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

RNA polymerase II-mediated rDNA transcription mediates rDNA copy number expansion in Drosophila

Ribosomal DNA (rDNA), which encodes ribosomal RNA, is an essential but unstable genomic element due to its tandemly repeated nature. rDNA's repetitive nature causes spontaneous intrachromatid recombination, leading to copy number (CN) reduction, which must be counteracted by a mechanism that recovers CN to sustain cells' viability. Akin to telomere maintenance, rDNA maintenance is particularly important in cell types that proliferate for an extended time period, most notably in the germline that passes the genome through generations. In Drosophila, the process of rDNA CN recovery, known as 'rDNA magnification', has been studied extensively. rDNA magnification is mediated by unequal sister chromatid exchange (USCE), which generates a sister chromatid that gains the rDNA CN by stealing copies from its sister. However, much remains elusive regarding how germ cells sense rDNA CN to decide when to initiate magnification, and how germ cells balance between the need to generate DNA double-strand breaks (DSBs) to trigger USCE vs. avoiding harmful DSBs. Recently, we identified an rDNA-binding Zinc-finger protein Indra as a factor required for rDNA magnification, however, the underlying mechanism of action remains unknown. Here we show that Indra is a negative regulator of rDNA magnification, balancing the need of rDNA magnification and repression of dangerous DSBs. Mechanistically, we show that Indra is a repressor of RNA polymerase II (Pol II)-dependent transcription of rDNA: Under low rDNA CN conditions, Indra protein amount is downregulated, leading to Pol II-mediated transcription of rDNA. This results in the expression of rDNA-specific retrotransposon, R2, which we have shown to facilitate rDNA magnification via generation of DBSs at rDNA. We propose that differential use of Pol I and Pol II plays a critical role in regulating rDNA CN expansion only when it is necessary.

Ribosomal DNA Copy Number Variation is Coupled with DNA Methylation Changes at the 45S rDNA Locus

The human ribosomal DNA (rDNA) copy number (CN) has been challenging to analyse, and its sequence has been excluded from reference genomes due to its highly repetitive nature. The 45S rDNA locus encodes essential components of the cell, nevertheless rDNA displays high inter-individual CN variation that could influence human health and disease. CN alterations in rDNA have been hypothesized as a possible factor in autism spectrum disorders (ASD) and were shown to be altered in Schizophrenia patients. We tested whether whole-genome bisulphite sequencing can be used to simultaneously quantify rDNA CN and measure DNA methylation at the 45S rDNA locus. Using this approach, we observed high inter-individual variation in rDNA CN, and limited intra-individual copy differences in several post-mortem tissues. Furthermore, we did not observe any significant alterations in rDNA CN or DNA methylation in Autism Spectrum Disorder (ASD) brains in 16 ASD vs 11 control samples. Similarly, no difference was detected when comparing neurons form 28 Schizophrenia (Scz) patients vs 25 controls or oligodendrocytes from 22 Scz samples vs 20 controls. However, our analysis revealed a strong positive correlation between CN and DNA methylation at the 45S rDNA locus in multiple tissues. This was observed in brain and confirmed in small intestine, adipose tissue, and gastric tissue. This should shed light on a possible dosage compensation mechanism that silences additional rDNA copies to ensure homoeostatic regulation of ribosome biogenesis.

Mild cognitive impairment is associated with low copy number of ribosomal genes in the genomes of elderly people

Introduction: Mild cognitive impairments (MCI) accompanying aging are associated with oxidative stress. The ability of cells to respond to stress is determined by the protein synthesis level, which depends on the ribosomes number. Ribosomal deficit was documented in MCI. The number of ribosomes depends, together with other factors, on the number of ribosomal genes copies. We hypothesized that MCI is associated with low rDNA CN in the elderly person genome.

Materials and Methods: rDNA CN and the telomere repeat (TR) content were determined in the DNA of peripheral blood leukocytes of 93 elderly people (61–91 years old) with MCI and 365 healthy volunteers (16–91 years old). The method of non-radioactive quantitative hybridization of DNA with biotinylated DNA probes was used for the analysis.

Results: In the MCI group, rDNA CN (mean 329 ± 60; median 314 copies, n = 93) was significantly reduced (p < 10^–15) compared to controls of the same age with preserved cognitive functions (mean 412 ± 79; median 401 copies, n = 168) and younger (16–60 years) control group (mean 426 ± 109; median 416 copies, n = 197). MCI is also associated with a decrease in TR DNA content. There is no correlation between the content of rDNA and TR in DNA, however, in the group of DNA samples with rDNA CN > 540, TR content range was significantly narrowed compared to the rest of the sample.

