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rDNA - the 3rd type of DNA

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Posted 09 April 2005 - 03:41 PM

A neoSENS target.

Other posts have discussed nuclear and mitochondrial DNA and how alterations is the information encoded therein can affect cell function. With the exception of a post by Wolfram in the early part of this year, the "3rd" type of DNA - ribosomal DNA - and how it influences aging has been largely ignored both within our community and somewhat by the biogerontology research community as an anti-senescence target.

Firstly some background: ribosomal DNA (rDNA) is DNA that encodes ribosomal RNA (rRNA) rather than messenger RNA (mRNA) which is ultimately translated into a protein. rDNA genes are found next to each other in stretches of hundreds of tandem repeats along one or more chromosomes. Once rDNA is transcribed into rRNA it associates to form ribosomes whose function is to translate the mRNA of any gene into an amino acid chain or protein. Hence ribosomes are directly responsible for protein manufacture. The rDNA tandem repeat region which is transcribed by RNA polymerase I becomes a discrete microscopically identifiable region inside the nucleus known as the nucleolus.

With the nucleolus being the region of ribosomal biogenesis which in turn is directly related to the capacity of the cell to translate mRNA, it stands to reason that mechanisms could exist to regulate the production of ribosomes and that the region of the chromosome where the rDNA tandem repeats are found is of vital importance to the cell's ability to manufacture protein. Just as telomerase negative cells become increasingly chromosomally unstable with each mitotic division that bring them closer to their Hayflick limit, so it could be that as time goes on, the progressive DNA damage that is occurring in the cell - most particularly in the rDNA region - reduces its ability to synthesize protein.

There is considerable evidence supporting the relationship between aging and reduced rDNA: it has been observed in humans ranging in age from infancy to 76 years that as age progresses the amount of hybridizable rDNA decreases at a rate of 0.5% per year (1) . Interestingly, the same test performed in dogs showed a ratio increase of 1:7 (2) - comparable to the well known lifespan ratio between humans and dogs. This age related reduction was confirmed in human fibroblasts using silver staining of nucleolar organizing regions (3). More recently, using PCR to quantitate rDNA, two components of the ribosome unit, the 28S and 5S subunit rDNA genes, were found to be reduced in copy number as age increased (4).

So what is causing this age dependent loss of rDNA? In rat germ and liver cells the reason appears to be hypermethylation (5). In Werners syndrome patients rDNA genes are found to be increasingly methylated (6). The observation that the 18S subunit gene is not decreased in aging suggests a possible recombination event (4) associated with loss of rDNA. In any case and whatever the mechanism of rDNA gene expression decrease, the effect of decreased ribosomal function could be devastating to cell physiology.

(1) Mechanisms of Ageing and Development, Volume 11, Issues 5-6, December 1979, Pages 371-378
Loss of hybridizable ribosomal DNA from human post-mitotic tissues during aging: I. Age-dependent loss in human myocardium
Bernard L. Strehler, Mei-Ping Chang and Lorin K. Johnson

(2) Mechanisms of Ageing and Development, Volume 11, Issues 5-6, December 1979, Pages 379-382
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
Bernard L. Strehler and Mei-Ping Chang

(3)Mechanisms of Ageing and Development 92 (1996) 101–109
A longitudinal study of human age-related ribosomal RNA gene activity as detected by silver-stained NORs Samuel Thomas, Asit B. Mukherjee

(4) The International Journal of Biochemistry & Cell Biology 37 (2005) 409–415 (Attached)
Preferential loss of 5S and 28S rDNA genes in human adipose tissue during ageing
A. Zafiropoulos, E. Tsentelierou, M. Linardakis, A. Kafatos, D.A. Spandidosa

(5) PNAS 100 No 4 (2003) 1775-1780
Aging results in hypermethylation of ribosomal DNA in sperm and liver of male rats
Christopher C. Oakes, Dominic J. Smiraglia, Christoph Plass, Jacquetta M. Trasler and Bernard Robaire

(6) FASEB 14 (2000) 1715-1724
Accelerated methylation of ribosomal RNA genes during the cellular senescence of Werner syndrome fibroblasts

#2 manofsan

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Posted 09 April 2005 - 05:10 PM

Hi, what do you suggest as a remedy?

What causes hypermethylation, and how does one stop it? Are there any natural built-in methods used by cells for protecting their rDNA from hypermethylation?

If all this methylation stuff is a fallout from the natural epigenetic regulatory mechanisms going awry, then it sounds like any cure will stem from better understanding of epigenetic processes.

You guys call it rDNA, but it's still located in the nucleus, isn't it? It sounds simply like a segment of nuclear DNA that's used to spawn the ribosomes, but you seem to be identifying it by function rather than by location, as with nDNA and mtDNA.

My point is that if it's just a section of nuclear DNA, why would it attract more methylation than any other part of nuclear DNA?

#3 kevin

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Posted 09 April 2005 - 10:30 PM

Genes transcribed by RNAPolIII.. tRNA's and rRNA's are affected by stress levels..


with constitutive inflammation being a hallmark of aging we might see a down regulation of these genes and the subsequent effects.

