Here’s another great advance in methylome sequencing. You all know about bisulfite sequencing, the “gold standard” method. Unfortunately it’s expensive.  It also requires a lot of sample, due to DNA degradation. There are enrichment methods, like MeDIP-seq, that are relatively cheap. However, there is the drawback of CpG density bias. Excitingly, there is a new enzyme based enrichment method, called TamC-Seq that requires less sample, less money, and provides excellent coverage for genome-wide profiling. The devlopers are from the He group, University of Chicago. The paper is Liang Zhang et al. Tet-mediated covlent labelling of 5-methylctosine for its genome-wide detection and sequencing. (2013) Nature Communications, (4) 1517

So how does it work? Their protocol uses mouse Tet (Ten-eleven translocation)-1, (or mTet1) enzyme expressed in a baculovirus system. First 5hmC is protected with a glucose using Beta-GT. Next, in a “One pot” procedure, the mTet1 converts 5hmC from 5mC, which is then immediately glycoslated by Beta-GT with a modified glucose moiety(6-N3-glucose) . Then all the original 5mC is labeled with biotin via click chemistry. Time for affinity biotin/streptavidin purification, followed by sequencing.

The researchers used mouse embryotic stem cells, as well as human breast cancer cell lines, to compare methylome data with other methods. TamC-Seq was efficient at providing more methylation site coverage than MeDIP-Seq. TamC-Seq captured a wider range of CpGs, showing less density bias than MeDIP-Seq. The TamC-Seq data was concordant with Bisulfite-Seq data.

The same research group is also working on RNA epigenetics. Interesting! Check out their web site.

Zhang L, Szulwach KE, Hon GC, Song CX, Park B, Yu M, Lu X, Dai Q, Wang X, Street CR, Tan H, Min JH, Ren B, Jin P, & He C (2013). Tet-mediated covalent labelling of 5-methylcytosine for its genome-wide detection and sequencing. Nature communications, 4 PMID: 23443545

Posted in Applications, DNA Methylation, Genomewide Methylation Profiling, Glycosylases, Hydroxymethylation, Methylation, New Lab Methods, Next Gen Sequencing | Tagged , , , , | Leave a comment

New England Biolabs is well known for its extensive in house research programs – churning out numerous publications every year. The role of hydroxymethylation as a possible cancer biomarker is a topic of keen interest for all Epigenetics researchers. So, NEB researchers are especially enthused about their recent publication in Cell, along with their collaborators from Emory University School of Medicine.

Sun, Z. et al. High-Resolution Enzymatic Mapping of Genomic 5-Hydroxymethylcytosine in Mouse Embryonic Stem Cells. (2013) Cell Reports 3, 567-576. describes the Aba-seq method, an AbaSI enzyme based high-resolution hydroxymethylome mapping. (Open access.)

In nature, AbaSI is a weapon in the arms race between bacteria and bacteriophages. Wildtype bacteriophages such as T4, are resistant to most restriction enzymes due to their 5-hmC (hydroxymethylated) and 5ghmC (glucosylhydroxymethylated) DNA. However this type of bacteriophage DNA “armor” is no match for AbaSI, or other members of a family of restriction enzymes produced by bacteria, to stop T4 replication.

NEB scientists had isolated, prepared and characterized AbaSI to show ~10,000 fold higher specificity between 5ghmC and 5-mC.  This feature brought the teams closer to the goal of developing a method to explore the mammalian hydroxymethome at near single base resolution.  See figure 1B for the Aba-seq method overview.

For epigenetics research, the Aba-seq method has advantages over other methods developed to analyze the hydroxymethlome at high resolution sequencing. Keep in mind, only a a tiny fraction of mammalian DNA is hydroxymethylated (~0.1%). This method is not harsh on DNA samples. Only a small amount of DNA is needed 100ng. 5HmC sites with low occupancy can be reliably detected. Also, data analysis is straightforward.

