Retrotransposons and aging
Genomes are polygons for evolutionary struggle. Perhaps nothing reflects this idea so well as the active confrontation between retrotransposons and the genomes they are part of. Retrotransposons, often called jumping genes, are mobile genetic elements that parasitize the host DNA replication mechanisms in order to replicate themselves throughout the genome. The retrotransposons that appeared more than 100 million years ago turned out to be very successful. For example, the genomes of modern mammals are dotted with elements that appeared as a result of the activity of the "copy-paste" mechanism used by retrotransposons. And the human genome consists of almost 50% of DNA of retrotransposon origin.
The most dangerous retrotransposon of mammalian genomes is the long dispersed nuclear element-1 (LINE-1, or L1). The length of L1 retrotransposons is slightly more than 6 kilobases (thousands of nucleotides, so-called), while they encode an RNA-binding protein and an enzyme endonuclease with reverse transcriptase activity, which provides the possibility of autonomous replication in the host genome through the synthesis of an intermediate RNA molecule. The human genome contains more than 500,000 copies of L1 retrotransposons. Despite the fact that the vast majority of them are inactivated as a result of shortening, mutation or internal reorganization, according to experts, approximately 100 copies of L1 retrotransposons per nuclear genome retain replication activity. However, despite their abundance, L1 retrotransposons are not so harmless. On the contrary, their activity and even their very presence poses a real threat to the host, increasing the risk of DNA damage, as well as the development of cancer and other diseases. Given the consequences of the activity of L1 retrotransposons, it is not surprising that genomes expend considerable efforts to suppress it. Each of the stages of the life cycle of L1 retrotransposons is hindered by any factors caused by the activity of the host genome, such as suppression of gene expression, virus protection mechanisms, small RNAs and autophagy.
Historically, almost all studies of "genomic parasites" have been devoted to the study of their activity in germ cells, any changes in the genome of which are transmitted to the next generations. Very little attention was paid to retrotransposition in somatic tissues, as they were considered to be an "evolutionary dead end". However, in recent years there has been evidence that L1 elements can be activated in various somatic tissues of humans and mice, including in the brain, skeletal muscles, heart and liver. The most interesting was the fact that the highest activity of L1 retrotransposons in many cases is observed in aging tissues, especially those prone to age-related pathologies, such as cancer. Based on this, it can be assumed that the activity of these genetic elements may contribute to the aging process.
The number of facts testifying in favor of this idea is constantly increasing. Aging tissues are characterized by an increase in the frequency of DNA damage and mutagenesis, whereas it is known that this results in an increase in the activity of L1 elements. In addition, the results of a small number of studies indicate that overexpression of L1 retrotransposons can lead to physiological aging of cells, which is a characteristic feature of aging tissues. The role of L1 elements in triggering age-related processes is currently an issue that requires detailed study.
Suppression of L1 retrotransposon expression
The most obvious threat that L1 retrotransposons conceal is the risk of mutagenic inserts. Depending on where in the genome it is embedded, a retrotransposon can, for example, make a cell predisposed to malignant degeneration. In fact, an increased number of copies and increased activity of L1 retrotransposons is a characteristic sign of genome malignancy. Moreover, it has been established that many human genetic diseases arise as a result of mutagenesis caused by L1 retrotransposons. However, L1 retrotransposons still have a whole arsenal of mechanisms for the destruction of the host genome. The endonuclease encoded by them can cause single-stranded DNA breaks, for example, the untranslated region of L1 retrotransposons 5’ (5’ UTR) is capable of disrupting the transcription of host genes adjacent to it, and the presence of extensive regions represented exclusively by the DNA of L1 retrotransposons can lead to recombination errors. Since genome instability and DNA damage are key characteristics of aging, it is not at all difficult to guess what role L1 retrotransposons may play in the molecular etiology of the aging process.