An interesting newer finding of an 'RNA polymerase IV' in plants which is involved in methylation of 5S genes.


In a series of genetic and biochemical tests , Pikaard and his collaborators discovered that Pol IV does not share in the duties of Pol I, II or III. But when the Pol IV subunits are knocked out, the most tightly packed DNA in the nucleus becomes less condensed, small RNAs called siRNAs corresponding to highly repeated 5S rRNA genes and retrotransposons (jumping genes) are completely eliminated and DNA methylation at 5S genes and retrotransposons is lost.

Methylation is a vital process involving a chemical modification in cytosine, one of the four chemical subunits of DNA. Without proper DNA methylation, higher organisms from plants to humans have a host of developmental problems, from dwarfing in plants to tumor development in humans to certain death in mice.

perhaps there is a vertebrate equivalent. Regardless it is abundantly clear that proteolysis and protein synthesis are linked and when you allow old proteins to hang around too long they are going to aquire damage that can eventually accumulate to gum up the system.


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Posted 10 April 2005 - 03:28 AM

You guys call it rDNA, but it's still located in the nucleus, isn't it? It sounds simply like a segment of nuclear DNA that's used to spawn the ribosomes, but you seem to be identifying it by function rather than by location, as with nDNA and mtDNA.

The chief distinction between mitochondrial DNA and nuclear DNA is its location (there are also other important differences such as histone presence, chromosomal structure versus circular structure, presence of introns, etc). The distinction between ribosomal DNA and nuclear/mitochondrial DNA is that ribosomal DNA is not transcribed into messenger RNA and then translated into protein (this is an overt simplification for illustrative purposes). Instead, ribosomal DNA, once it is transcribed into RNA (not mRNA) will fold into various functional configurations which may then associate into more complex structures such as ribosomes.

You're asking the important questions, Manofsan:
- what causes hypermethylation?
- why are some areas preferentially methylated?

We know that methylation, which is the addition of a methyl group to a cytosine residue, is associated with CpG islands which are regions associated with promoters. Promoter methylation silences the transcription of the gene downstream of it. The enzymes that methylate DNA are known as DNA methyltransferases. We know that as a cell ages, the incidence of methylation increases across various promoters and not just the rDNA/nucleolar region. You can imagine the results of silencing tumor suppressor and DNA repair genes. Some investigators are looking at inhibiting methyltransferases as a cancer therapeutic strategy (1) but one must be very specific with targeting such enzymes to ensure that undesirable genes such oncogenes are not also activated. I have included a good recent review cancer and DNA methylation (2).

The only remedy I can envisage for age-dependent rDNA loss is in the SENS tradition of intervention with as little knowledge as possible ;) : use gene therapy to replace the hypermethylated and/or damaged rDNA with a clean stretch of rDNA. Note that it would have to replace the old rDNA and not be ectopically expressed since the nucleolus has some other interesting functions (to be discussed shortly, but here is a reference anyway (3)) which could be affected if it is not allowed to form properly.

(1) Cancer Biol Ther. 2004 Nov;3(11):1062-8. Epub 2004 Nov 12.
Mechanism of inhibition of DNA methyltransferases by cytidine analogs in cancer therapy.
Gowher H, Jeltsch A.

(2) The Journal of Pathology (2005) Volume 205, Issue 2 (p 172-180) (Attached)
Dormant hypermethylated tumour suppressor genes: questions and answers
Manel Esteller

(3) Int Rev Cytol. 2002;219:199-266
Conventional and nonconventional roles of the nucleolus.
Olson MO, Hingorani K, Szebeni A.

#5 Karomesis

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Posted 10 April 2005 - 04:25 AM

prometheus, The only remedy you can envision? In your opinoin, could it be that we may bypass the genetic interventions altogether? [:o] What is feasible with nanobots? I ask not to be demanding, but rather, to inqure as to the machinations of your reasoning.

Do you have any observations to note of genetic therapy to be used to replace rDNA? What would you guess if you had to?


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Posted 10 April 2005 - 05:17 AM

inqure as to the machinations of your reasoning

The NeoSENS approach aims to achieve SENS objectives using technology and science that is available today. In my view, if SENS is to enable escape velocity then NeoSENS is designed to achieve the initial boost. On the other hand, whilst the prospect of nanoechnology to many, myself included, represents the ultimate solution of molecular engineering, it is too immature and the science knowledgebase too limited to seriously consider any possible therapeutic interventions which can be tested using today's technology. Therefore when I say envision, it is within the scope of technology that we have available today. For example, it is possible to introduce a "healthy" segment of DNA into a cell that via a process known as homologous recombination that will replace a damaged target sequence. This has not been particularly succesful in vivo but it does work in vitro.

#7 manofsan

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Posted 10 April 2005 - 09:37 AM

I was reading about this drug Abraxane


"...idea was to ditch the solvent and attach the drug to tiny nano-particles of protein instead "

I want to know if this idea of bonding a drug to a protein for delivery purposes is related to that Protein Transduction Sequence stuff that Dr Smigrodzki was working on. Anybody know?

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