44 replies to this topic

[kevin]

Link: http://www.eurekaler...l-sos042204.php

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Public release date: 22-Apr-2004

Contact: Heather Cosel
coselpie@cshl.org
Cold Spring Harbor Laboratory

Something old, something new
Scientists glean new insight from prematurely old mice

The relationship between genome integrity and aging is the subject of a new report in the upcoming issue of Genes & Development. Drs Lin-Quan Sun and Robert Arceci at Johns Hopkins University School of Medicine have developed a novel mouse model to study premature aging, and the genetic events that contribute to normal development and longevity.

"The inability of an organism to maintain the integrity of its genome has been postulated to be an important cause of aging, developmental abnormalities and predisposition to cancer," explains Dr. Arceci, corresponding author and professor of pediatrics and oncology at The Johns Hopkins Kimmel Cancer Center.

Dr. Arceci and his colleagues focused on PASG (Proliferation Associated SNF2-like Gene). PASG encodes a SWI/SNF protein family member that facilitates DNA methylation (the addition of a methyl (CH3) group to cytosine) – an effective means to silence genes in the eukaryotic genome. As an organism develops, global patterns of DNA methylation change in order to accommodate the changing patterns of gene expression.

Now, for the first time, Drs Sun and Arceci provide in vivo evidence that the loss of PASG results in a reduced level of global genomic methylation and premature aging in mice.

"In order to elucidate the function of PASG, we generated a "knockout" mouse carrying a hypomorphic mutation of PASG. Using homologous recombination, exons 10, 11 and 12 containing helicase domains II, III and IV were deleted," states Dr. Arceci.

These PASG-mutant mice displayed numerous abnormalities, including developmental growth retardation and characteristics associated with premature aging, including graying and loss of hair, reduced skin fat deposition, osteoporosis, cachexia and, ultimately, an untimely death. On a cellular level, PASG-mutant animals displayed reduced levels of genomic methylation, as well as increased expression of senescence-associated tumor suppressor genes, like p16INK4a.

Dr. Arceci is hopeful that "the mutant mice provide a potentially useful model for the study of aging as well as the mechanisms regulating epigenetic patterning during development and postnatal life. They may also serve as a potential model for examining the role of epigenetic change and chromatin remodeling in cancer predisposition with implications for possible therapeutic targeting."


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Edited by Kevin Perrott, 11 April 2006 - 01:53 PM.

[manofsan]

This is interesting -- so lack of methylation can result in faster aging? I thought methylation was meant to selectively disable genes, to alter the pattern of gene expression. In which case, why would inability to suppress some genes lead to aging? Wouldn't you expect the opposite -- that inability to express some genes would lead to the deterioration in the body?

I guess this relates to what some people have previously said, about how if certain genes overexpress, then it triggers immune response against oncogenes, because your immune system is worried that cancerous activity is happening.

[kevin]

Hi manofsan,

A biogerontologist by the name of Richard Cutler, who is also a participant in the Methuselah Mouse Prize by the way, proposed some time ago that aging is the result of the 'dysdifferentiation' of tissues by various mechanisms which can damage DNA. He basically states that cells lose their function as a result of improper gene expression. From what I understand, as stem cells move through increasing stages of differentiation to their final tissue cell type, some genes are silenced while others are activated with methylation which is able to both activate and deactivate depending on the configuration of the gene switching mechanism. Regardless whether a gene is turned on or off by methylation, the fact that methylation levels decrease as we age leads one to think it is possible that a muscle cell may begin to express genes for liver and so on and so on.. thus leading to a state of 'dysdifferentiation'. We are multicellular organisms and one thing which is not perhaps focused enough on is that our cells are really independent entities which have 'agreed' to fulfill a certain function. This cooperation and communication takes a LOT of energy and I believe there are signals sent out from our reproductive systems, (in line with what Kenyon proposes), which might allow the beginning of the breakdown of our maintenance systems. Rather than it being an 'active' self-destruct mechanism however, I think it is more like a scaling back of life-promoting expression which is eventually overcome by the normal wear and tear.

We all need to start having children later in life.. ! NOT!

Epigenetic controls on gene expression from methylation as well as the interaction of small interfering RNA's are possibilitities that should be looked at in the maintenace of the integrity of our genomes.

[manofsan]

Well, from cloning experiments going awry, we know that imprinting mechanisms (which seem largely based on the epigenetic methylation) are supposed to be much more subtle and fragile in comparison to actual DNA copying.

So even if we copy the DNA robustly, the much more delicate methylation stuff can still get screwed up. Whether the screwups happen right at conception (in the case of cloning) or as we reach old age (ie. natural aging), this represents an entropy that takes away from our highly ordered, highly specialized structure.

So if it's Methylation vs Methuselah (ie. if methylation is the weak link in the senescence chain which causes the breakdown in bodily function) then we really need to learn more about this whole methylation business.