The 5hmC pattern found in mouse embryonic stem cells by the researchers suggests a dependence on TET enzymes accessibility in some areas, and a demethylation intermediate or poised epigenetic state in others. The ease of this enzymatic method certainly contrasts to the complicated nature of epigenomes!

Sun Z, Terragni J, Borgaro JG, Liu Y, Yu L, Guan S, Wang H, Sun D, Cheng X, Zhu Z, Pradhan S, & Zheng Y (2013). High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells. Cell reports, 3 (2), 567-76 PMID: 23352666

Posted in Applications, Biomarkers, DNA Methylation, Enzymology, Genomewide Methylation Profiling, Hydroxymethylation, Methylation Sensitive Restriction Enzymes, New Lab Methods, Oncology, Stem Cells | Tagged , , , , , | Leave a comment

Recent surprising evidence has shown that metastatic tumors usually do not vary in their genomes within an individual. Yet, these tumors behave differently at different sites around the body. Does that mean that epigenetic profiling will be too variable to target for cancer treatment? In a word, no.

Martin J. Aryee et al., from Johns Hopkins, have published their work in DNA Methylation Alterations Exhibit Intraindividual Stability and Interindividual Heterogeneity in Prostate Cancer Metastases in Science Translational Medicine. They looked at methylation signatures, including total methylation and allele-specific methylation (ASM) in lethal metastatic prostate cancer, among tumors from 24 donors. Methylated DNA was enriched from the genomic DNA using a Methyl-CpG Binding Domain (MBD) -based capture. Their MBD-SNP assay provided total methylation, ASM and copy number concurrently for each sample. Microarray analysis and computational analysis were used downstream to produce “cityscapes” of visualized data.

The epigenetic and genetic data varied a lot among the individual donors. Yet intriguingly, static epigenetic profiles were seen among metastatic tumors for each individual donor. This means that although metastatic prostate cancer tumors are somehow able to overcome treatments like the removal of androgens (surgical or medical castration), there are still “non-moving” epigenetic biomarkers targets to aim at to develop new treatments. The authors point out that it will be important to distinguish between the driver and passenger DNA methylation alterations in carcinogenesis. So there’s all that to still sort through in functional studies to determine targets with casuality in the disease progression. The stable methylomes within individuals supports the goals of personalized medicine in prostate cancer treatment – so it’s definitely worth the effort.

Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, Esopi D, Irizarry RA, Getzenberg RH, Nelson WG, Luo J, Xu J, Isaacs WB, Bova GS, & Yegnasubramanian S (2013). DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Science translational medicine, 5 (169) PMID: 23345608

Posted in Biomarkers, Epigenome, Methylated DNA Capture, Microarray, Oncology | Tagged , , , | Leave a comment

The beginning of a new year is a time for reflection. There have been two news items which have struck me in regard to epigenetics and cancer research, recently.

Dr. James Watson, Nobel Prize winner, and co-discoverer of the double helix structure of DNA, has published a controversial, open access paper in the journal Open Biology. Cancer research has not produced cures, but merely temporary life extentions for those facing metastatic cancers. The sequencing of the human genome and identification of individual cancer cell mutation drivers of disease, have not produced cures. Dr. Watson points out that once cancer turns metastatic, resistance to gene-targeted drugs is rampant. In the metastatic process, DNA sequence mutations often don’t change. Rather their expression changes. Multiple molecular pathways are enabling drug resistance to tumors in new surrounding environments. Dr. Watson recommends research focuses on the protein Myc, (supported by Bromodomain 4) as a common driver of resistance pathways. Dr. Watson also was quoted saying that “The time has come to seriously ask whether antioxidant use much more likely causes than prevents cancer.” The basis of this idea is that chemotherapy and radiation treatments rely on oxidized free radicals to kill cancer cells. You can read the full paper here.

