Decreased transcription of neuronal polyadenylated RNA during senescence in nuclei from rat brain cortex

Genome-wide RNA polymerase stalling shapes the transcriptome during aging

Gene expression profiling has identified numerous processes altered in aging, but how these changes arise is largely unknown. Here we combined nascent RNA sequencing and RNA polymerase II chromatin immunoprecipitation followed by sequencing to elucidate the underlying mechanisms triggering gene expression changes in wild-type aged mice. We found that in 2-year-old liver, 40% of elongating RNA polymerases are stalled, lowering productive transcription and skewing transcriptional output in a gene-length-dependent fashion. We demonstrate that this transcriptional stress is caused by endogenous DNA damage and explains the majority of gene expression changes in aging in most mainly postmitotic organs, specifically affecting aging hallmark pathways such as nutrient sensing, autophagy, proteostasis, energy metabolism, immune function and cellular stress resilience. Age-related transcriptional stress is evolutionary conserved from nematodes to humans. Thus, accumulation of stochastic endogenous DNA damage during aging deteriorates basal transcription, which establishes the age-related transcriptome and causes dysfunction of key aging hallmark pathways, disclosing how DNA damage functionally underlies major aspects of normal aging.

Transcriptional Signatures of Aging

Genome-wide studies of aging have identified subsets of genes that show age-related changes in expression. Although the types of genes that are age regulated vary among different tissues and organisms, some patterns emerge from these large data sets. First, aging is associated with a broad induction of stress response pathways, although the specific genes and pathways involved differ depending on cell type and species. In contrast, a wide variety of functional classes of genes are downregulated with age, often including tissue-specific genes. Although the upregulation of age-regulated genes is likely to be governed by stress-responsive transcription factors, questions remain as to why particular genes are susceptible to age-related transcriptional decline. Here, we discuss recent findings showing that splicing is misregulated with age. While defects in splicing could lead to changes in protein isoform levels, they could also impact gene expression through nonsense-mediated decay of intron-retained transcripts. The discovery that splicing is misregulated with age suggests that other aspects of gene expression, such as transcription elongation, termination, and polyadenylation, must also be considered as potential mechanisms for age-related changes in transcript levels. Moreover, the considerable variation between genome-wide aging expression studies indicates that there is a critical need to analyze the transcriptional signatures of aging in single-cell types rather than whole tissues. Since age-associated decreases in gene expression could contribute to a progressive decline in cellular function, understanding the mechanisms that determine the aging transcriptome provides a potential target to extend healthy cellular lifespan.

Analysis of Gene Expression in Human Dermal Fibroblasts Treated with Senescence-Modulating COX Inhibitors

We have previously reported that NS-398, a cyclooxygenase-2 (COX-2)-selective inhibitor, inhibited replicative cellular senescence in human dermal fibroblasts and skin aging in hairless mice. In contrast, celecoxib, another COX-2-selective inhibitor, and aspirin, a non-selective COX inhibitor, accelerated the senescence and aging. To figure out causal factors for the senescence-modulating effect of the inhibitors, we here performed cDNA microarray experiment and subsequent Gene Set Enrichment Analysis. The data showed that several senescence-related gene sets were regulated by the inhibitor treatment. NS-398 up-regulated gene sets involved in the tumor necrosis factor β receptor pathway and the fructose and mannose metabolism, whereas it down-regulated a gene set involved in protein secretion. Celecoxib up-regulated gene sets involved in G2M checkpoint and E2F targets. Aspirin up-regulated the gene set involved in protein secretion, and down-regulated gene sets involved in RNA transcription. These results suggest that COX inhibitors modulate cellular senescence by different mechanisms and will provide useful information to understand senescence-modulating mechanisms of COX inhibitors.

Neurotoxic mechanisms of DNA damage: focus on transcriptional inhibition

Although DNA damage-induced neurotoxicity is implicated in various pathologies of the nervous system, its underlying mechanisms are not completely understood. Transcription is a DNA transaction that is highly active in the nervous system. In addition to its direct role in expression of the genetic information, transcription contributes to DNA damage detection and repair as well as chromatin organization including biogenesis of the nucleolus. Transcription is inhibited by DNA single-strand breaks and DNA adducts. Hence, transcription inhibition may be an important contributor to the neurotoxic consequences of such types of DNA damage. This review discusses the existing evidence in support of the latter hypothesis. The presented literature suggests that neuronal DNA damage interferes with the RNA-Polymerase-2-dependent transcription of genes encoding proteins with critical functions in neurotransmission and intracellular signaling. The latter category includes extracellular signal-regulated kinase-1/2 mitogen-activated protein kinase phosphatases whose lowered expression results in chronic activation of extracellular signal-regulated kinase-1/2 and its reduced responsiveness to physiological stimuli. Conversely, DNA damage-induced inhibition of RNA-Polymerase-1 and the subsequent disruption of the nucleolus induce p53-mediated apoptosis of developing neurons. Finally, decreasing nucleolar transcription may link DNA damage to chronic neurodegeneration in adults.