But most experts still say that it's a cocktail of things which drag us down -- eg. glycosylation, methylation, copying errors, oxidative destruction, physical wear and tear. And our biological algorithm tells our gut to keep growing and our hips to get wider, which is not stimulated by the environment.

Heh, I see what you mean about having the kids later in life, but our information technology is now progressing to the point where it can do the Darwinist algorithm for us, instead of us having to wait for nature to act it out. We just need to computationally simulate lots of genomes, and see which one works better and lasts longer. If we can do this for regular binary computer programs, we can do it for genome-based programs too. Hey, we're only talking about 2.6 billion bases and maybe 30K-100K genes, which should be a lot easier than simulating the weather.

The first I heard of this delicate epigenetic methylation control stuff, was in connection with that Callipyge goat and its unique phenotype, which shows that methylation can be responsible for natural variation as well. I'm not sure whether it's possible for 2 creatures to be genetically identical, and yet differ due to methylation. But at the very least, minor genetic differences can have an amplified effect due to the resultant epigenetic methylation differences.

[kevin]

Link: http://www.eurekaler...s-dof121404.php


In the post above I mentioned that decreasing methylation of chromatin occurs with aging. One thing nobody knew is how demethylation occured as in 40 years no 'demethylase' enyzme has been found. Genetic regulation just took a huge leap forward with the discovery below.

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Public release date: 16-Dec-2004
Contact: John Lacey
public_affairs@hms.harvard.edu
617-432-0442
Harvard Medical School

Discovery of first demethylase molecule, a long-sought gene regulator
Could be target for cancer therapeutics
BOSTON, MA-Researchers have discovered an enzyme that plays an important role in controlling which genes will be turned on or off at any given time in a cell. The novel protein helps orchestrate the patterns of gene activity that determine normal cell function. Their disruption can lead to cancer.

The elusive enzyme, whose presence in cells was suspected but not proven for decades, came to light in the laboratory of Yang Shi, HMS professor of pathology, and is described in a study published in the Dec. 16 online edition of Cell and appearing in the Dec. 29 print edition.

"This discovery will have a huge impact on the field of gene regulation," said Fred Winston, an HMS professor of genetics who was not involved with the work. "Shi and his colleagues discovered something that many people didn't believe existed."

The enzyme, a histone demethylase, removes methyl groups appended to histone proteins that bind DNA and help regulate gene activity. "Previously, people thought that histone methylation was stable and irreversible," said Shi. "The fact that we've identified a demethylase suggests a more dynamic process of gene regulation via methylation of histones. The idea of yin and yang is universal in biology; our results show that histone methylation is no different."

In the cell, yarnlike strands of DNA wrap around protein scaffolds built of histones. The histones organize DNA into a packed structure that can fit into the nucleus, and the packing determines whether the genes are available to be read or not. Acetyl, methyl, or other chemical tags appended to the histones determine how the histones and DNA interact to form a chromatin structure that either promotes gene activity or represses it.

Some histone tags, particularly acetyl groups, are known to be easily added and removed, helping genes to flick on and off when needed. But the addition of methyl groups was considered a one-way process that could only be reversed by the destruction of histones and their replacement with new ones. Part of the reason scientist believed this was that no one had isolated a demethylase, despite an active search.

The Shi lab was not among those in the hunt, but they stumbled onto the demethylase while probing the function of a new gene repressor protein. Postdoctoral fellow Yujiang Shi had exhausted the likely possibilities for how the mystery protein worked to suppress gene activity, so one day he tried an unlikely experiment. He had the purified protein in a test tube and decided to feed it methylated histones. His finding, that the enzyme could efficiently chew off the methyl group, leaving behind intact, unmodified histone left the postdoc Shi shaking with excitement. "Forty years ago some scientists speculated that histone demethylases existed," he said. "At first, I thought it was impossible that this protein was it." After reproducing the results using several different biochemical techniques, he began to feel comfortable that they had found the first demethylase.

Their enzyme didn't remove just any methyl group from histone. Instead, it removed a very specific methyl found on lysine 4 (K4) of histone 3 (H3). H3K4 methylation is associated with active transcription, so its removal would be consistent with the gene repression function they had identified.

Now that the first demethylase has been recognized, researchers will certainly find more. "This cannot be the only demethylase," said Shi.

Genes turning on at the wrong time or in the wrong place is a hallmark of cancer cells. In some tumors, high levels of methylation of H3K4 seem to play a role in activating genes that drive abnormal cell growth. The discovery of this H3K4 demethylase suggests a way to counterbalance this progrowth signal in some tumors. And if previous experience with histone deacetylases is any guide, the demethylases could one day be targets for cancer therapeutics.

"These findings will impact every walk of biology," said David Allis of Rockefeller University, a leader in studying the regulation and biological roles of histone tags. "Histone modifications are highly dynamic on-off switches that the cell throws a lot. These modifications affect everything DNA does, and getting the enzyme means you've got one upstream point of regulation. This will open up a wealth of new experiments."