The second paper that turned my head over the holidays was Kreso A. et al. Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer (2012) Science This work was surprising because it demonstrated how tumors with the same genomes were behaving quite differently based on their environments. Again, functional drug resistance is based more on epigenetics than genetics.

Undoubtedly, scientists will reflect on these ideas and become even more resolved to apply epigenetics and cell signaling research in the “war on cancer”. It is critical that scientists collaborate to incorporate data from of all molecular systems to propel cancer research forward. The complexity of this disease will likely require equally complex combinational treatments to attain a real cure.

Watson J (2013). Oxidants, antioxidants and the current incurability of metastatic cancers. Open biology, 3 (1) PMID: 23303309

Posted in Epigenome, Genetics, History & Trends, Oncology | Tagged , , , , | Leave a comment

Finally there’s research comparing the epigenetic marks of human brain neurons to those of other primates, and it’s found real differences that make us function in a unique way. Do these epigenetic modifications help give us the brainpower for reflection, sentience, sapience, consciousness, and so forth? I’m not a gambler, but since primate neuron-specific genes don’t show a whole lot of difference from one another in their protein-coding sequences, that’s where I’d put my money. If I really had to.

With only one study to look at so far, this line of inquiry is in its infancy, to be sure. No one else has looked at the epigenetic component of human brain evolution. Hennady Shulha, Jessica Crisci, and Schahram Akbarian at the University of Massachusetts Medical School — and colleagues — took that first step with research they published in PLoS Biology late last month.

[Update 12/20/2012: Twitter friend @ed vautier points me to this study in Epigenetics, which documents the evolution of additional CpGs in humans, compared to non-human primates, and looks at their relative methylation levels. It's not neuron-specific, but it's in the same bucket as this study, so I thought I'd note it here. And so I have. And there you have it.]

What they find is this: Human prefrontal cortex neurons sport 33 epigenetic modifications — histone H3 trimethylated at lysine 4, or H3K4me3 — in genomic locations where macaques and chimps are much less likely to feature them. These H3K4me3 marks tended to appear near each other, and when the research team used chromosome conformation capture to look more closely at the region around one gene, DPP10, they discovered that chromosome looping appears to allow two nearby H3K4me3 modifications to come into contact.

But although H3K4me3 marks often lead to higher gene expression levels, this interaction seems to cause down-regulation of DPP10 through an interesting mechanism. As it turns out, increased anti-sense DPP10 RNA might be the answer. When the team did RNA-seq and quantitative RT-PCR on cortex neuron samples from separate human subjects, they found high levels of DPP10‘s anti-sense RNA and lower levels of DPP10 sense mRNA, as compared to the analogous macaque and chimp neurons.

The team also found the anti-sense RNA at higher levels in the human subjects’ neuron-rich prefrontal cortex layers II-IV, but not in neuron-poor layer I, white matter, or cerebellar cortex.

What’s more, the researchers discovered that the sequence of anti-sense DPP10 RNA has GC-rich areas that could allow it to form a stem-loop structure to interact with Polycomb 2 and transcription start sites — qualities that would support the RNA’s role in regulation.

Now, there’s no disease known to result from any DPP10 epigenetic modifications. But the authors note that rare variants “confer strong genetic susceptibility to autism, while some of the gene’s more common variants contribute to a significant risk for bipolar disorder, schizophrenia, and asthma.” That is, it’s a pretty good candidate for a gene that affects cortex function: Also according to the authors, it encodes a dipeptidyl peptidase-related protein that regulates potassium channels and neuronal excitability.

(It goes beyond DPP10, too. Five other genes associated with some of the 33 human-specific H3K4me3 peaks have ties to psychiatric diseases.)

So does all this point to an epigenetic role in human brain evolution? It starts to look even more convincing, considering what the researchers report about genetic changes in the DNA around these H3K4me3 marks, since the DNA sequence might very well have an important influence on histone binding and other functions. Compared to macaques, chimps, gorillas, and orangutans, the human versions of these DNA sequences have undergone major changes, with nucleotide substitution rates of 2- to 5-fold.

