A study of DNA methylation and age

This 2014 Finnish human study compared and contrasted the DNA methylation levels of young adults with people age 90:

“We identified 8540 high-confidence CpG [cytosine and guanine separated by only one phosphate link] sites that show a large difference in methylation levels between nonagenarians and young controls and that present high statistical significance in a regression model adjusted for the leukocyte proportion.

The majority of frequently reported CpG sites are hypermethylated with increasing age.

Ageing-associated hypermethylation is concentrated in genes associated with developmental processes as well as DNA-binding and transcription of genes, whereas hypomethylation is not enriched among a specific set of genes.

The largest percentage of the variation in our methylation data was associated with the proportions of different leukocyte subtypes.

We found that only a minority of ageing-associated CpG sites showed an association between methylation and expression levels. Furthermore, only a minority of these genes have been identified as differentially expressed between nonagenarians and young individuals.”

The finding concerning:

“Ageing-associated hypermethylation is concentrated in genes associated with developmental processes as well as DNA-binding and transcription of genes”

was in concert with a referenced 2013 review Aging is not programmed that stated:

“Aging is not and cannot be programmed. Instead, aging is a continuation of developmental growth, driven by genetic pathways.

Aging is a shadow. Its shape is determined by the developmental growth.

Genetic programs determine developmental growth and the onset of reproduction. When these programs are completed, they are not switched off.

Aging has no purpose (neither for individuals nor for group), no intention. Nature does not select for quasi-programs. It selects for robust developmental growth.

Whereas the growth of the body is programmed, the emergence of the shadow is not. Natural selection cannot eliminate the shadow without hurting the “body”.”


The researchers made several points relating the current study and other epigenetic studies.

Regarding DNA methylation and gene expression:

“Due to the methods applied in the present study, not all the effects of DNA methylation on gene expression could be detected; this limitation is also true for previously reported results.

The textbook case of DNA methylation regulating gene expression (the methylation of a promoter and silencing of a gene) remains undetected in many cases because in an array analysis, an unexpressed gene shows no signal that can be distinguished from background and is therefore typically omitted from the analysis.”

Regarding biological age and chronological age:

“It remains to be investigated whether these [CpG] sites are only associated with chronological age or if there are also associations with phenotypic changes related to (successful) ageing.

If these frequently reported sites are only markers of chronological age, markers of biological age are yet to be identified.”

Regarding the rapid progression of technology used in epigenetic studies, they noted several times how what they used was significantly improved over pre-2014 technologies with statements such as:

“Global hypomethylation has been associated with an increasing risk of frailty, but very few other associations between phenotype and DNA methylation have been reported. However, this may be due to technical concerns, as the study by Bell et al. was performed with the 27K array, which almost exclusively contains promoter-associated probes that are not methylated at baseline and can therefore primarily acquire hypermethylation. Phenotype association studies performed with the 450K array or using sequencing techniques are necessary to clarify if hypomethylation is associated with typical ageing-associated phenotypes.”

Compare that with the limitations of the same 450K array acknowledged in A human study of changes in gene expression 2015 study:

“This array queries only 1.6% of all CpGs in the genome and the CpG selection is biased towards CpG islands. Other techniques – whole-genome bisulfite sequencing and methylC-capture (MCC) sequencing, for example – have definite technical advantages (higher resolution and no CpG island selection bias).”

http://www.biomedcentral.com/1471-2164/16/179 “Ageing-associated changes in the human DNA methylome: genomic locations and effects on gene expression”

A molecular study of the epigenetic regulation of memory

This 2015 Norwegian rodent study provided:

“New insights into the molecular underpinnings of synaptic plasticity.

We report the first global transcriptome [all RNA found in specific cells] analysis of in vivo synaptic plasticity, using the well-established model of LTP [long-term potentiation, an increase in synaptic strength that underlies memory] in the rat dentate gyrus [a region of the hippocampus where neurogenesis occurs].

We have identified a number of novel lncRNAs [long (more than 200 nucleotides) noncoding (non-protein coding) RNA] that are dynamically regulated in response to LTP. In addition, we also observed an altered expression of multiple classes of repeat elements [mobile DNA sequences often involved in mutations] including retrotransposons [a repeat element type formed by copy-and-paste mechanisms].

