stress to about the same degree that function is lost in various human organ systems during aging, as defined by Shock and others.

Loss of hybridizable ribosomal DNA from human post-mitotic tissues during aging: II. Age-dependent loss in human cerebral cortex--hippocampal and somatosensory cortex comparison

DNA was isolated from the hippocampal and from the somatosensory cortex of 13 humans (at autopsy). In both the cortex and hippocampus, the loss of ribosomal DNA (rDNA), as measured through hybridization in the liquid phase, approximates about 0.9% per year. The r value for somatosensory cortex was about -0.7 and that for the hippocampus was about -0.91. The correlation coefficient between the sets of two samples derived from the same individual (two different areas) in +0.945. These results are consistent with those reported concurrently for human myocardium and with earlier studies conducted with beagle dogs, in which only post-mitotic tissues (brain, heart and skeletal muscle) showed measurable decrements in these key genes. To the degree that the synthesis of new proteins is essential for sustained mental activity, these results are consistent with the observations that Nissl substance is more slowly replenished, following exhaustive work by motor cortical cells, and the fact that many older persons experience mental fatigue during continuous mental work at earlier times than do younger persons. The mechanism of loss is not certain, but may well be related to inadequacies in DNA repair systems, thereby allowing deletion of tandemly duplicated genes through cross-over "episome" formation, followed by degradation of the excised DNA segments. The ratio of loss of rDNA hybridizability in human and dogs in about 1 to 7, which approximates the relative ratios of their lifespans (reciprocals).

Aging research: current and future

The key events that lead to organismic senescence appear to occur in cells that have been genetically programmed to arrest their own proliferation. After arrest, a variety of subcellular events occur, among the more important of which are the accumulation of waste product pigments, an increase in the fraction of inactive enzymes, and (probably of central importance) the loss of key genes, specifically those that code for rRNA. An understanding of the senescence of the epidermis and dermis would almost certainly provide answers to related problems in those organ systems whose sudden or slow failure leads to individual death.

The relationship between lipofuscin pigment and ageing in the human nervous system

The cytoplasmic RNA content, nucleolar volume and lipofuscin content of nerve cells of the inferior olivary and dentate nuclei, Purkinje cells and pyramidal cells of the hippocampus has been measured in 82 persons of age range 2--91 years, who were free from overt neurological disease at the time of death. All 4 cell types accumulate lipofuscin in a linear manner throughout life, but to markedly differing extents. Both the RNA content and nucleolar volume of dentate, olivary and hippocampal cells decrease, with advancing age, in a similar way in all of these 3 cell types, despite the widely differing extents of pigment accumulation, with losses of RNA and nucleolar volume at 90 years of age of 15 and 30% respectively. Olivary cells which contain most pigment show a different pattern of change with losses of RNA and nucleolar volume of about 60%. It seems, therefore, that, if there is a causal relationship between lipofuscin accumulation and reductions in RNA and nucleolar volume, it is rather obscure. It cannot simply be a matter of the absolute amounts of pigment present in any one cell type, but rather might be that there is a critical concentration of such material in the cytoplasm.

Changes in the pattern of RNA synthesis in mouse limb cartilage during early development

Patterns of RNA synthesis using tritiated uridine were studied in organ cultures of mouse embryonic limb cartilage and epiphyseal cartilage from mice 5 days of age. The cold phenol-sodium dodecyl sulfate extracted RNA was characterized by methylated albumin kieselguhr chromatography and polyacrylamide gel electrophoresis. The general pattern of synthesis indicates the persistence of primarily low molecular weight tRNA and a diminishing synthesis of rRNA in the older cartilage. Data show that the increased radioactivity in the low molecular weight fraction is not due to the accumulation of rRNA breakdown products. These findings are discussed in relation to other age-related studies on RNA biosynthesis.

Ribosomal RNA gene dosage as a function of tissue and age for mouse and human

The average number of rRNA genes per haploid genome (rRNA gene dosage) of the cells present in liver and brain was determined throughout the lifespan of the inbred C57BL/6J mouse strain and of human. Ribosomal RNA gene dosage was determined using the RNA-excess DNA - RNA hybridization technique. DNA was extracted and purified using a CsCl/chloroform method with a high percent yield (over 90%) to minimize any possible effects of tissue and age-dependent selective loss or gain of rRNA genes. Radioactive rRNA was from the liver of the youngest age group for either mouse or human in all hybridization experiments, with DNA from the different tissues and age groups being the only variable. In the young mouse (35-49 days), the rRNA gene dosage was 36% higher in brain (114 genes), as compared to liver (84 genes). The rRNA gene dosage remained essentially constant as a function of age for mouse brain; but between the age of about 220 to 440 days, it increased in liver, attaining approximately an equal value to that of brain. No significant difference was found in the rRNA gene dosage of brain or liver between different mice of the same age. In contrast to this result, a significant difference was found between human tissues of similar age. The rRNA gene dosage ranged about 2-fold (148-289) between 2 months to 75 years of age. An age-dependent trend, similar to that for mouse liver, was found when the averages of four different age groups totaling 20 individuals were compared. However, this was not statistically significant. No difference in the rRNA gene dosage as a function of sex or tissue was apparent. Several models are discussed to account for these results.

Percent satellite DNA as a function of tissue and age of mice

A selective loss of satellite DNA was found to occur to different extents as a function of tissue and age of mice using several common DNA extraction and purification procedures. This result emphasizes a serious problem that may be encountered in comparative studies of DNA structure and composition if selective loss of specific DNA sequences occurs. We have developed a DNA extraction and purification procedure that is simple and reliable and gives a high percent DNA yield, which substantially reduces the selective loss of heterochromatin DNA sequences. The method features a centrifugation step of a proteolytic digest of chromatin in 2.4 M CsCl. Percent DNA yield of 82-98% are routinely obtained with no apparent loss of satellite DNA sequences from different tissues or ages of mice. Utilizing this method, percent satellite DNA was found to remain essentially constant at 11 +/- 1% for spleen, kidney, and brain tissues obtained from mice of 10-780 days of age. However, for liver, percent satellite DNA remained at about 7-8% from 10 to 300 days of age and then increased to about 12-13% from 300 to 600 days of age. During this latter time interval (300-600 days), an increase of DNA per nucleus of about 3-fold occurred, due to the formation of tetra- and octaploid cell types. A steady loss in the total number of nuclei per gram of liver as a function of age was also found. These two opposing effects resulted in a nearly constant amount of DNA per gram and per organ for liver throughout the lifespan of the mouse.