Perhaps the most obvious evidence of the involvement of retrotransposons in the aging process is the existence of a relationship between the activity of the SIRT6 longevity gene and the suppression of the activity of L1 retrotransposons in somatic tissues. SIRT6 encodes an enzyme necessary for the prevention of aging that maintains telomere length, promotes the repair of DNA damage, regulates metabolism, prevents oncogenesis and suppresses inflammation. All these mechanisms are associated with the prevention of age-related extinction of the body. Mice without the SIRT6 gene suffer from severe premature aging syndrome, whereas mice with SIRT6 overexpression are distinguished by longevity. More recently, it was found that SIRT6 plays a key role in maintaining the inactive state of L1 retrotransposons in the tissues of young mice and human cells that have not entered the phase of physiological aging by packing retrotransposons into chromatin inaccessible for transcription [1]. To do this, SIRT6 binds to the 5’ UTR region of the L1 element and triggers the assembly of heterochromatin proteins in the region of the retrotransposon promoter. Upon completion of assembly, this mechanism of gene activity suppression saturates the 5’ UTR region of the L1 element and associated chromatin with epigenetic modifications that prevent the launch of retrotransposon expression.
Deprived of the ability to express L1, the retrotransposon is unable to synthesize the parasitic mechanisms necessary to trigger its own replication. This protects the host cell from the appearance of new mutations. In addition, heterochromatinization limits the ability of the L1 retrotransposon to alter the expression of host genes and induce recombination errors. When the SIRT6 gene is removed from mouse cells or knocked out in human cells, the 5’ UTR region of L1 elements avoids heterochromatinization, which leads to a pronounced increase in the transcription of L1 retrotransposons and the appearance of new inserts of these elements into DNA.
An interesting fact is that with age, the mechanism by which SIRT6 suppresses the activity of L1 retrotransposons loses its effectiveness. During aging, SIRT6 disappears from the 5’ UTR regions of L1 retrotransposons, which leads to the de-heterochromatinization of these genetic elements (see Figure).
The disappearance of the activity-suppressing chromatin returns to L1 retrotransposons the ability to transcribe in many tissues of aging mice, as well as in human cells that have entered the phase of physiological aging. However, what exactly is happening in the aging process that deprives SIRT6 of the ability to effectively protect aging cells from dangerous genomic parasites?
One explanation for this failure may be related to the key role of SIRT6 in repairing DNA damage. The results of several studies indicate that SIRT6 catalyzes the repair of many types of DNA damage, including single- and double-stranded breaks. A characteristic feature of aging cells is an increase in the amount of DNA damage. It is possible that under normal conditions SIRT6 remains bound to the L1 promoter of the retrotransposon to suppress the activity of the genomic parasite, however, when DNA damage occurs, this enzyme leaves the sequence of the L1 element in order to facilitate the process of DNA repair in the damaged area. This gives L1 retrotransposons the opportunity to replicate. This model is confirmed by observations according to which, when cells are exposed to DNA-damaging agents such as hydrogen peroxide or the herbicide paraquat, SIRT6 disappears from the L1 retrotransposon sequences, which is accompanied by an increase in its concentration in the damage zones.
Several other factors may potentially reduce the ability of SIRT6 to suppress the activity of L1 retrotransposons in aging cells. For example, SIRT6 cannot exhibit its enzymatic activity in the absence of a substrate known as NAD+. The level of this metabolite decreases in aging cells, which may lead to a decrease in the efficiency of SIRT6 functioning. Moreover, the level of SIRT6 expression in various types of cells and tissues decreases with age. The lower availability of this protein may also exacerbate the age-related decrease in the level of suppression of the activity of L1 elements.
Involvement in the aging process
The change in the localization of SIRT6 occurring in stressed or aging cells is consonant with the theory of aging, known as the theory of changes in the localization of chromatin modifiers. This theory was originally proposed in 1998 by Japanese researchers Hiroaki Kitano and Shinichiro Imai [2] and finally formulated a decade later by Philipp Oberdoerffer and David Sinclair from Harvard University Medical School [3]. According to this theory, while the mobilization of chromatin-modifying proteins, such as SIRT6, occurring in response to stressful influences, is beneficial for young organisms, the redistribution of these elements can trigger disastrous age-related changes. From this point of view, the mobilization of SIRT6 into DNA damage zones and the subsequent release of L1 retrotransposons can lead to the manifestation of age-related phenotypes and pathologies. For example, increased activity of L1 retrotransposons may contribute to the appearance of genome instability, which is a key phenotype of aging cells. This is the result of DNA mutagenesis, manifested by the appearance of new inserts, and the start of the process of DNA damage mediated by the expression of L1 endonuclease of retrotransposons. Moreover, the exit of SIRT6 from L1 elements caused by DNA damage triggers a vicious circle: DNA damage induced by L1 retrotransposons causes SIRT6 to leave all new L1 elements, which further enhances the activity of L1 retrotransposons and, accordingly, leads to the appearance of new DNA damage. Similarly, L1 retrotransposons can disrupt cell homeostasis by inducing the process of dysregulation of gene expression or blocking the transcription mechanisms of the host cell. This is confirmed by observations according to which the overexpression of exogenous L1 retrotransposons is sufficient to trigger the entry of human fibroblasts and stem cells into the stress-induced phase of physiological aging [4].