The results presented here reveal a vast extension of mRNAs [messenger RNA, a large RNA that carries codes for protein production] previously not associated with neuronal plasticity; the discovery of extensive, dynamic regulation of lncRNAs, repeat elements, and tRNA [transfer RNA that links mRNA and amino acids during protein production] following LTP induction in the adult rat brain.

These findings provide a broader foundation for elucidating the transcriptional and epigenetic regulation of synaptic plasticity.”

Regarding lncRNA:

“We annotate a total of 10,256 novel lncRNAs in the rat transcriptome.

To infer possible functions of lncRNAs, we correlated [71] differentially expressed lncRNAs with regulated protein coding genes.

There are no established rules for predicting the function of lncRNAs.”

Regarding repeat elements:

“It is intriguing to consider that expression of repeat elements during LTP is the first step toward retrotransposition and reshaping of the neuronal genome. A hypothetical mechanism for how these repeat elements could be linked to memory, would be that a certain stimuli, whether it is stress or a learning task (here LTP), deregulate the repression of repeat elements which are then rapidly and transiently transcribed. These elements reinsert themselves back into the genome of stimulated neurons where they influence the expression of neighboring genes.

The present work supports the intriguing hypothesis that dynamic retrotransposition may act as a molecular means to reprogram the neuronal genome as part of long-term synaptic plasticity and memory formation.”

See RNA as a proxy signal for context-specific biological activity for more about lncRNA.

http://journal.frontiersin.org/article/10.3389/fnins.2015.00351/full “Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity”

Is the purpose of research to define opportunities for interventions?

In this 2014 review, a social scientist first presented an interpretive history of what he found to be important in the emergence of epigenetics. He proceeded into his ideas of “a possible agenda of the social studies of the life-sciences” in the “postgenomic age” with headings such as “Postgenomic biopolitics: “upgrade yourself” or born damaged for ever?”

This perspective included:

“The upgradable epigenome may become the basis for a new motivation to intervene, control and improve it through pharmacological agents or social interventions.

An important trend is the use of epigenetic and developmental findings in the so-called early-intervention programmes.

It is possible that epigenetic findings will become increasingly relevant in social policy strategies.”


In this blog I often highlight research that may help us understand details of how each of us is a unique individual. It’s my view that insofar as research helps each of us understand our unique, real self, we may be able to empathetically understand others’ unique qualities.

Click individual differences for a sample of how researchers explain away uniqueness in order to converge on a study’s desired objectives. There’s seldom an attempt to further understand what caused each subject to develop their unique qualities.

Why would this reviewer advocate that

  • Researchers,
  • People working in the social sciences,
  • People employed or involved in social services, and
  • Their sponsors and employers

intentionally disregard another individual’s unique qualities?

I’ll answer this question from a perspective that explains how this common, reflexive action derives from a person being unable to face the facts of their own life. Pertinent fundamentals of Dr Arthur Janov’s Primal Therapy are:

  1. Pain motivates a person’s unconscious act-outs of their underlying problems.
  2. The behavior that caused a problem is sometimes also the act-out behavior.
  3. Act-outs enable a person to re-experience the feelings of their historical struggles, in a vain attempt to resolve them.
  4. Due to pain barriers, people seldom become consciously aware of and – more importantly – address the causes for their own problematic behavior.
  5. “The patient has the power to heal himself.”

A consequent hypothesis is that a person will often glorify their unconscious act-outs and surround themself with justifications for these actions. For example, a person who can’t sit still may refer to their incessant activity with socially acceptable phrases such as “I’m always busy” or “I love to travel.” They’ll structure their life to enable their unconscious behavior, never questioning how they were attracted to an always-on-the-go occupation such as flight attendant, only vaguely feeling that they were made for it.

The behavior relevant to the current review may be exhibited by a person with a history of having no control over their own life. Following the above first two fundamentals, the pain of historically not having control over their life may motivate them to control other people’s lives.