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HARVARD MEDICAL SCHOOL
http://hms.harvard.edu/
Harvard Medical School has more than 5,000 full-time faculty working in eight academic departments based at the School's Boston quadrangle or in one of 47 academic departments at 18 Harvard teaching hospitals and research institutes. Those Harvard hospitals and research institutions include Beth Israel Deaconess Medical Center, Brigham and Women's Hospital, Cambridge Hospital, The CBR Institute for Biomedical Research, Children's Hospital Boston, Dana-Farber Cancer Institute, Forsyth Institute, Harvard Pilgrim Health Care, Joslin Diabetes Center, Judge Baker Children's Center, Massachusetts Eye and Ear Infirmary, Massachusetts General Hospital, Massachusetts Mental Health Center, McLean Hospital, Mount Auburn Hospital, Schepens Eye Research Institute, Spaulding Rehabilitation Hospital, VA Boston Healthcare System.

[manofsan]

So these demethylation agents are doing a necessary job, acting to switch off genes when necessary. But is there any possibility that they are malfunctioning and turning off too many genes, at times when this is undesirable? Is there any possibility of excess buildup/accumulation of these agents occurring over time, contributing to our aging process?

[kevin]

Link: http://www.eurekaler...s-nrp021005.php

I think we might expect to find an Rna PolIV like this in humans, or something like it.

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Public release date: 10-Feb-2005

Contact: Tony Fitzpatrick
tony_fitzpatrick@wustl.edu
314-935-5272
Washington University in St. Louis

New RNA polymerase discovered in plants
Plays roles in flowering, methylation
Biologists at Washington University in St. Louis have discovered an entirely new cellular "machine" in plants that plays a significant role in plant flowering and DNA methylation, a key chemical process essential for an organism's development.

A team headed by Craig Pikaard, Ph, D., Washington University professor of biology in Arts & Sciences, has discovered a fourth kind of RNA polymerase found only in plants and speculated to have been a plant feature for more than 200 million years.

RNA polymerase is an enzyme, or protein machine, essential for carrying out functions of cells and for expression of biological traits. It does its job by copying a template of DNA genetic information in order to make RNAs that encode proteins or that function directly in the cell.

Biologists have studied three kinds of RNA polymerase for decades in organisms ranging from brewer's yeast to humans. In all eukaryotes, the RNA polymerases Pol I, II, and III perform the same distinct , though separate, functions in different species.

But then along came Pol IV. Pikaard first noticed the evidence for a fourth polymerase when analyzing gene sequences after Arabidopsis thaliana , the "laboratory rat" of the plant world, was sequenced in 2001. It originally looked to him like an alternative form of either Polymerase I (Pol I), which makes the largest of the ribosomal RNAs, Pol II which makes RNAs for protein-coding genes, or Pol III, a specialist in making the shortest of the ribosomal RNAs and tRNAs.

The big 'subunit'

He and his colleagues looked specifically at two polypeptides that would be the key subunits if the fourth polymerase were functional, namely the largest and second largest subunits, what Pikaard refers to as the catalytic, or "business end" of any known polymerase.

"So, we took a reverse-genetics approach" said Pikaard. " We thought: 'What happens if we knock these genes out?' So, we knocked out the genes responsible for these subunits and there were no huge consequences. The plants survived, but there were slight delays in flowering and some strange floral defects. The plants were having trouble with organ identity – stamens tried to turn into petals, for instance. Our first hypothesis was that the fourth polymerase was involved with what are known as micro RNAs, which are known to regulate flower development, but that proved wrong."

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.

Pikaard thinks that Pol IV helps make siRNAs that then direct DNA methylation to sequences matching the siRNAs.

The results were published in Cell online, Feb. 10, 2005 and will appear in the March, 2005 print version of the journal.

"Pol IV is somehow involved in maintaining the integrity of the Arabidopsis genome, principally in keeping the silent DNA silent," Pikaard said. "Plants can get by without Pol IV, whereas they can't do without the other three. We don't see anything obviously like Pol IV in any other genome, but it's possible it might have been overlooked."

While Pikaard and his collaborators have indirect evidence that Pol IV is a distinct RNA polymerase, they still have many aspects of Pol IV to unravel.

"We know what happens when its gone, but not how it behaves, at this point," he said. "We don't know its template, or what kind of RNA – long or short – it makes. Presumably, because it is inherently different from the other RNA polymerases, the rules of activity are different for Pol IV."

Pikaard said the Pol IV has a perfect match in rice, the only other plant genome to be sequenced, despite rice being a monocotyledon and Arabidopsis a dicotyledon.

"These two plants diverged 200 million years ago, and there is some speculation that this form of polymerase might extend twice as far back in evolution,' Pikaard said.

Pikaard said that it is strange that so far this kind of polymerase has been found only in plants.

"Why would plants only have these?" he questioned. "It is a bit of a mystery how other organisms that use small RNAs and that also do methylation get by without a Pol IV. It might be possible that they have something equivalent, and maybe we haven't looked hard enough. "


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[kevin]

Link: http://www.eurekaler...c-neo121905.php

and the plot thickens...