Compromise in mRNA processing machinery in senescent human fibroblasts: implications for a novel potential role of Phospho-ATR (ser428)

Ataxia-Telangiectasia and Rad3 related kinase (ATR) is a major gatekeeper of genomic stability and has been the subject of exhaustive study in the context of cell cycle progression and senescence as a DNA damage-induced response. Conditional knockout of the kinase in adult mice results in accelerated aging phenomena, such as such hair graying, alopecia, kyphosis, osteoporosis, thymic involution, fibrosis, and other abnormalities. In addition to that, recent reports strongly implicate signaling mediated by this kinase in the regulation of alternative splicing of certain, mostly cancer-associated transcripts. Interest to the function of mRNA synthesis and processing is constantly increasing as severe degenerative diseases, such as cancer, cystic fibrosis and Hutchinson-Gilford progeria syndrome are at least partly attributed to these abnormalities. In light of the above, we investigate the RNA processing machinery in senescent fibroblasts as opposed to young, either exponentially proliferating or quiescent, further focusing on the distribution and localization of active, phosphorylated ATR at ser428. This study implicates the spatiotemporal presence of the phosphorylated kinase in the regulation of mRNA splicing and polyadenylation. This function appears perturbed in senescent cells, accompanied by a distinct pattern of phospho-ATR in the senescent nucleus.

Tubulin and actin mRNAs in the young-adult and the aged rat brain: effects of repeated administration with bifemelane hydrochloride

In an attempt to identify the age-dependent changes in the potential synthesis of cytoskeletal proteins, we investigated changes in messenger RNA (mRNA) of alpha-tubulin and beta-actin in the young-adult and the aged rat brain using Northern blot analysis. alpha-Tubulin mRNA levels in the frontal cortex and hippocampus, and beta-actin mRNA levels in the hippocampus were significantly decreased in the aged rat brain. Age-dependent decreases in these mRNAs may be related to the neuronal dysfunction associated with aging, in addition to the reduction of several kinds of receptors previously reported. Repeated administration of bifemelane hydrochloride (4-(2-benzylphenoxy)-N-methylbutylamine hydrochloride) for 14 days increased the levels of beta-actin mRNA in the frontal cortex and the striatum of both young-adult and aged rats, although the effect of bifemelane treatment was smaller and not significant in the aged group. These results suggest that bifemelane treatment may enhance the synthesis of cytoskeletal protein and promote neural plasticity by inducing neurite growth or synapse formation.

Polyadenylate polymerase (PAP) and 3' end pre-mRNA processing: function, assays, and association with disease

Polyadenylate polymerase (PAP) is one of the enzymes involved in the formation of the polyadenylate tail of the 3' end of mRNA. Poly (A) tail formation is a significant component of 3' processing, a link in the chain of events, including transcription, splicing, and cleavage/polyadenylation of pre-mRNA. Transcription, capping, splicing, polyadenylation, and transport take place as coupled processes that can regulate one another. The poly(A) tail is found in almost all eukaryotic mRNA and is important in enhancing translation initiation and determining mRNA stability. Control of poly(A) tail synthesis could possibly be a key regulatory step in gene expression. PAP-specific activity values are measured by a highly sensitive assays and immunocytochemical methods. High levels of PAP activity are associated with rapidly proliferating cells, it also prevents apoptosis. Changes of PAP activity may cause a decrease in the rate of polyadenylation in the brain during epileptic seizures. Testis-specific PAP may play an important role in spermiogenesis. PAP was found to be an unfavorable prognostic factor in leukemia and breast cancer. Furthermore, measurements of PAP activity may contribute to the definition of the biological profile of tumor cells. It is crucial to know the specific target causing the elevation of serum PAP, for it to be used as a marker for disease. This review summarizes the recently accumulated knowledge on PAP including its function, assays, and association with various human diseases, and proposes future avenues for research.