Unfortunately for everyone who’s affected, such unconscious act-outs don’t resolve anything:

  1. The initiator may achieve some symbolic satisfaction by controlling others’ lives.
  2. This temporary satisfaction doesn’t make the initiator’s underlying problems less painful.
  3. The motivation impelling these unconscious act-outs isn’t thereby reduced.
  4. So the initiator soon repeats their controlling behavior, stuck in a loop of unresolved feelings.
  5. Since the self-chosen interests of someone who’s being controlled are lesser concerns to the initiator than exercising control, the controlled person may or may not be helped by the controller’s act-outs.

Research provides abundant evidence that we are unique individuals.

This is a strong indicator of who is best qualified to direct each of our unique lives.

A person who is driven to control others’ lives won’t accept epigenetic research as instructive for understanding, honoring, and respecting others as unique individuals. They’ll use research as a way to enable their own unconscious act-outs, and view it as offering opportunities for interventions into the lives of others.

This is the way that “pharmacological agents or social interventions” are often the intended “use of epigenetic and developmental findings.” Interventions receive justifications with “a possible agenda of the social studies of the life-sciences.”

Becoming aware of one’s own act-outs – and then individually addressing one’s own underlying problems – often take backseats to employment and other concerns to keep enabling one’s own behavior. That makes it likely that interventions justified by “epigenetic findings..in social policy” will continue, whether or not the subjects agree that they’re being helped.

For examples, take a look at a few of the YouTube presentations by people employed in the social sciences and social services on a topic of epigenetics. Compare them with the current state of epigenetic research in Grokking an Adverse Childhood Experiences (ACE) score.

What did you notice? How many presentations emphasized disrupted prenatal development – a period when problems can be prevented? Did you instead see that many more of the presentations emphasized controlling behavior?

http://journal.frontiersin.org/article/10.3389/fnhum.2014.00309/full “The social brain meets the reactive genome: neuroscience, epigenetics and the new social biology

A human study of changes in gene expression

This 2015 international human study of genetic and epigenetic factors was the largest in its field:

“We perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age.

We further used the gene expression profiles to calculate the ‘transcriptomic age’ of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features.”

Items of interest:

  • About 1,450 of the “1,497 genes that are differentially expressed” are newly identified;
  • The subjects’ mean age was 55.81 with a pooled standard deviation of 11.59;
  • The mean difference “between transcriptomic age and chronological age” was 7.84 years; and
  • Native American, Mexican American, and African American studies were used as replication cohorts.

It was refreshing to see the peer-review influence of numerous coauthors on the study. Papers that are written by only one or two researchers don’t often have frank limitation explanations such as:

“A potential limitation of our study is that we relied on a linear regression model to identify age-associated genes. A linear model assumes constant change over age, which may not be always correct in biological processes that stretch over several decades (adulthood). A recent study demonstrated that a quadratic regression model has a higher statistical fit to cross-sectional gene expression datasets over linear model.

A limitation of our study is that we used the Illumina Infinium Human Methylation 450K Bead Chip Array for measuring methylation levels: this array queries only 1.6% of all CpGs in the genome and the CpG selection is biased towards CpG islands.

In addition, we did not examine non-CpG methylated sites, which have recently been suggested to play a role in regulating gene expression as well.

Other techniques—whole-genome bisulfite sequencing and methylC-capture (MCC) sequencing, for example—have definite technical advantages (higher resolution and no CpG island selection bias), but these have currently not been applied to a large number of samples.”

http://www.nature.com/ncomms/2015/151022/ncomms9570/full/ncomms9570.html “The transcriptional landscape of age in human peripheral blood”

Transgenerational epigenetic programming with stress and microRNA

This 2015 Pennsylvania rodent study found:

“Sperm miRs [microRNAs, a small non-coding RNA that has a role in gene expression] function to reduce maternal mRNA [messenger RNA, a large RNA that carries codes for protein production] stores in early zygotes, ultimately reprogramming gene expression in the offspring hypothalamus and recapitulating the offspring stress dysregulation phenotype.”

The researchers caused stress-induced changes at an early stage of embryonic development with microRNA injections. The resultant adverse effects weren’t observed until the subjects were adults!