Conclusion: Mild cognitive impairment is associated with low ribosomal genes copies in the elderly people genomes. A low level of rDNA CN may be one of the causes of ribosomal deficit that was documented in MCI. The potential possibilities of using the rDNA CN indicator as a prognostic marker characterizing human life expectancy are discussed.

Assessment of cell cycle regulators in human peripheral blood cells as markers of cellular senescence

Cellular senescence has gained increasing interest during recent years, particularly due to causal involvement in the aging process corroborated by multiple experimental findings. Indeed, cellular senescence considered to be one of the hallmarks of aging, is defined as a stable growth arrest predominantly mediated by cell cycle regulators p53, p21 and p16. Senescent cells have frequently been studied in the peripheral blood of humans due to its accessibility. This review summarizes ex vivo studies describing cell cycle regulators as markers of senescence in human peripheral blood cells, along with detection methodologies and associative studies examining demographic and clinical characteristics. The utility of techniques such as the quantitative reverse transcriptase polymerase chain reaction (qRT-PCR), microarray, RNA sequencing and nCounter technologies for detection at the transcriptional level, along with Western blotting, enzyme-linked immunosorbent assay and flow cytometry at the translational level, will be brought up at salient points throughout this review. Notably, housekeeping genes or proteins serving as controls such as GAPDH and β-Actin, were found not to be stably expressed in some contexts. As such, optimization and validation of such genes during experimental design were recommended. In addition, the expression of cell cycle regulators was found to vary not only between different types of blood cells such as T cells and B cells but also between stages of cellular differentiation such as naïve T cells and highly differentiated T cells. On the other hand, the associations of the presence of cell cycle regulators with demographics (age, gender, ethnicity, and socioeconomic status), clinical characteristics (body mass index, specific diseases, disease-related parameters) and lifestyle vary in groups of participants. One envisions that increased understanding and insights into the assessment of cell cycle regulators as markers of senescence in human peripheral blood cells will help inform prognostication and clinical intervention in elderly individuals.

First discovered, long out of sight, finally visible: ribosomal DNA

With the advent of long-read sequencing, previously unresolvable genomic elements are being revisited in an effort to generate fully complete reference genomes. One such element is ribosomal DNA (rDNA), the highly conserved genomic region that encodes rRNAs. Genomic structure and content of the rDNA are variable in both prokarya and eukarya, posing interesting questions about the biology of rDNA. Here, we consider the types of variation observed in rDNA - including locus structure and number, copy number, and sequence variation - and their known phenotypic consequences. With recent advances in long-read sequencing technology, incorporating the full rDNA sequence into reference genomes is within reach. This knowledge will have important implications for understanding rDNA biology within the context of cell physiology and whole-organism phenotypes.

Variability of Human rDNA

In human cells, ribosomal DNA (rDNA) is arranged in ten clusters of multiple tandem repeats. Each repeat is usually described as consisting of two parts: the 13 kb long ribosomal part, containing three genes coding for 18S, 5.8S and 28S RNAs of the ribosomal particles, and the 30 kb long intergenic spacer (IGS). However, this standard scheme is, amazingly, often altered as a result of the peculiar instability of the locus, so that the sequence of each repeat and the number of the repeats in each cluster are highly variable. In the present review, we discuss the causes and types of human rDNA instability, the methods of its detection, its distribution within the locus, the ways in which it is prevented or reversed, and its biological significance. The data of the literature suggest that the variability of the rDNA is not only a potential cause of pathology, but also an important, though still poorly understood, aspect of the normal cell physiology.

Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans

The ribosomal RNA genes (rDNA) are tandemly arrayed in most eukaryotes and exhibit vast copy number variation. There is growing interest in integrating this variation into genotype-phenotype associations. Here, we explored a possible association of rDNA copy number variation with autism spectrum disorder and found no difference between probands and unaffected siblings. Because short-read sequencing estimates of rDNA copy number are error prone, we sought to validate our 45S estimates. Previous studies reported tightly correlated, concerted copy number variation between the 45S and 5S arrays, which should enable the validation of 45S copy number estimates with pulsed-field gel-verified 5S copy numbers. Here, we show that the previously reported strong concerted copy number variation may be an artifact of variable data quality in the earlier published 1000 Genomes Project sequences. We failed to detect a meaningful correlation between 45S and 5S copy numbers in thousands of samples from the high-coverage Simons Simplex Collection dataset as well as in the recent high-coverage 1000 Genomes Project sequences. Our findings illustrate the challenge of genotyping repetitive DNA regions accurately and call into question the accuracy of recently published studies of rDNA copy number variation in cancer that relied on diverse publicly available resources for sequence data.