Meanwhile, nearby protein-coding sequences remained relatively unchanged in humans, as compared with the other primates. Also, compared to our close hominid relatives Homo denisova and Neanderthals, the nucleotide substitution rate near human H3K4me3 is much lower — about half the rate that the comparisons with non-human primates revealed. So the authors speculate that …

Taken together, these results suggest that at least a subset of the TSS regions with H3K4me3 enrichment in human (compared to non-human primates) were exposed to evolutionary driven DNA sequence changes on a lineage of the common ancestor of H. sapiens and the archaic hominins, but subsequently were stabilized in more recent human evolution, after splitting from other hominins.

What I like about this research is that the team used real human brain cells. No, not from living people, of course. Cadavers. And they didn’t just grind up a lump of brain in the blender, either. They painstakingly separated prefrontal cortex neurons from glial cells and other types to get at the real differences in the cells that matter, from the brain region that makes executive decisions and fancy associations.

What’s more, they may have sidestepped the problem with dead tissue — sample degradation – by measuring histone methylation. Apparently these marks don’t appear to change much after their host has died.

What I don’t like about the study is pretty standard. The human brain samples came from only 11 subjects — seven children and four adults.

The research team focused only on H3K4me3 peaks that all the humans had in common, so although they might’ve missed some peaks, it’s not that bad of a shortcoming. But there’s also the problem that the human subjects’ brains had already developed — as the authors hint in their discussion, fetal neuronal gene regulation could hold many of the important secrets, since the period of actual brain development is when you’ll probably find a lot of human-specific differences.

I’m anxious to see more of these kinds of studies, and I bet they’re in the works right this minute. It seems that there’s finally a big enough set of lab tools to get at the nitty-gritty parts of big questions.

[Flickr user IsaacMao's picture "Child Brain" is used here under a Creative Commons license.]

Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC, Yao WD, Myers RH, Chen JF, Preuss TM, Rogaev EI, Jensen JD, Weng Z, & Akbarian S (2012). Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS biology, 10 (11) PMID: 23185133

Posted in Applications, Chromatin Structure, Chromosome conformation capture, Conformation Capture, Divergent Transcription, Evolutionary Epigenetics, Gene Regulation, Histone Modifications, Neuroscience | Tagged , , , , , | Leave a comment

When it comes to acetylation and epigenetics your mind probably goes right to histones. Acetylated histones are associated with relaxed, transcriptionally active DNA. However, acetylation is an important post-translational modification of lysine in many cellular proteins. It is as widespread as phosphorylation. It is reversable. Functionally, acetylation is known to be involved in the effects of calorie restriction on metabolism and aging. Now the first direct evidence of a mechanism underlying this process has been reported.

The journal Molecular Cell has recently published Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome, authored by scientists from the University of Wisconsin-Madison and the University of Tokyo. They used model mice with age-related hearing loss for this study. This hearing loss is prevented by calorie restriction (CR). They explored the liver mitochondrial protein acetylome by developing a new quantitative, acetyl-proteomic method. The Sirtuin family of deacetylases were already linked to CR. And  Sirtuin3 was recently shown to be induced during CR. So the researchers explored the regulatory role of tSIRT3 during CR. They identified multiple pathways where SIRT3 is involved in reprogramming mitochondria during CR via acetylation. Interestingly for “Epiexperts”, among those ID’d were mitochondria DNA expression and maintenance pathways.  Part of that SIRT3 led CR reprogramming, is through regulation of mtDNA transcription factors, mtRNA polymerases and mitochondrial ribosome proteins. Please see Table 1. in the pub for the list of SIRT3 targets in this functional group.  The reprogramming during CR of these targets leads to enhanced mtDNA transciption, mtDNA translation and protein quality control.