Most of the news coverage focused on it being a male’s stress, not a female’s, that affected the developing embryo. Either or both sexes can epigenetically disadvantage a fetus – okay.

Demonstrating how a damaging influence can begin immediately after conception, but the symptoms didn’t present until adulthood, was what made this study newsworthy.


Although the term “transgenerational” was used in the study’s title, abstract, and elsewhere, the study demonstrated that the epigenetic effects were intergenerational rather than transgenerational. Per the definition in A review of epigenetic transgenerational inheritance of reproductive disease, for the term to apply, the researchers needed to provide evidence in at least the next 2 male and/or 3 female generations of:

“Altered epigenetic information between generations in the absence of continued environmental exposure.”


From the press release, a coauthor of the study who also coauthored How to make a child less capable even before they are born: stress the pregnant mother-to-be stated:

“Bale suspects that when a male experiences stress it may trigger the release of miRs contained in exosomes from the epithelial cells that line the epididymis, the storage and maturation site for sperm between the testes and the vas deferens. These miRs may be incorporated into the maturing sperm and influence development at fertilization.”

Not all stress-related gene expression in the pituitary and adrenal glands differed.

http://www.pnas.org/content/112/44/13699.full “Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress”

The roles of DNA methylation and demethylation in forming memories

This 2015 Alabama combined animal and human review noted:

“Memories can last a lifetime, yet the proteins that enable synaptic plasticity, allowing for the establishment and maintenance of the memory trace, are subject to perpetual turnover.

DNA methylation may likely serve as the principle cellular information storage device capable of stably and perpetually regulating cellular phenotype.”

The authors developed a framework for understanding disparate findings of DNA methylation and demethylation concerning memory.


The dependencies expressed in the framework among the numerous factors – with their relative strengths, timings, and durations – reminded me of this video:

1) If such an error-prone framework accurately reflected the evolved architecture of our memory, we wouldn’t have the variety and number and intensity of memories that we have.

2) The framework neither accounted for prenatal memory processes nor differentiated emotional memories, although some of the referenced studies’ findings were applicable.

3) DNA methylation and demethylation aren’t the entirety of memory formation explanations. For example, they don’t explain state-dependent memories that can be instantiated, reactivated, and amnesia induced without involving “the proteins that enable synaptic plasticity” described in the authors’ framework. For completeness, the authors could have assessed the relative contributions of other memory processes, or at least enumerated them.

4) DNA methylation and demethylation explanations don’t cover all epigenetic biochemical processes. There are also placental interactions, histone/protein interactions, microRNA interactions, etc. For completeness, the authors could have placed the review’s topic within appropriate contexts of other epigenetic processes that influence memory.

This review of DNA methylation and demethylation roles in memory formation opened up a few slats in the blind covering one window. There’s more to be done to fully open that blind, and more window blinds to be opened before the workings of our memory are illuminated.

http://nro.sagepub.com/content/21/5/475.full “DNA Methylation in Memory Formation: Emerging Insights”

A review of the epigenetic basis for mental illness

This 2015 New York combined animal and human review of epigenetic studies noted:

“While genetic factors are important in the etiology of most mental disorders, the relatively high rates of discordance among identical twins, particularly for depression and other stress-related syndromes, clearly indicate the importance of additional mechanisms.

Environmental factors such as stress are known to play a role in the onset of these illnesses.

Exposure to such environmental insults induces stable changes in gene expression, neural circuit function, and ultimately behavior, and these maladaptations appear distinct between developmental versus adult exposures.

Increasing evidence indicates that these sustained abnormalities are maintained by epigenetic modifications in specific brain regions.”

Placing the “maladaptations” and “sustained abnormalities” phrases into their contexts:

  • A fetus biologically adapted to their environment – however toxic it was – in order to best survive.
  • These adaptations for survival were subsequently viewed as Disrupted Neurodevelopment and “maladaptations” from the perspectives of normal development and environments.
  • The “sustained abnormalities” caused within the earlier environments “are maintained by epigenetic modifications.” An improved environment wasn’t impetus enough to change developmental “maladaptations.”