Age-Dependent Ribosomal DNA Variations in Mice

The rRNA gene, which consists of tandem repetitive arrays (ribosomal DNA [rDNA] repeat), is one of the most unstable regions in the genome. The rDNA repeat in the budding yeast Saccharomyces cerevisiae is known to become unstable as the cell ages. However, it is unclear how the rDNA repeat changes in aging mammalian cells. Using quantitative single-cell analyses, we identified age-dependent alterations in rDNA copy number and levels of methylation in mice. The degree of methylation and copy number of rDNA from bone marrow cells of 2-year-old mice were increased by comparison to levels in 4-week-old mice in two mouse strains, BALB/cA and C57BL/6.

The rRNA gene, which consists of tandem repetitive arrays (ribosomal DNA [rDNA] repeat), is one of the most unstable regions in the genome. The rDNA repeat in the budding yeast Saccharomyces cerevisiae is known to become unstable as the cell ages. However, it is unclear how the rDNA repeat changes in aging mammalian cells. Using quantitative single-cell analyses, we identified age-dependent alterations in rDNA copy number and levels of methylation in mice. The degree of methylation and copy number of rDNA from bone marrow cells of 2-year-old mice were increased by comparison to levels in 4-week-old mice in two mouse strains, BALB/cA and C57BL/6. Moreover, the level of pre-rRNA transcripts was reduced in older BALB/cA mice. We also identified many sequence variations in the rDNA. Among them, three mutations were unique to old mice, and two of them were found in the conserved region in budding yeast. We established yeast strains with the old-mouse-specific mutations and found that they shortened the life span of the cells. Our findings suggest that rDNA is also fragile in mammalian cells and that alterations within this region have a profound effect on cellular function.

Dosage effects of human ribosomal genes (rDNA) in health and disease

Human ribosomal RNA genes encoding a pre-transcript of the three major ribosomal RNA (18S, 5.8S, and 28S rRNA) are tandemly repeated in human genome. Their total copy number varies from 250 to 670 per diploid genome with a mean of approximately 420 copies, but only a fraction of them is transcriptionally active. The functional consequences of human ribosomal RNA gene dosage are not widely known and often assumed to be negligible. Here, we review the facts of rRNA gene dosage effects on normal growth and aging, stress resistance of healthy individuals, and survivability of patients with chromosomal abnormalities, as well as on the risk and severity of some multifactorial diseases with proven genetic predisposition. An original hypothesis that rRNA gene dosage can be a modulating factor involved in the pathogenesis of schizophrenia and rheumatoid arthritis is put forward.

Copy Number of Human Ribosomal Genes With Aging: Unchanged Mean, but Narrowed Range and Decreased Variance in Elderly Group

Introduction: The multi-copied genes coding for the human 18, 5.8, and 28S ribosomal RNA (rRNA) are located in five pairs of acrocentric chromosomes forming so-called rDNA. Human genome contains unmethylated, slightly methylated, and hypermethylated copies of rDNA. The major research question: What is the rDNA copy number (rDNA CN) and the content of hypermethylated rDNA as a function of age?

Materials and Methods: We determined the rDNA CN in the blood leukocyte genomes of 651 subjects aged 17 to 91 years. The subjects were divided into two subgroups: “elderly” group (E-group, N = 126) – individuals over 72 years of age (the age of the population’s mean lifetime for Russia) and “non-elderly” group (NE-group, N = 525). The hypermethylated rDNA content was determined in the 40 DNA samples from the each group. The change in rDNA during replicative cell senescence was studied for the cultured skin fibroblast lines of five subjects from NE-group. Non-radioactive quantitative dot- and blot-hybridization techniques (NQH) were applied.