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Contact: L. H. Lang
llang@med.unc.edu
919-843-9687
University of North Carolina School of Medicine

Novel enzyme offers new look at gene regulation
UNC scientists' findings have diverse implications

Scientists at the University of North Carolina at Chapel Hill have purified a novel protein and have shown it can alter gene activity by reversing a molecular modification previously thought permanent.

In the study, the authors showed that a protein called JHDM1A is able to remove a methyl group from histone H3, one of four histone proteins bound to all genes. Until just last year, the addition of a methyl group to a histone had been regarded as irreversible.

"That histones can become methylated has been known for over three decades, and just now we're learning that those methyl groups can also be removed," said Dr. Yi Zhang, the lead author.

Zhang is professor of biochemistry and biophysics at UNC's School of Medicine and the university's first Howard Hughes Medical Institute investigator. He also is a member of the UNC Lineberger Comprehensive Cancer Center.

The new study is now online in the journal Nature.

"Human genes are so tightly compact within the nucleus that if the DNA of a single cell were unwound and stretched, it would be a line of about two meters in length," said Zhang. "Histones are necessary to package the DNA so that it fits inside a cell's nucleus."

Because they are so intimately associated with DNA, even slight chemical alterations of histones can have profound effects on nearby genes. Depending on the precise location and how many methyl groups are added, their presence can either switch affected genes on or off.

The first enzyme to remove methyl groups from histones, or histone demethylase, was identified last year. This was a breakthrough in the study of histone modifications, but Zhang thought pieces of the puzzle were still missing.

"We hypothesized that there were more demethylase enzymes out there for two reasons," Zhang said. "For one, the previous demethylase identified, called LSD1, could not remove a chain of three methyl groups from a histone, or a trimethyl group. Secondly, common baker's yeast does not have LSD1, although it does have proteins adding methyl groups to histones."

Zhang devised a biochemical strategy to isolate proteins that could remove methyl from histones inside a test tube. The result was the identification of a novel protein, JHDM1A, named for JmjC histone demethylase 1A. A similar protein exists in baker's yeast and has the potential to remove trimethyl groups.

JmjC is only a section of the entire JHDM1A protein, but is required for its demethylase activity. The authors showed that disruption of JmjC prevents JHDM1A from removing histone methyl groups.

Importantly, the JmjC section of JHDM1A, or "JmjC domain," can be found in other proteins, even when the proteins share little else in common. Database searches predict more than 100 total proteins found in organisms as diverse as bacteria and man contain the JmjC domain. This suggests that many other proteins may act similarly to methyl groups from histones or other proteins.

The implications of the new findings are as diverse as the proteins that contain a JmjC domain. For example, hair loss occurs in individuals with mutations in the JmjC domain of a protein called "hairless," possibly due to defects in the appropriate removal of histone methyl groups.

"Given the large numbers of JmjC domain-containing proteins that exist in diverse organisms ranging from yeast to human, our discovery will keep many people in the field busy for the years to come," said Zhang.


###
Contributing to the work were Drs. Yu-ichi Tsukada and Jia Fang, two postdoctoral scientists in Zhang's lab. Other collaborators include research associate Dr. Maria Warren and assistant professor Dr. Christoph Borchers, both of UNC's department of biochemistry and biophysics, as well as Dr. Hediye Erdjument-Bromage and Dr. Paul Tempst from the Memorial Sloan-Kettering Cancer Center.

The work was supported by funding from the Howard Hughes Medical Institute and a grant from the National Institutes of Health.

Note: Contact Zhang at (919) 843-8225 or 8228 or yi_zhang@med.unc.edu.

School of Medicine contact: Les Lang, (919) 843-9687 or llang@med.unc.edu

[kevin]

Link: http://sageke.scienc...ll/2005/51/nf91

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Loose Chromosomes Sink Cells
Gene-silencing mechanism falters in patients with premature aging disorder

Mitch Leslie

Just relax" might be good advice for stressed-out holiday travelers, but it could be disastrous for chromosomes, according to work presented at the American Society for Cell Biology meeting in San Francisco, California, on 13 December. The study suggests that chromosomes uncoil somewhat in patients with a disease that resembles premature aging, an alteration that could unleash genes whose products aren't needed.

Children with the fatal genetic disease Hutchinson-Gilford progeria syndrome (HGPS) seem to grow old before their time. They lose their hair, their skin thins, their bones grow brittle, and their arteries clog (see "Of Hyperaging and Methuselah Genes"). Most afflicted individuals die in their teens from a stroke or heart attack. In 2003, researchers fingered the genetic flaw that triggers HGPS: a mutation in the gene for lamin A (see "Lamin-tation"). The protein weaves a mesh that supports the cell's nucleus, and it's also necessary for copying DNA and making messenger RNA. A 2004 study by cell biologist Robert Goldman of Northwestern University's Feinberg School of Medicine in Chicago, Illinois, and colleagues suggested a connection between HGPS and gene control. Cells mothball stretches of DNA that they are not currently using. They accomplish the feat by coiling the strands tightly in a structure called heterochromatin. Goldman's work hinted that heterochromatin vanishes from HGPS cells. The researchers sought to confirm its disappearance and determine whether mutant lamin A was involved.