Recall, mitochondria function to produce ATP from sugar and oxygen, powering the cell. This process also creates oxidative free radicals that contribute to aging. Mitochondria have their own DNA and can make their own proteins. During calorie restriction, mitochondria performance is actually enhanced. They use less oxygen and produce less damaging free radicals. Again, in the model mice this results in prevention of hearing loss.

This is a great paper worth reading. Mainly because it establishes that SIRT3, (of the sirtuins deacetylases family) is directly linked to anti-aging effects. But also because it shows SIRT3 is potentially a significant regulator of mitochondrial epigenetics.  It’s like by eating less, SIRT3 directs mitochondria to become environmentally friendly power stations with high energy efficiency ratings.

Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon AJ, Higbee AJ, Westphall MS, Pagliarini DJ, Prolla TA, Assadi-Porter F, Roy S, Denu JM, & Coon JJ (2012). Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome. Molecular cell PMID: 23201123

Posted in Animal Models, Mass Spec, Regenerative Medicine | 1 Comment

Microbiologists rushed to respond to the 2011 pathogenic E.coli (0104:H4) outbreak in Europe. The new strain’s DNA was sequenced within 3 days time. The trace back investigation identified an organic bean sprouts field as the source. Now, Pacific Biosciences with collaboration from New England Biolabs, reports Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing in the journal, Nature Biotechnology (open access paper).

Epigenetic analysis reveals the potential for restriction modification methyltransferase enzymes (RM MTases) to have important roles in this pathogenic phenotype. 0104:H4 phenotype virulence has been defined by its production of high levels of Shiga toxin. AND it turns out that this strain has specific MTases that can promote that production.

SMRT sequencing was used to simultaneously map both the E.coli DNA sequence and strand-specific methylation patterns, yielding functional information. From this data sequence motifs for strain specific methyltransferase enzymes were deduced. New MTase activities were ID’d by correlating the methylation patterns with transcriptome profiles. The functions of these MTases were probed. In one experiment when a phage encoding both the shiga toxin and an 0104:H4 MTase was incorporated into the genome of a non-pathogenic E.coli strain, 1/3 of its transcriptome changed and it was able to produce the Shiga toxin. In another experiment, knocking out a 0104:H4 specific MTase from the strain showed significant epigenetic changes affecting multiple systems.

It’s impressive how the third generation SMRT sequencing technology can be applied to discovering bacterial epigenetic processes key to establishing pathogenicity. Hopefully these techniques will enable the development of new medicines for hemorrhagic colitis and hemolytic uremic syndromes to save lives!

Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ, Deikus G, Clark TA, Luong K, Murray IA, Davis BM, Keren-Paz A, Chess A, Roberts RJ, Korlach J, Turner SW, Kumar V, Waldor MK, & Schadt EE (2012). Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nature biotechnology PMID: 23138224

Posted in DNA Methylation, Genomewide Methylation Profiling, Methyltransferases, Microbial Epigenetics, New Lab Methods, Next Gen Sequencing | Tagged , , , , | Leave a comment

Behold! The noble turkey.

In honor of the U.S. national day of gustatory indulgence, I thought I’d write about girth and fat. EpiExperts Twitter friend Graham Burdge and colleagues at the University of Southampton in the United Kingdom just published an interesting paper exploring how the fat content of a mother rat’s diet affects the polyunsaturated fats in her offspring’s cells and plasma, as well as how that diet may accomplish that feat — apparently it involves promoter methylation of the gene Fads 2.

But first, girth. My co-blogger Nicole recently tweeted a blog post from U.S. National Institutes of Health Director Francis Collins, who shared a map by the U.S. Centers for Disease Control showing how obesity has swept the country since 1985. It’s bracing, to say the least.

Here’s an animated version by BuzzFeed. [Ed. -- For some reason I'm having trouble embedding the video. The text link leads to that video, while the picture link below leads to Collins's blog post again.]

Obesity in the U.S., 2010

(For reference, adults with a BMI of 30 – 39.9 kg/m² are defined as obese. Calculate your BMI by multiplying your weight [in pounds] by 703, dividing that number by your height in inches, then dividing that answer again by your height in inches.)