Results: In the subjects from the E-group the mean rDNA CN was the same, but the range of variation was narrower compared to the NE-group: a range of 272 to 541 copies in E-group vs. 200 to 711 copies in NE-group. Unlike NE-group, the E-group genomes contained almost no hypermethylated rDNA copies. A case study of cultured skin fibroblasts from five subjects has shown that during the replicative senescence the genome lost hypermethylated rDNA copies only.

Conclusion: In the elderly group, the mean rDNA CN is the same, but the range of variation is narrower compared with the younger subjects. During replicative senescence, the human fibroblast genome loses hypermethylated copies of rDNA. Two hypotheses were put forward: (1) individuals with either very low or very high rDNA content in their genomes do not survive till the age of the population’s mean lifetime; and/or (2) during the aging, the human genome eliminates hypermethylated copies of rDNA.

Visualization of aging-associated chromatin alterations with an engineered TALE system

Visualization of specific genomic loci in live cells is a prerequisite for the investigation of dynamic changes in chromatin architecture during diverse biological processes, such as cellular aging. However, current precision genomic imaging methods are hampered by the lack of fluorescent probes with high specificity and signal-to-noise contrast. We find that conventional transcription activator-like effectors (TALEs) tend to form protein aggregates, thereby compromising their performance in imaging applications. Through screening, we found that fusing thioredoxin with TALEs prevented aggregate formation, unlocking the full power of TALE-based genomic imaging. Using thioredoxin-fused TALEs (TTALEs), we achieved high-quality imaging at various genomic loci and observed aging-associated (epi) genomic alterations at telomeres and centromeres in human and mouse premature aging models. Importantly, we identified attrition of ribosomal DNA repeats as a molecular marker for human aging. Our study establishes a simple and robust imaging method for precisely monitoring chromatin dynamics in vitro and in vivo.

Mechanism of regulation of 'chromosome kissing' induced by Fob1 and its physiological significance

Protein-mediated "chromosome kissing" between two DNA sites in trans (or in cis) is known to facilitate three-dimensional control of gene expression and DNA replication. However, the mechanisms of regulation of the long-range interactions are unknown. Here, we show that the replication terminator protein Fob1 of Saccharomyces cerevisiae promoted chromosome kissing that initiated rDNA recombination and controlled the replicative life span (RLS). Oligomerization of Fob1 caused synaptic (kissing) interactions between pairs of terminator (Ter) sites that initiated recombination in rDNA. Fob1 oligomerization and Ter-Ter kissing were regulated by intramolecular inhibitory interactions between the C-terminal domain (C-Fob1) and the N-terminal domain (N-Fob1). Phosphomimetic substitutions of specific residues of C-Fob1 counteracted the inhibitory interaction. A mutation in either N-Fob1 that blocked Fob1 oligomerization or C-Fob1 that blocked its phosphorylation antagonized chromosome kissing and recombination and enhanced the RLS. The results provide novel insights into a mechanism of regulation of Fob1-mediated chromosome kissing.

Age-changes in gene expression in primary mixed glia cultures from young vs. old rat cerebral cortex are modified by interactions with neurons

Astrocytic GFAP expression increases during normal aging in many brain regions and in primary astrocyte cultures derived from aging rodent brains. As shown below, we unexpectedly found that the age-related increase of GFAP expression was suppressed in mixed glia (astrocytes+microglia). However, the age-related increase of GFAP was observed when E18 neurons were co-cultured with mixed glia. Thus, the presence of microglia can suppress the age-related increase of GFAP, in primary cultures of astrocytes. To more broadly characterize how aging and co-culture with neurons alters glial gene expression, we profiled gene expression in mixed glia from young (3 mo) and old (24 mo) male rat cerebral cortex by Affymetrix microarray (Rat230 2.0). The majority of age changes were independent of the presence of neurons. Overall, the expression of twofold more genes increased with age than decreased with age. The minority of age changes that were either suppressed or revealed by the presence of neurons may be useful to analyze glial-neuron interaction during aging. Some in vitro changes are shared with those of aging rat hippocampus in studies from the Landfield group (Rowe et al., 2007; Kadish et al., 2009).