Heterochromatin condenses when DNA wraps tightly around the proteins called histones. Cinching up the chromosomes requires that a specific amino acid in one type of histone acquires methyl groups. To track heterochromatin, the scientists reared skin cells from a girl with HGPS and added an antibody that grabs the methyl-carrying amino acid. Using cells from females makes it easy to detect compacted DNA, Goldman notes, because they harbor one inactive X chromosome in each cell that is "a mass of heterochromatin." After duplicating for several generations, cells from the HGPS patient had shed their methyl groups, but cells from her healthy sister retained the molecular adornment. Normal cells engineered to pump out the faulty form of lamin A dropped their methyl marks, too. HGPS cells pump out less of the messenger RNA that codes for the methyl-adding enzyme, the researchers showed, which could explain the loss of methylated histones. Heterochromatin usually bears a coating of RNA. Although this layer didn't vanish in the HGPS cells, it showed signs of fraying. That finding suggests that although the chromosomes in the HGPS cells didn't unravel, they had started to loosen up. Overall, the work indicates that faulty lamin A meddles with histone methylation, Goldman says.

The work deserves praise for homing in on a change that might trigger HGPS defects, says cell biologist Susan Michaelis of Johns Hopkins University in Baltimore, Maryland. Now, the trick is to tease out which of the alterations researchers have identified cause the symptoms of HGPS, she says. For example, Goldman's group also found that faulty lamin A remains stuck to the nuclear membrane during cell division; in contrast, the normal protein disperses. Cell biologist Harald Herrmann of the German Cancer Research Center in Heidelberg describes the study as "a real breakthrough" because it shows that the protein can tamper with chromosome organization. Next, researchers need to establish that faulty lamin A activates silenced genes, he says. Further work might reveal whether uptight chromosomes keep cells healthy.

December 21, 2005

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[Mind]

Where does methylation and its under/over expression fit into the SENS model. Obviously, you could consider it a mutation or mutation promoting mechanism and thus in SENS it would fall under Mito Mutation or Nuclear Mutation, but is this a chicken and egg scenario? Does damage (wear and tear) and accumulated junk lead to a disruption of methylation, or does genetic mutation happen first and disrupt cellular repair? Maybe it doesn't matter.

Reading the last article got me to thinking about the "primary" cause of aging or what may be the most significant factor. People with the "relaxed" chromosomes (Hutchinson-Gilford progeria syndrome) aquire the symptoms of normal aging much faster. So do regular people have a slower acting form of Hutchinson-Gilford progeria syndrome? Is that a logical way to think about it? Is faulty Lamin A a "key" component of the agging process? I suppose it is hard to speculate until more data comes in, but has anyone else thought of it in these terms?

[ag24]

> Where does methylation and its under/over expression fit into the SENS model.

Same place as mutations, as you guessed. "Epimutations" is the term that I like for adventitious but persistent changes to DNA methylation and histone modifications: it was coined by Holliday but never really caught on. Epimutations are unknown in mtDNA, but even if they exist allotopic expression would rended them harmless. In the nuclear DNA, they potentially matter just as much as mutations -- but luckily this applies to cancer too, so the logic that evolution has made our maintenance machinery unnecessarily good for most genes in order to be good enough to avoid cancer applies to epimutations just as to mutations. (Incidentally, I've finally written that argument up in detail and it's in press in Mech Ageing Dev; various people, including the inestimable Jan Vijg, will be writing responses so we'll see how it stands up.)

> do regular people have a slower acting form of Hutchinson-Gilford progeria syndrome?

In a way -- it just depends how much slower. This is the perenial problem with accelerating damage: even if you see a wide range of aging symptoms, you can't infer that that type of damage is the dominant contributor to aging in a normal lifetime because you don't know by what factor you've accelerated the primary damage. Accelerated mtDNA damage and accelerated stem cell death also cause many types of acceleratedaging in people and/or mice.

SENS indeed steers clear of gene regulation, just as it steers clear of all metabolism, and as prometheus says, that's because we don't understand it well enough to have much chance of intervening significantly without doing more harm than good. More generally though, I'm reviewing SENS all the time -- it is certainly open to change.

[ag24]

Send me your email address and I'll send you the submitted version. In brief, however: the reason why this is an exception to what you rightly note is the rule that no maintenance system is unnecessarily good is that there is no easily definable way to distinguish between genes in which mutations would promote cancer and genes irrelevant to cancer. Possibly these classes of gene could be distinguished by very sophisticated genetic machinery -- but then evolution faces the choice of whether to maintain that machinery or whether to forget the distinction and just maintain every gene as well as it needs to maintain any gene. The latter seems to have won out, as judged from both the level and the rate of increase of mutations seen in aging in mammals, most thoroughly explored by Vijg but also explored by several other groups. The general rule about nothing being done unnecessarily well arises because each aspect of aging is combated by a set of genes that only partly overlap with the set for any other aspect of aging, so that if one aspect of aging is being defended against unnecessarily well, the genes that participate in that defence but not in the defence against aspects of aging that do kill the organism (are being combated only just well enough) will accumulate mild mutations in the germ line because there will be no selection against such mutations (no shortening of health or life). When no such genes exist (because the two aspects of aging in question are combated by exactly the same genes), this logic fails.