Aging is associated with divergent effects on Nf-L and GFAP transcription in rat brain

We studied the effects of advancing age on the expression of several proteins important in the structure and function of the nervous system. Brains of young (3 month), middle-aged (13 month), and old (29 month) male Fischer 344 rats were examined. Run-on transcription and Northern blot hybridizations were used to determine gene-specific transcription rates and mRNA levels, respectively. With advancing age, there was a decrement in the transcription rate and mRNA levels for neurofilament-light subunit (Nf-L), but an increment in the transcription rate and mRNA levels for glial fibrillary acidic protein (GFAP). Proteolipid protein (PLP) mRNA levels were attenuated between 3 and 13 months of age, whereas amyloid precursor protein (APP) mRNA levels were attenuated in the middle-aged but not the old animals. Transcription rates for alpha-actin and fos, and mRNA levels for alpha-actin, were unaffected. These observations indicate divergent transcriptional regulation of several genes, notably Nf-L and GFAP, in the aging mammalian forebrain.

Age-related changes in gene expression in the rat brain revealed by differential display

We have used the polymerase chain reaction (PCR)-based technique of differential display to analyse changes in gene expression during ageing of the rat brain. In this approach we have compared three young adult (6 months) with three old adult (20 months) animals. RNA preparations from the homogenised brains were subjected to reverse transcriptase (RT)-PCR using 36 different combinations of primer pairs. Any PCR product which was consistently found to be more prominent in the three young brains compared to the three old brains, and vice versa, was scored as potentially representing a gene which was differentially expressed during the ageing of this tissue. Out of a possible 2000+ PCR products we identified 44 that might represent genes that exhibit differential expression during ageing of the rat brain. An initial screen of these fragments, by Southern-blotting the PCR products and hybridising them with cDNA probes derived from either young or old brain RNA preparations, indicated that 40% of them represented genes that were differentially expressed. This approach is likely to prove invaluable for identifying cohorts of genes that show differential expression during the ageing process.

Axonal atrophy in aging is associated with a decline in neurofilament gene expression

Neurofilaments (Nfs) are major determinants of axonal caliber. Nf transcript levels increase during development and maturation, and are associated with an increase in Nf protein, Nf numbers, and caliber of axons. With aging there is axonal atrophy. In this study we asked whether the axonal atrophy of aging was associated with a decline in Nf transcript expression, Nf protein levels, and Nf numbers. Expression of transcripts for the three Nf subunits was evaluated in dorsal root ganglia (DRG) of Fischer-344 rats aged 3-32 months by Northern and in situ hybridization. There was an approximately 50% decrease in Nf subunit mRNA levels in DRG of aged (> 23 months) as compared to young and mature (3 and 12 months) rats, whereas expression of another neuronal mRNA, GAP-43, showed no decline. Western analysis showed a corresponding decrease in Nf subunit proteins and no decline in GAP-43. Morphometric analysis showed a 50% decrease in Nf numbers within axons. The decrease in Nf gene expression and Nf numbers was accompanied by a decrease in cross-sectional area and circularity of all myelinated fibers, with the largest fibers showing the most marked changes, and a shrinkage in the perikaryal area of large neurons. Furthermore, we found a concomitant decrease in the expression of transcripts for the nerve growth factor receptors trkA and p75 with aging. Although the mechanisms leading to the decrease in Nf gene expression with aging are not known, a decrease in the availability of growth factors, or the neuron's ability to respond to them, may play a role in this process.

Gene expression in Alzheimer neocortex as a function of age and pathologic severity

Previous studies have shown a marked decline in neuronal and an increase in glial gene expression in Alzheimer's disease (AD) neocortex. Severity of pathologic changes may be greater in presenile AD (PAD) than in senile AD (SAD). We evaluated whether changes in transcript expression were altered as a function of age or pathologic severity. Northern analysis revealed a marked (> 50%) decline in expression of transcripts for the neurofilament light subunit and the major amyloid precursor protein (APP) isoforms in both PAD and SAD. Expression of these neuronal transcripts declined as a function of age in AD and control cases. Expression of the glial fibrillary acidic protein (GFAP) transcript was increased in AD, particularly in the presenile group. AD cases with larger numbers of neurofibrillary tangles had higher levels of GFAP transcript; AD cases with larger numbers of senile plaques had higher levels of APP695 transcript. We conclude that the neuronal mRNA decrements of AD are superimposed on an age-related decline. Age-related shift in expression of certain genes may account for the differences in pathologic severity of PAD and SAD.