Validation of suitable internal control genes for expression studies in aging

Quantitative data from experiments of gene expression are often normalized through levels of housekeeping genes transcription by assuming that expression of these genes is highly uniform. This practice is being questioned as it becomes increasingly clear that the level of housekeeping genes expression may vary considerably in certain biological samples. To date, the validation of reference genes in aging has received little attention and suitable reference genes have not yet been defined. Our aim was to evaluate the expression stability of frequently used reference genes in human peripheral blood mononuclear cells with respect to aging. Using quantitative RT-PCR, we carried out an extensive evaluation of five housekeeping genes, i.e. 18s rRNA, ACTB, GAPDH, HPRT1 and GUSB, for stability of expression in samples from donors in the age range 35-74 years. The consistency in the expression stability was quantified on the basis of the coefficient of variation and two algorithms termed geNorm and NormFinder. Our results indicated GUSB be the most suitable transcript and 18s the least for accurate normalization in PBMCs. We also demonstrated that aging is a confounding factor with respect to stability of 18s, HPRT1 and ACTB expression, which were particularly prone to variability in aged donors.

Autophagy, organelles and ageing

As a result of insufficient digestion of oxidatively damaged macromolecules and organelles by autophagy and other degradative systems, long-lived postmitotic cells, such as cardiac myocytes, neurons and retinal pigment epithelial cells, progressively accumulate biological 'garbage' ('waste' materials). The latter include lipofuscin (a non-degradable intralysosomal polymeric substance), defective mitochondria and other organelles, and aberrant proteins, often forming aggregates (aggresomes). An interaction between senescent lipofuscin-loaded lysosomes and mitochondria seems to play a pivotal role in the progress of cellular ageing. Lipofuscin deposition hampers autophagic mitochondrial turnover, promoting the accumulation of senescent mitochondria, which are deficient in ATP production but produce increased amounts of reactive oxygen species. Increased oxidative stress, in turn, further enhances damage to both mitochondria and lysosomes, thus diminishing adaptability, triggering mitochondrial and lysosomal pro-apoptotic pathways, and culminating in cell death.

Preferential loss of 5S and 28S rDNA genes in human adipose tissue during ageing

Loss of genomic rDNA has been associated with cellular and organismal ageing. The rDNA locus in humans comprises multiple copies of the 5.8S, 28S and 18S genes. Aim of the present study was to test the effect of aging on the copy number of the three rDNA genes individually in post-mitotic human tissue. We utilized real time polymerase chain reaction relative quantification to measure the copy number of 5.8S, 28S and 18S rDNA genes individually. We obtained adipose tissue from 120 male individuals aged from 9 to 94 years. The available data of each subject corresponding to the time of tissue sampling included: age, height, weight and calculated body mass index. Each rDNA gene was directly tested with Pearson correlation against age and body mass index. We found a significant negative correlation of the gene copy of 5.8S (P < 0.001) and 28S (P < 0.003) with age. Interestingly 18S gene copy displayed a different pattern with no statistically significant correlation with age. Conversely, we observed a significant negative correlation of the 18S gene copy with body mass index (P = 0.004) and a marginally non-significant negative correlation of the 5.8S (P = 0.097) gene copy with body mass index. In summary our results indicate that the rDNA recombination events in humans can be differentially targeted and regulated in response to ageing and/or fat accumulation. The proposed model generates possible implications regarding the effects of each rDNA gene loss in cell function as well as the mechanism of recombination targeting.

Slipped-strand DNAs formed by long (CAG)*(CTG) repeats: slipped-out repeats and slip-out junctions

The disease-associated expansion of (CTG)*(CAG) repeats is likely to involve slipped-strand DNAs. There are two types of slipped DNAs (S-DNAs): slipped homoduplex S-DNAs are formed between two strands having the same number of repeats; and heteroduplex slipped intermediates (SI-DNAs) are formed between two strands having different numbers of repeats. We present the first characterization of S-DNAs formed by disease-relevant lengths of (CTG)*(CAG) repeats which contained all predicted components including slipped-out repeats and slip-out junctions, where two arms of the three-way junction were composed of complementary paired repeats. In S-DNAs multiple short slip-outs of CTG or CAG repeats occurred throughout the repeat tract. Strikingly, in SI-DNAs most of the excess repeats slipped-out at preferred locations along the fully base-paired Watson-Crick duplex, forming defined three-way slip-out junctions. Unexpectedly, slipped-out CAG and slipped-out CTG repeats were predominantly in the random-coil and hairpin conformations, respectively. Both the junctions and the slip-outs could be recognized by DNA metabolizing proteins: only the strand with the excess repeats was hypersensitive to cleavage by the junction-specific T7 endonuclease I, while slipped-out CAG was preferentially bound by single-strand binding protein. An excellent correlation was observed for the size of the slip-outs in S-DNAs and SI-DNAs with the size of the tract length changes observed in quiescent and proliferating tissues of affected patients-suggesting that S-DNAs and SI-DNAs are mutagenic intermediates in those tissues, occurring during error-prone DNA metabolism and replication fork errors.