You ask an interesting but different question re death in the wild. Yes, few animals die of cancer in the wild. But few die of other aspects of aging in the wild either. Evolution seems to feel that the optimal degree of maintenance is that which keeps death from aging (i.e. from lack of maintenance) really quite low -- perhaps because the energy involved in this maintenance is slight.

[kevin]

Link:
http://www.ncbi.nlm....l=pubmed_docsum

p21(Waf1/Cip1) plays a critical role in modulating senescence through changes of DNA methylation.

Zheng QH, Ma LW, Zhu WG, Zhang ZY, Tong TJ.

Peking University Research Center on Aging, Peking University Health Science Center, Beijing, China.

It has been reported that genomic DNA methylation decreases gradually during cell culture and an organism's aging. However, less is known about the methylation changes of age-related specific genes in aging. p21(Waf1/Cip1) and p16(INK4a) are cyclin-dependent kinase (Cdk) inhibitors that are critical for the replicative senescence of normal cells. In this study, we show that p21(Waf1/Cip1) and p16(INK4a) have different methylation patterns during the aging process of normal human 2BS and WI-38 fibroblasts. p21(Waf1/Cip1) promoter is gradually methylated up into middle-aged fibroblasts but not with senescent fibroblasts, whereas p16(INK4a) is always unmethylated in the aging process. Correspondently, the protein levels of DNA methyltransferase 1 (DNMT1) and DNMT3a increase from young to middle-aged fibroblasts but decrease in the senescent fibroblasts, while DNMT3b decreases stably from young to senescent fibroblasts. p21(Waf1/Cip1) promoter methylation directly represses its expression and blocks the radiation-induced DNA damage-signaling pathway by p53 in middle-aged fibroblasts. More importantly, demethylation by 5-aza-CdR or DNMT1 RNA interference (RNAi) resulted in an increased p21(Waf1/Cip1) level and premature senescence of middle-aged fibroblasts demonstrated by cell growth arrest and high beta-Galactosidase expression. Our results suggest that p21(Waf1/Cip1) but not p16(INK4a) is involved in the DNA methylation mediated aging process. p21(Waf1/Cip1) promoter methylation may be a critical biological barrier to postpone the aging process. J. Cell. Biochem. © 2006 Wiley-Liss, Inc.

PMID: 16514663 [PubMed - as supplied by publisher]

[mitohunter]

Dr. de Grey,
I was shocked to hear that your conference/debates with Kenyon were denied by her (if i am wrong, let me know). Maybe she has patent interests in mind, or is closed-minded....who knows. Everyone who fights the WOA must collaborate and exchange ideas/debate at every possible opportunity, regardless.
I will be a player (and have been in subtle ways for years) in the WOA, and have plans "A" through "Z" to back it up.

[kevin]

If I read this correctly, aberrant epigenetic methylation recruits Sirt1 which deacetylates and silences tumour suppressors, tying the activity of Sirt1 to methylation, which I don't recall hearing about before.

http://www.ncbi.nlm....l=pubmed_docsum

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PLoS Genet. 2006 Mar;2(3):e40. Epub 2006 Mar 31. Related Articles, Links
Inhibition of SIRT1 Reactivates Silenced Cancer Genes without Loss of Promoter DNA Hypermethylation.

Pruitt K, Zinn RL, Ohm JE, McGarvey KM, Kang SH, Watkins DN, Herman JG, Baylin SB.

The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, United States of America.

The class III histone deactylase (HDAC), SIRT1, has cancer relevance because it regulates lifespan in multiple organisms, down-regulates p53 function through deacetylation, and is linked to polycomb gene silencing in Drosophila. However, it has not been reported to mediate heterochromatin formation or heritable silencing for endogenous mammalian genes. Herein, we show that SIRT1 localizes to promoters of several aberrantly silenced tumor suppressor genes (TSGs) in which 5' CpG islands are densely hypermethylated, but not to these same promoters in cell lines in which the promoters are not hypermethylated and the genes are expressed. Heretofore, only type I and II HDACs, through deactylation of lysines 9 and 14 of histone H3 (H3-K9 and H3-K14, respectively), had been tied to the above TSG silencing. However, inhibition of these enzymes alone fails to re-activate the genes unless DNA methylation is first inhibited. In contrast, inhibition of SIRT1 by pharmacologic, dominant negative, and siRNA (small interfering RNA)-mediated inhibition in breast and colon cancer cells causes increased H4-K16 and H3-K9 acetylation at endogenous promoters and gene re-expression despite full retention of promoter DNA hypermethylation. Furthermore, SIRT1 inhibition affects key phenotypic aspects of cancer cells. We thus have identified a new component of epigenetic TSG silencing that may potentially link some epigenetic changes associated with aging with those found in cancer, and provide new directions for therapeutically targeting these important genes for re-expression.