Per the below link, it’s been a month since this review was published. Why has there been ZERO news coverage of it?

One reason may be that the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, didn’t issue a press release or otherwise publicize it. Another reason may be the groups that are opposed to its findings:

  • Parents who provided harmful environments for their children, beginning at conception;
  • People who feel threatened when scientific causal evidence resonates with what happened in their own lives, and in response, limit their empathetic understanding of others’ problems;
  • Social workers, psychologists, and others in industries whose paychecks depend on efforts that aren’t directed towards ameliorating the causes for these later-life effects;
  • Psychiatrists and medical personnel whose livelihoods depend on pharmaceutical and other treatments that only alleviate symptoms;
  • Researchers whose funding depends on producing non-etiologic findings.

Despite resistance to this review’s findings, a large number of people would benefit from publicizing evidence for:

“These sustained abnormalities are maintained by epigenetic modifications in specific brain regions.”

http://nro.sagepub.com/content/early/2015/09/24/1073858415608147 “Epigenetic Basis of Mental Illness”

Grokking an Adverse Childhood Experiences (ACE) score

What does it take to empathetically understand, to make a part of oneself, to grok an ACE score?

The ACE effort was initiated in 1985 in an era before epigenetics was well-studied. Its artifacts included the ACE pyramid:

The_ACE_PyramidThe historical ACE lifespan continuum on the left began at conception. The pyramid on the right promoted a limited view of ACE that assigned childhood as the pyramid’s base.

Current official depictions of the ACE pyramid assign an expanded view of ACE as the pyramid’s base. The viewer’s attention is directed to “Scientific Gaps” between pyramid layers, but the largest gap remains: the continuum starts at conception but the pyramid still starts at childhood. The narrative claims:

“To provide scientific information that would be useful for developing new and more effective prevention programs.”

The official ACE pyramid doesn’t accurately reflect current science documented in, for example, Epigenetic effects of early life stress exposure. By downplaying Disrupted Neurodevelopment that may begin at conception, governing agencies implicitly endorse approaches that fail to address prenatal causes for later-life adverse effects.


If the ACE diagram was drawn thirty years later in 2015 to incorporate evidence for epigenetics, Disrupted Neurodevelopment wouldn’t be a consequent layer to an ACE base. The potential start of Disrupted Neurodevelopment would coincide with conception:Updated for 2015 to show Disrupted Neurodevelopment

What’s an example of current ACE-related scientific evidence that wasn’t present three decades ago and also isn’t represented in the official ACE pyramid? Prenatal Disrupted Neurodevelopment may be considered today as a possible consequence of a “Yes” answer to half of the original ACE questions:

  • Were your parents were too drunk or high to take care of you or take you to the doctor?
  • Were your parents ever separated or divorced?
  • Was your mother often or very often pushed, grabbed, slapped, or had something thrown at her?
  • Did you live with anyone who was a problem drinker or alcoholic or who used street drugs?
  • Was a household member depressed or mentally ill?

These threats and other stresses cause a fetus to biologically adapt. When such adaptations occur during prenatal development, they may:

  • Have much larger impacts and
  • Cause Biological Impairments that
  • Don’t unassistedly disappear over time.

Emphasizing Disrupted Neurodevelopment that may begin at conception would encourage:

  • Research that’s directed toward producing causal evidence for adaptations that largely occur during the early periods of an individual’s lifespan; and
  • Research on how these adaptations consistently influence our later-life ideas, biology, and behavior.

The above recommendations for research are neither the current focus of ACE research nor the direction of related efforts to assist affected individuals. Relevant studies that I’ve curated on this blog often only produced symptomatic evidence.

If a study couched its findings in non-etiologic phrases such as “is associated with” or “is linked to” or “may relate to,” it didn’t address ACE originating causes.

“New and more effective prevention programs” seldom address Disrupted Neurodevelopment and Biological Impairments with efforts to reduce the source of the damage. At best, they only alleviate the symptoms.

If a program’s presentation showed multivariate analyses with ACE score probabilities and percentages, it didn’t address originating causes.

Here’s a YouTube search of ACE + adverse. Evaluate the current focus of ACE efforts by people employed in the social sciences and services. What did you notice?