In memoriam Bernard Strehler--genomic instability in ageing: a persistent challenge

Genomic instability comprises a broad spectrum of mutational alterations in the genome, such as point mutations in DNA, microsatellite expansions or contractions, amplifications and deletions of DNA sequences, gene rearrangements and structural or numerical chromosomal aberrations. A substantial body of data demonstrates an increase of genomic instability during normal ageing. This includes cytogenetic changes; loss of rDNA; formation of extrachromosomal circular DNA species; loss of telomeric repeats; increased microsatellite instability; as well as point mutations and deletions in global nuclear and mitochondrial DNA. Evidence has accumulated supporting a causative role of genomic instability in ageing. Genomic instability can be counteracted by a number of proteins including antioxidant enzymes, the WRN protein (deficient in Werner syndrome), telomerase, poly(ADP-ribose) polymerase-1 and a range other others, as well as by multi-protein systems such as DNA mismatch repair, base-excision repair and nucleotide-excision repair. Important research tasks for the future will be to elucidate how and what extent the various expressions of genomic instability contribute to the ageing process and to understand the molecular mechanisms and regulation of the above factors and pathways involved in limiting the induction of ageing-associated genomic instability.

Garbage catastrophe theory of aging: imperfect removal of oxidative damage?

Increasing evidence suggests an important role of oxidant-induced damage in the progress of senescent changes, providing support for the free radical theory of aging proposed by Harman in 1956. However, considering that biological organisms continuously renew their structures, it is not clear why oxidative damage should accumulate with age. No strong evidence has been provided in favor of the concept of aging as an accumulation of synthetic errors (e.g. Orgel's 'error-catastrophe' theory and the somatic mutation theory). Rather, we believe that the process of aging may derive from imperfect clearance of oxidatively damaged, relatively indigestible material, the accumulation of which further hinders cellular catabolic and anabolic functions. From this perspective, it might be predicted that: (i) suppression of oxidative damage would enhance longevity; (ii) accumulation of incompletely digested material (e.g. lipofuscin pigment) would interfere with cellular functions and increase probability of death; (iii) rejuvenation during reproduction is mainly provided by dilution of undigested material associated with intensive growth of the developing organism; and (iv) age-related damage starts to accumulate substantially when development is complete, and mainly affects postmitotic, cells and extracellular matrix, not proliferating cells. There is abundant support for all these predictions.

Accelerated methylation of ribosomal RNA genes during the cellular senescence of Werner syndrome fibroblasts

Ribosomal DNA (rDNA) metabolism has been implicated in cellular and organismal aging. The role of rDNA in premature and normal human aging was investigated by measuring rDNA gene copy number, the level of rDNA methylation, and rRNA expression during the in vitro senescence of primary fibroblasts from normal (young and old) donors and from Werner syndrome (WS) patients. In comparison to their normal counterparts, WS fibroblasts grew slowly and reached senescence after fewer doublings. The rDNA copy number did not change significantly throughout the life span of both normal and WS fibroblasts. However, in senescent WS and normal old fibroblasts, we detected rDNA species with unusually slow electrophoretic mobility. Cellular aging in Saccharomyces cerevisiae is accompanied by the formation and accumulation of rDNA circles. Our analysis revealed that the rDNA species observed in this study were longer, linear rDNA molecules attributable to the inhibition of ECO:RI cleavage by methylation. Furthermore, isoschizomeric restriction analysis confirmed that in vitro senescence of fibroblasts is accompanied by significant increases in cytosine methylation within rDNA genes. This increased methylation is maximal during the abbreviated life span of WS fibroblasts. Despite increased methylation of rDNA in senescent cells, the steady-state levels of 28S rRNA remained constant over the life span of both normal and WS fibroblasts.

Age-related changes in cellular activity in human submandibular glands as evaluated by argyrophilic nucleolar organizer regions

OBJECTIVE

To examine the age-related changes in cellular activity of epithelial components of human submandibular glands, evaluated on the basis of argyrophilic nucleolar organizer regions (AgNORs).