PMID: 16596166 [PubMed - in process]

[stephen_b]

[Moved from methylation mini-stack discussion.]

There is also the question of whether DMG or TMG is a better source of methyl donors:

Q: So in your research,should MB-12, folinic acid, etc. "kick start" the methyl. cycle? What about TMG or DMG?

A: TMG/DMG is controversial. TMG (Betaine) does seem to help the blood level of the methylation-related metabolites, but it might actually be a hindrance to the cognitive benefits that the MB-12 otherwise would bring. Methionine synthase and BHMT (betaine hydroxymethyltransferase) are in competition when you introduce the TMG, it actually makes the body produce more BHMT. In the brain, the BHMT doesn’t help the dopamine stimulated methylation. If you “starve” the BHMT and let the MB-12 work its magic with methylation, that’s what really seems to help the dopamine.
...
Q: Would DMG be as bad as TMG in affecting the two enzymes you referred to earlier? My daughter tolerates DMG much better than TMG. Thank you.

A: DMG should be tolerated better – it doesn’t affect the enzymes and interfere with the dopamine mechanism. It’s TMG that could interfere.

He has written that his experience is anecdotal from his practice, not from a controlled study. For me, it tips the scales towards DMG. YMMV.

Stephen

[Luna]

If the problem is mainly gene expression, isn't an easy tempoery fix would be to simply insert a good copy of the gene every X years?
And later find a better mechanism to secure the genes.

[VictorBjoerk]

Mrs. Ruth Emblow of New York, born February 6, 1898 died on March 16, 2008 at 110 years and 39 days. Ruth's twin sister, Rhea lived to be 100, providing more evidence that the phenotype of longevity is inherited. But, if they were identical twins reared together [?], one might rightly ask, "Why didn't they die together on the same day?" The answer to this question lies in epigenetics, the random distribution of methyl groups decorating the DNA, which are not inherited at birth, but acquired during life. Thus, among twins, they start off with the same methyl groups in all their cells, but drift increasingly apart with age. This gives each twin unique gene expression patterns and thus a different rate of cellular aging.

[Sasuke]

Lots of interesting reading material in this thread which I haven't gotten through yet, so I'm only responding to these first two posts. Sorry if I say anything redundant.

This is interesting -- so lack of methylation can result in faster aging? I thought methylation was meant to selectively disable genes, to alter the pattern of gene expression. In which case, why would inability to suppress some genes lead to aging? Wouldn't you expect the opposite -- that inability to express some genes would lead to the deterioration in the body?

I don't think the experiment in the first post demonstrated that lack of methylation results in faster aging (assuming I'm not missing something important from the primary paper, I only read what was in the post). Methylation is one of the most important ways of controlling gene expression, so the result of the study was not surprising. An organism with severely disfunctional control over gene expression is going to have all sorts of problems. Death is not surprising. It would have been more interesting, to me, if they did the same test but only activated the hypomorphic PASG mutation after development. During development gene expression is more critical and more delicate. Perhaps they will study it in adults later.

If lack of methylation leads to faster aging, it might be because the expression of the methylated regions of DNA leads to its degradation. Methylation is also considered to be a "strategy" of many prokaryotes to protect their DNA from viruses. In this case, the methylation can prevent the opening of DNA at cut sites used by viruses. It might offer protection against aging by being a general protectant. In general, methylation makes the DNA harder to access for anything, so perhaps we could simplistically say that one of the functions is to protect DNA when it is not in use.

Despite those things, I don't think that there is a direct cause between methylation and aging, but perhaps via "dysdifferentiation" methylation plays an indirect role. The "dysdifferentiation" idea seems interesting. I think it is likely to provide some sort of interesting result, because even if it does not explain aging, it is hard to imagine it not being important to health, if in a lesser extent. I say this in ignorance though, I haven't read up on it yet, but it seems highly likely that gene expression encounters such problems in old age (our evolved expression management has had no evolutionary pressure to manage itself indefinitely, and it is so complex I find it easy to imagine developing conflicts as we age), and that is bound to cause problems.

Edited by Sasuke, 02 June 2008 - 01:30 AM.

[Mind]

Another study measuring methylation changes

The team repeated the analysis using samples collected from 126 individuals from 21 families living in Utah in the United States. The average interval between samples was 16 years. As well as looking at methylation across the genome, they used a different test to analyse changes in 807 specific genes.

The results were similar: two-fifths of the individuals showed a change in methylation of at least 5%, with a range of change from -49% to +39%.

In the Utah sample, members of the same family tended to show the same direction of change. “We were surprised to see such clusters,” says Feinberg.