How many presentations emphasized prenatal Disrupted Neurodevelopment, a period during which problems may be prevented by addressing causes? Did you instead see that these were outnumbered by many more presentations that emphasized Health and Social Problems symptom interventions?


So, what does it take to empathetically understand, to make a part of oneself, to grok a person’s ACE score?

Regarding empathy – it’s best to avoid the advice of studies such as:

People who are helped may not recognize it at first, but over time, they’ll sense whether the helper’s empathy is genuine.

Regarding understanding – I feel that people first need to ameliorate the origins of their own problems. Then they may be able to help others therapeutically address causes for ACE symptoms.

Need proof? Think of someone you’ve met whose thoughts and feelings and behavior were caught up in and motivated by their own problems:

  • Did you feel they could empathetically understand others?
  • Wasn’t the welfare of the people who may have been helped truly incidental and secondary to someone who was acting out their own problems?

Conclusions without evidence regarding emotional memories

The last sentence in the Significance section of this 2015 Emory/Harvard rodent study was:

“These data highlight the potential to exploit sensory system plasticity as a means of ameliorating negative emotional memories that may be tied to peripheral sensory systems.”

The “ameliorating negative emotional memories” part of this statement was incongruent with what the study actually found, as summarized by the Abstract’s last sentence:

“These data suggest that learning-induced freezing behavior, structural alterations, and enhanced neural sensory representation can be reversed in adult mice following extinction training.”

The study performed fear extinction experiments. The researchers and reviewer knew or should have known about prior studies such as Fear extinction is the learned inhibition of retrieval of previously acquired responses whose findings demonstrated that fear extinction doesn’t depend on memory retrieval.

Based on the previous research, the subjects’ “negative emotional memories” possibly weren’t affected at all by the current study’s extinction experiments!

The researchers provided neither direct evidence for “ameliorating negative emotional memories” nor studied areas of the subjects’ brains that contained or processed emotional memories, such as the hippocampus, amygdala, and prefrontal cortex. But – after all – Harvard.

What purposes did it serve for the researchers to make a Significance statement about “ameliorating negative emotional memories” when this wasn’t supported by the study’s findings? What part did the reviewer play in approving this statement?


Where was the study’s evidence to support the headline and statements in the news release such as:

“New Study Indicates That Sense of Smell Could Play Major Role in New Approaches to Treating PTSD

It’s possible for fear behaviors associated with emotional learning to be reversed through exposure-based talk therapy.”

Could this rodent study’s olfactory system findings be properly extrapolated to human talk therapy?

NO! But – Harvard.

http://www.pnas.org/content/112/41/12846.full “Extinction reverses olfactory fear-conditioned increases in neuron number and glomerular size”

Stress-induced epigenetic DNA modifications may be inherited

This 2015 Australian plant summary study made several points:

“Non-transmission of epigenetic marks through meiosis may be regarded as an epigenetic modification in itself. We should understand the implications for plant evolution in the context of both selection for and selection against transgenerational epigenetic memory.

Both epigenetic inheritance and resetting are mechanistically directed and targeted. Stress-induced epigenetic modifications may buffer against DNA sequence-based evolution to maintain plasticity, or may form part of plasticity’s adaptive potential.

In some cases the signature of the stress experience remains in the epigenome after relief from the stress, providing a “memory.” If this memory conditions the response to stress during subsequent development, the organism is said to be epigenetically primed. If the memory of the stress experienced by a parent conditions the response of its progeny, this epigenetic priming may be transgenerational.

Epigenetic and genetic variation co-evolve. Epigenetic plasticity does not completely buffer evolvability and reduce the correlation between fitness and genotype, slowing selection.”

One of the summarized studies found that a transgenerational epigenetic change eventually silenced itself after the 40th copy!

The Are stress-induced epigenetic changes to DNA inherited across generations? study was cited, although it argued for the opposing viewpoint.

http://journal.frontiersin.org/article/10.3389/fpls.2015.00699/full “Transgenerational inheritance or resetting of stress-induced epigenetic modifications: two sides of the same coin”