DESIGN

Epithelial components of human submandibular glands were divided into serous acinar cells, mucous acinar cells, intercalated duct cells, striated duct cells, and interlobular duct cells. The mean AgNOR number of each cell type was compared among six age groups.

SETTING

The study was conducted at the Department of Oral Pathology, Tohoku University School of Dentistry, Japan.

SUBJECTS

Necropsy specimens from 66 males and 57 females 1 to 97 years old.

RESULTS

In all cell types except for intercalated duct cells, the mean AgNOR number was lowest in the 0-14 year-old group and highest in the 15-29 year-old group. The value then gradually decreased with advancing age and ultimately reached a similar level to that in the 0-14 year-old group. In intercalated duct cells, the mean AgNOR number did not differ significantly between any age group. There were no significant sex-related differences.

CONCLUSIONS

The cellular activity of almost all components of human submandibular glands rises in adolescence and young adulthood and then decreases with aging. These results suggest that intercalated duct cells are capable of not only proliferation but also division into other components; these cells may thus compensate for the reduced activity of other components in elderly subjects.

Assessment of DNA-protein crosslinks in the course of aging in two mouse strains by use of a modified alkaline filter elution applied to whole tissue samples

Two different mouse strains have been used for determination of age dependence of DNA-protein crosslinks by alkaline filter elution: a long lived laboratory strain, NMRI and an accelerated senescence-prone, short lived strain, SAMP1. Five organs were selected: Brain, kidney, lung, heart and liver. Remarkably in all five organs of short lived SAMPI mice crosslinks increased significantly with age. In NMRI however only in brain and heart a significant rise in old age has been observed, while in the other organs there was no increase in DNA-protein crosslinking. Appreciable mitotic activity which is lacking in brain and heart could be the reason for this difference. Poor repair in all five organs could be an important component for the multiple ailments and shortened life span in SAMP1 mice.

Elimination of replication block protein Fob1 extends the life span of yeast mother cells

A cause of aging in yeast is the accumulation of circular species of ribosomal DNA (rDNA) arising from the 100-200 tandemly repeated copies in the genome. We show here that mutation of the FOB1 gene slows the generation of these circles and thus extends life span. Fob1p is known to create a unidirectional block to replication forks in the rDNA. We show that Fob1p is a nucleolar protein, suggesting a direct involvement in the replication fork block. We propose that this block can trigger aging by causing chromosomal breaks, the repair of which results in the generation of rDNA circles. These findings may provide a novel link between metabolic rate and aging in yeast and, perhaps, higher organisms.

Nucleolar localization of the Werner syndrome protein in human cells

Werner Syndrome (WS) is a human genetic disorder with many features of premature aging. The gene defective in WS (WRN) has been cloned and encodes a protein homologous to several helicases, including Escherichia coli RecQ, the human Bloom syndrome protein (BLM), and Saccharomyces cerevisiae Sgs1p. To better define the function of WRN protein we have determined its subcellular localization. Indirect immunofluorescence using polyclonal anti-human WRN shows a predominant nucleolar localization. Studies of WRN mutant cells lines confirmed the specificity of antibody recognition. No difference was seen in the subcellular localization of the WRN protein in a variety of normal and transformed human cell lines, including both carcinomas and sarcomas. The nucleolar localization of human WRN protein was supported by the finding that upon biochemical subcellular fractionation, WRN protein is present in an increased concentration in a subnuclear fraction enriched for nucleolar proteins. We have also determined the subcellular localization of the mouse WRN homologue (mWRN). In contrast to human WRN protein, mWRN protein is present diffusely throughout the nucleus. Understanding the function of WRN in these organisms of vastly differing lifespan may yield new insights into the mechanisms of lifespan determination.

Telomeres, the nucleolus and aging

Reactivation of telomerase in cultured human cells extends their replicative life span beyond the Hayflick limit. How telomere shortening triggers cell senescence and whether it contributes to aging in vivo are under investigation. Studies in yeast have revealed another site critical to cellular aging: the nucleolus. The accumulation of ribosomal DNA circles is a cause of aging in this organism. The possible relevance of this mechanism to human aging is also being considered.

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.