The four individuals who showed the biggest loss of methylation all belonged to one family. “It would be worth studying the genetics of this family on its own,” says James Flanagan, who studies epigenetic influences on cancer at University College London, UK.

[caston]

I think we need a big colorful diagram showing all the different types and levels of cellar mutations. Perhaps as a pyramid (if it's that simple which I doubt) but more likely perhaps some sort of flowchart. This does not include junk... it is the damage to all the parts of the cell. Everything from poorly repaired DNA, RNA screwups, to misfolded proteins, epigentic changes, what can happen to all the organelles and so on.

This is so the people here that are having trouble taking all of this in may have a chance of being able to visualize all this.

Edited by caston, 26 June 2008 - 01:42 PM.

[maestro949]

I think we need a big colorful diagram showing all the different types and levels of cellar mutations. Perhaps as a pyramid (if it's that simple which I doubt) but more likely perhaps some sort of flowchart. This does not include junk... it is the damage to all the parts of the cell. Everything from poorly repaired DNA, RNA screwups, to misfolded proteins, epigentic changes, what can happen to all the organelles and so on.

This is so the people here that are having trouble taking all of this in may have a chance of being able to visualize all this.

Excellent idea.

Let us know when it's ready

[caston]

Excellent idea.

Let us know when it's ready

Well I can try but you might be waiting several years... If anyone knows of anything like what I'm talking about (ie the big colorful cellular mutations diagram thingy) that may have been prepared earlier please post it. If not all in favor of trying to make one that might have the foggiest idea on where to start don't be shy!

Edited by caston, 26 June 2008 - 02:08 PM.

[maestro949]

Well I can try but you might be waiting several years...

Ten years at most but no more

If anyone knows of anything like what I'm talking about (ie the big colorful cellular mutations diagram thingy) that may have been prepared earlier please post it.

It's not epimutation centric but it's is an interesting view of the interrelations of damage at a higher level.

http://www.legendary...html#Mechanisms

Many of the pathways that lead to epigenetic damage types are still unknown but there is a lot of research going on here, particularly for cancer. Eventually we can leverage much of these data sets for designing targets that suppress aging.

If not all in favor of trying to make one that might have the foggiest idea on where to start don't be shy!

Read the following book (just in time for some light summer reading) and then work your way through pubmed articles linking all of the damage related to chromatin remodeling, histone modifications, DNA methylation, siRNAs, gene silencing, X-chromosome inactivations, etc. to the diagram above.

http://www.amazon.co...s/dp/0879697245

OK. Maybe you can have 15 years.

Edited by maestro949, 26 June 2008 - 03:53 PM.

[caston]

Thanks Maestro: i'll take your 15 years and raise you another 5 for studying proteomics and prions

[caston]

Here's a nice article:

New revelations in epigenetic control shed light on breast cancer
http://www.embl.org/...ar08/index.html


Maybe for now we can try lots of different experiments on cells and see what helps restore epi-genetic regulation. For instance providing better enzymes for autophagy. From there we can try to work out the types of damage autophagy can't fix.
We may find that some perfectly good cells sometimes screw up when given the wrong information.

It is possible to fix something without understanding everything about how it works. As long as we're not afraid to "break" the cells that we are experimenting on there is nothing wrong with lots of mischievous tinkering and trying stuff.

The only reason we are forced to read all the theory is because it would be more expensive to give hands on training and let people loose in the lab to learn that way. Theory is all well and good but it's a kind of augmented reality. You don't really learn until you actually do something for yourself.



If the science isn't there yet at least let art have a go

$$$$$

How about a lab-athon! Lab experiments are broadcast live over the internet and people can pledge money, resources, inter discipline technical advice and services, ideas and so on. We may even end up with celebrity lab workers just like we have celebrity chefs
Teams could be given prizes (cash and or trophy or medal-like ) when they make breakthroughs.

An ideal place to host lab-athons might be at universities.

It might work better than the current situation:

http://ouroboros.wor...nday-funnies-5/

Edited by caston, 28 June 2008 - 04:30 AM.

[caston]

Guys I just had an idea about how we might be able to fix epigentic mutations!

Flying in the face of growth factors to encourage cell division lets do experiments in cell fusion!

Somehow fitting cell fusion into a strategy to intervene in the aging process is the general idea. Hopefully the seperate nuclei will form together to make a single nuclei.

I'm not sure how it could (or would) work but one suggestion is coaxing the organism to start returning to a zygote state. So we press rewind for a little but then hit play again.

Has this been suggested before?



Heterokaryon: A cell with two separate nuclei formed by the experimental fusion of two genetically different cells. (Heterokaryons, for example, composed of nuclei from Hurler syndrome and Hunter syndrome, both diseases of mucopolysaccharide metabolism, have normal mucopolysaccharide metabolism proving that the two syndromes affect different proteins and so can correct each other in the heterokaryon)

Edited by caston, 04 July 2008 - 11:07 AM.

[Mind]

More attention being given to non-coding regions of DNA

Sorry, in my haste that I misclassified this article. Need to move it to a more approriate thread.