Uptake of 1-methyl-4-phenylpyridinium and dopamine in the mouse brain cell nuclei

The neurotoxin N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) causes, via its metabolite 1-methyl-4-phenylpyridinium (MPP+), parkinsonism in humans, monkeys, and mice but not in rats. When incubated with mouse brain homogenates, [3H]-MPP+ is recovered in relatively large concentrations in the brain cell nucleus. Although isolated cell nuclei from rat and mouse brain contain uptake systems for dopamine (DA), only brain cell nuclei from mice avidly take up [3H]MPP+. This nuclear uptake is ATP dependent and can be blocked by ouabain and N-ethylmaleimide. It is not, however, affected by neuronal and vesicular blockers such as benztropine, mazindol, and reserpine. Selective uptake of MPP+ into brain cell nuclei may provide a new avenue for future investigation into the complex modes of action of the neurotoxin MPTP.

Testosterone reverses a senescent decline in extrahypothalamic vasopressin mRNA

The biosynthetic activity of extra-hypothalamic vasopressin (VP) neurons in the bed nucleus of the stria terminalis (BNST) is regulated by gonadal steroids. These neurons have also been implicated in a number of behaviors that are impaired in aging. We previously reported that VP mRNA labelling in the BNST is decreased in senescent rats. We hypothesized that the age-related decrease in VP mRNA labelling is due to the decline in circulating testosterone (T) levels in aged animals. T or saline was administered peripherally for 1 month in physiologic or superphysiologic doses to 3 month old or 24 month old Fischer 344 male rats. In situ hybridization and quantitative autoradiography for VP mRNA in the BNST were performed using a 48-base 35S-labelled oligonucleotide probe. Administration of T completely reversed the decline in VP mRNA labelling in the aged animals. Superphysiologic T further increased VP gene expression in both age groups. These data are consistent with a previous report of T-induced increase in VP immunoreactive fiber density in other extrahypothalamic regions of the brain in aged rats. This study offers further evidence that alterations in the hormonal milieu may play an important role in modulating neuronal biosynthetic activity in senescence.

Gene expression in different cell types of aging rat brain

"Bound" and "free" RNA polymerase activities were assessed in the nuclear fraction of cerebral cortical, neuronal, astroglial, and oligodendroglial cells obtained from rats of young, adult, and old ages. Significant decreases in both the bound and free polymerase II activities were noticed in old brain, as compared to adult brain, in neuronal and oligodendroglial nuclei. In astroglia, only the free polymerase II was found to be affected. No effect of aging could be seen on the activity of bound RNA polymerase I + III. The free RNA polymerase I + III activity was increased from adult to old age in neuronal nuclei, but unchanged in oligodendroglial and astroglial nuclei. The age-dependent reduction in RNA polymerase II was maximum in oligodendroglial cells, whereas it was least, although still significant, in neuronal cells. DNA isolated from old brain was unable to enhance the transcriptional activity when added to chromatin preparations obtained from rat brains of any of the above ages and the "old" chromatin was unable to accept even the "young" DNA as additional exogenous template. It is concluded that the reduced gene expression noticed in old brain nuclei is due to both altered chromatin/DNA structure and inadequate levels of free RNA polymerase II.

Age-dependent changes of nucleic acid labeling in different rat brain regions

The effects of aging on in vivo DNA and RNA labeling and on RNA content in various brain regions of 4-, 12-, and 24-month-old rats were investigated. No difference in [methyl-14C]thymidine incorporation into DNA of cerebral cortex and cerebellum during aging was observed. The ratio of RNA/DNA content significantly decreased from 4 to 24 months of age in cerebral cortex, cerebellum and striatum. RNA labeling decreased by 15% in cerebral cortex of 24-month-old animals while in the other brain areas examined (cerebellum, hippocampus, hypothalamus, brainstem, striatum) did not change during aging. In the cerebral cortex, the ratio of the specific radioactivity of microsomal RNA to that of nuclear RNA, determined by in vivo experiments, was not affected by the aging process. A significant decrease of total, poly(A) RNA and poly(A) RNA content was observed in the same brain area of 24-month-old rats compared to 4-month-old ones. Moreover, densitometric and radioactivity patterns obtained by gel electrophoresis of labeled RNA after in vitro experiments (tissue slices of cerebral cortex) showed a different ribosomal RNA processing during aging. In vivo chronic treatment with CDP-choline was able to increase RNA labeling in corpus striatum of 24-month-old animals.