The tissue specificity of the age-related changes in alkali-induced DNA-unwinding

To determine if the age-related changes in chromatin digestibility are tissue-specific, fluorometric analysis of the alkali-induced DNA unwinding technique was adapted for soft-tissue chromatin studies. The rate of DNA unwinding in the brain and liver of young Fischer 344 male rats (3 months of age) was significantly greater than the rates measured in middle-aged (15 months) or aged rats (26 months). In contrast, the rate of DNA unwinding in the intestinal epithelium, a continuously replicating tissue, did not significantly vary with age. Although this assay is capable of detecting DNA strand breaks in vivo following N-nitrosodimethylamine administration, the age-related changes could not be attributed to reduced DNA strand lesions in the aged animals. The % double-stranded DNA at time 0 of incubation in alkali was lower in the brain and liver of aged rats indicating that DNA strand breaks may actually increase with aging. These results indicate that proliferative activity of the tissue is an important determinant of age-related changes in chromatin structure.

The number of silver-staining NORs (rDNA) in lymphocytes of newborns and its relationship to human development

The number of silver-staining NORs (rDNA)/cell and their pattern of distribution were studied in phytohaemagglutinin-stimulated blood lymphocyte chromosomes of different age group individuals starting from newborns to old age (0-75 years) in order to investigate if the number of Ag-NORs or rDNA genes varies during development in humans. The results indicate presence of a relatively high modal number of NORs in newborns and infants (9.00 and 8.00/cell, respectively) and a significantly reduced number in old individuals (6.00/cell) as compared to that of normal adults (7.00/cell). These data are complimentary as well as comparable to the previous findings of Denton et al. (Mech. Ageing Dev., 15 (1981) (1-7). It is suggested that at young age due to an obvious enhanced growth and differentiation more gene sites may be transcriptionally active showing higher number of silver-stained NORs but as the development proceeds and the age advances many of these may be gradually repressed or inactivated.

Age-dependent changes in proteins of Drosophila melanogaster

Several molecular theories of aging postulate that there are age-dependent changes in gene expression and that these changes contribute to the reduction in the viability of senescent cells. High-resolution, semiautomated, quantitative two-dimensional gel electrophoresis of many soluble proteins was used to test this hypothesis in Drosophila. Two-dimensional protein gel patterns were analyzed for each of three age groups of [(35)S]methionine-labeled adult male Drosophila melanogaster, which, except for their spermatocytes, consist entirely of fixed postmitotic cells. Seven relatively abundant polypeptides expressed in middle-aged (28-day-old) flies were absent in both young(10-day-old) and old (44-day-old) flies. Quantitative analyses of an additional 100 polypeptides were carried out by computer-assisted microdensitometry of fluorograms of the gel preparations. These analyses revealed a significant age-related heterogeneity in the quantitative distribution of radiolabel in these proteins. The data indicate that the qualitative pattern of gene expression is identical in young and old flies, but that profound quantitative changes occur in the expression of proteins during the Drosophila life-span.

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.

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.

Loss of DNA and euchromatin in senescing leaf cells of Allium

The leaves of the chive, Allium schoenoprasum, have an average life-span of 53 days, then they fade from top to bottom, in the same sequence as cells originated. Starting during the adult phase, the amount of DNA per nucleus decreases significantly. Nuclei of senescent cells exhibit about 15% less DNA than nuclei of juvenile cells. Electron-microscopic investigations have shown that the diffuse chromatin is lost from the nuclei, followed by shrinkage of the space left. Quantitation was achieved by measurement of the percentage of condensed chromatin per nucleus. Senescence starts in different tissues, and in individual cells of a tissue, asynchronously. Chloroplasts undergo structural changes after initiation of aging in the nuclei. The short life-span, in spite of a relatively high DNA content (11.8 pg), is suggestive of a programmed senescence in Allium leaves.

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.

The relationship between aging and ribosomal gene activity in humans as evidenced by silver staining

Silver selectively stains nucleolar organizer regions (NORs) distributed on the D and G chromosomes of man. The number of NORs is fairly constant for a given individual but is highly variable within populations. When 2540 metaphases from lymphocytes were examined from 127 normal subjects, a mean NOR number of 7.3 was obtained with a mode of 7. No significant difference was found in mean NOR number between females and males. However, regression lines do show a decrease in NOR number with aging for both sexes but the rate of decline is more evident in females. Also, G chromosome NORs appear more stable than those in D chromosomes. Since silver--NOR staining is indicative of ribosomal gene activity, it is proposed that lymphocyte rDNA becomes less sensitive to phytohemagglutinin stimulation during aging. It is unique that this gene repression can be visualized with conventional staining and light microscopy.

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 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).