The usual suspects in this ongoing demographic train wreck are sedentary lifestyles, stress, and poor eating habits. And in that last category, the adoption of Western-style diets high in saturated fats and sugars is often associated with the obesity scourge’s spread to other countries.

On to the paper by Samuel Hoile, Graham Burdge, et. al, which is an attempt to see just what happens in animals who do a bit of that fat-eating.

What’s interesting is that it sheds light on what happens when a mother rat’s diet influences the mixture of fatty acids that her offspring’s cells make and store in their cell membranes (and release into plasma) in the form of phosphatidylcholine and its molecular relatives. To be clear, it’s mostly already established that a mama rat’s high-fat diet changes offspring fatty acid metabolism — lower levels of arachidonic acid (ARA) and docosahexaenoic acid (DHA), in this line of research – the new paper links that phenomenon to epigenetic influence through the gene Fad2. In fact, it appears that although a pregnant mama rat’s high-fat diet can cause persistent changes in how much ARA and DHA her offspring make, a non-pregnant adult rat can experience the same diet-related metabolic changes, but they’re only temporary.

And of course, if epigenetic influence is responsible for these specific ARA- and DHA-related metabolic differences, then epigenetics is a decent candidate for explaining how a mother rat’s diet causes other changes in offspring metabolisms, such as vascular problems, difficulties with glucose metabolism, and so forth.

Now, it’s tempting to use these rat results to draw conclusions about the ramifications of fat in human diets, but there’s too much metabolic difference between the species for that. Also, while the Burdge group’s results achieved statistical significance, this study used six rats per diet cohort, and a larger sample size would of course provide a bit more certainty about the conclusions.

So what’s the health effect on these rat offspring who have lower levels of ARA and DHA in the cell walls of their aortas and livers, as well as in their plasma? Even in rats, the ramifications aren’t clear. Levels of  ARA and DHA affect physical membrane qualities — possibly changing vascular pliability, for example. And they contribute to the pool of precursor fatty acids from which cells make lipid second-messengers, so any change might affect how much of each product gets made.

Additionally, there’s also the role of DHA in forming the nervous system tissue of a developing fetus. In rats (and humans), females keep elevated levels of DHA in their livers and plasma, compared to males — and even higher levels during pregnancy. As Burdge and colleagues — and others — suggest, a higher day-to-day level might help females more easily ramp up DHA to the pregnancy level. As a result, it’s possible that when a mother rat eat a high-fat diet during pregnancy, she’s not only impairing her daughter’s ability to synthesize certain fatty acids, she’s hindering her daughter’s ability to provide the right fatty acids to the grandchild generation in utero.

Or is it “grandpups?”

In any case, Burdge and colleagues fed each of their six-rat groups with either butter or fish oil in different amounts: 3.5%, 7%, or 21%. These six diet-cohorts continued on their regimens from two weeks before conception until weaning, while the offspring all ate a diet of 4% soybean oil.

Surprisingly, at least for me, when it came to reducing the ARA and DHA in her offspring, it didn’t make a big difference whether a mama rat ate a high-fat butter diet or a high-fat fish oil diet. After all, fish oil is high in DHA. But on either regimen, a high-fat diet meant lower levels of these two polyunsaturated fats in the livers and plasma of her adult pups.

[Update Nov. 21, 2012: In an email conversation, Dr. Burdge points out that they'd purposefully fed only ARA and DHA precursors to adult offspring in order to test their ability to synthesize these fats themselves. There's no reason to think that a mother rat's high-DHA diet is going to encourage her offspring to keep DHA levels high, and I see that's what I implied in the paragraph above. Still, it's surprising that both butter and fish oil lead to offspring with same low DHA and ARA fatty-acid synthesis regimes.]