The assumption that the restoration of L1 retrotransposon activity may contribute to the development of age-related pathologies looks especially plausible if we take into account the fact that the brain tissues (especially the hippocampus and striatum), liver and skeletal muscles are especially characterized by an age-related increase in the activity of L1 elements. Each of these tissues plays an important role in maintaining the body's homeostasis at the level of a variety of signaling pathways and demonstrates a pronounced decline in functions as it ages. For example, the assumption that increased activity of L1 retrotransposons and associated DNA damage, inflammation and disruption of transcription mechanisms contribute to the development of atrophy and insensitivity to insulin-mediated signals characteristic of skeletal muscles of an aging organism looks very attractive. Similarly, L1 retrotransposition in the cells of the aging brain may be another curious but little-understood mechanism that can explain many manifestations associated with aging of the nervous system.
The results of a number of studies indicate that new retrotransposon inserts in the nervous system predominantly affect actively transcribed genes in brain cells, especially the genes of dopamine receptors, amino acid carriers and genes regulating synaptic transmission. Considering this fact in combination with the estimated data, according to which the number of new inserts of L1 retrotransposons on a nerve cell in certain regions of the brain can reach from 80 to 800 [5], we can talk about the existence of a powerful mechanism by which these retrotransposons are able to modulate neurological activity and contribute to the age-related extinction of neurological functions. In accordance with this idea, a number of neurological diseases, including Rett syndrome, Smith-Magenis syndrome and schizophrenia, are characterized by increased activity of L1 retrotransposons [6]. Taking into account the observation that the activity of L1 elements is increased in the aging brain, it suggests that the restoration of the activity of L1 retrotransposons may contribute to the development of age-related pathologies of the nervous system, ranging from cancer to neurodegenerative diseases, especially various types of dementia associated with aging.
In general, two clear pictures describing the biology of L1 retrotransposons are emerging. Firstly, L1 elements are undoubtedly active in somatic tissues. Since historically they have been ignored in the somatic context, the spectrum of their activity requires serious research devoted to the study of the biological importance of these genetic elements. Secondly, the activity of L1 retrotransposons may be of exceptional importance in the context of aging biology. The increased activity of L1 elements is associated with the aging of many tissues, and the discovery that SIRT6 is a link between L1 retrotransposons and aging provides researchers with a platform for further study of the relative contribution of L1 retrotransposon activity to the mechanisms of aging.
There are several therapeutic vectors that allow researchers to weaken the activity of L1 retrotransposons and possibly slow down the development of pathologies associated with aging caused by them. For example, during a series of experiments, the researchers found that SIRT6 overexpression is sufficient to suppress the activity of L1 retrotransposons and their return to an inactive state in cells that have already entered the phase of physiological aging. While it may not be so easy to achieve SIRT6 overexpression in a therapeutic context, the activity of this gene can be increased with a low-calorie diet, reduced glucose intake or increased bioavailability of NAD+. All these interventions have already demonstrated their potential in increasing the life expectancy of animal models. Such interventions also demonstrate the potential to slow down the progress of some age-related neurodegenerative diseases (see the article “Nurishing the Aging Brain"). The results of one of the studies indicate that a low-calorie diet is sufficient to suppress the age-related increase in the activity of L1 retrotransposons [7]. Another very interesting idea involves the use of reverse transcriptase inhibitors. In the absence of this enzyme, L1 retrotransposons cannot self-replicate; at the same time, there are already a number of powerful reverse transcriptase inhibitors on the market that effectively suppress the activity of L1 retrotransposons. Assessment of the scale of the contribution made by L1 retrotransposons to aging, as well as the search for methods to block their activity in the coming years are important tasks for researchers engaged in the study of aging issues.
For links to publications in scientific journals, see the original article.
Evgeniya Ryabtseva
Portal "Eternal youth" http://vechnayamolodost.ru based on the materials of The Scientist:
Michael Van Meter, Andrei Seluanov, and Vera Gorbunova. Wrangling Retrotransposons.
06.03.2015