Measuring mRNA expression of the gene Fads2 — which encodes the enzyme Δ6 desaturase (the rate-limiting enzyme in rats’ polyunsaturated fat synthesis) — the Burdge group found it to be low in rats born from mothers who ate high-fat diets, but higher in rats who ate less fat during pregnancy. That lower gene expression wasn’t dramatic enough to account for all the ARA and DHA reduction, though.

At the epigenetic level, the University of Southampton researchers found that in the liver promoter of Fad2 in adult offspring, methylation of three CpG sites was associated with lower Fad2 mRNA expression. And methylation at one of those CpGs coincided with low ARA and DHA in liver and plasma, accounting for the majority of this fatty-acid variation in both male and female rats.

The Burdge group feels this might show that Fad2 epigenetic regulation plays an important role in controlling ARA and DHA levels. And in fact, when the team tested the effect of fatty diets on non-pregnant rats, they found the same effects on Fad2 mRNA, promoter methylation, and liver ARA levels.

But perhaps most interesting is that in non-pregnant fat-fed rats — versus the offspring of fat-fed rats — these effects wore off. In the offspring of fat-fed rats, the low levels of polyunsaturated fats, low Fad2 mRNA, and higher Fad2 promoter methylation appeared to be long-lasting. As Burdge, et. al put it:

These findings suggest that there is epigenetic plasticity in the Fads2 gene in adulthood and that fat intake can alter the DNA methylation of its promoter. However, unlike exposure to an HF diet during development that induced a persistent change on Fads2 methylation and expression, there appears in adulthood to be a homeostatic mechanism that returns the level of methylation and transcription of the original state after the period of HF feeding ended.

And there’s the happy ending, as well as my opening for a tangential reference to this Thursday’s eating festival: At least in non-pregant rats, it’s possible to really overdo it for quite awhile and still avoid at least one long-term negative consequence.

Happy Thanksgiving!

[The fat turkey picture at the top is by Flickr user Dendroica cerulea, and it's reproduced here under a Creative Commons license.]

Hoile, S., Irvine, N., Kelsall, C., Sibbons, C., Feunteun, A., Collister, A., Torrens, C., Calder, P., Hanson, M., Lillycrop, K., & Burdge, G. (2012). Maternal fat intake in rats alters 20:4n-6 and 22:6n-3 status and the epigenetic regulation of Fads2 in offspring liver The Journal of Nutritional Biochemistry DOI: 10.1016/j.jnutbio.2012.09.005

Posted in DNA Methylation, Metabolism | Tagged , , , | Leave a comment

Methylome determination of G. metallireducens GS-15

The most recent pub from the stream of research put forth by New England Biolabs scientists, is a collaboration with scientists from Pacific Biosciences . See this open access paper Iain A. Murray et al. The methylomes of six bacteria. (2012) Nucleic Acids Research. It demonstrates how the 3rd generation SMRT DNA sequencing system is used to explore bacterial methylomes. Many exciting discoveries about microbe epigenetic systems are sure to follow this technological advance!

So why is DNA methylated in bacteria? Mainly it functions as part of restriction modification systems. But bacterial methyltransferases also take part in gene expression, host-pathogen interactions, DNA damage, and DNA repair. Microbe methylation modifications include N6-methyladenine (6-mA), N4-methylcytosine (4-mC) & 5-methylcytosine (5-mC).

Single-molecule, real-time sequencing, or SMRT, analyzes DNA as it is sequenced by collecting light pulses emitted as a byproduct of labelled nucleotide incorporation. Algorithmic analysis is subtle enough to detect certain base modifications. A caveat to methylation analysis is that 5-mC is still a bit too subtle.  However, for this study, associated methyltransferase genes were cloned and analyzed separately, where appropriate, to ID 5mC sites.  The researchers were able to perform methyltransferase (MTase) recognition motif analysis. The recent upgrade of the PacBio® RS High Resolution Genetic Analyzer software also made this project possible.

Richard Roberts, Ph.D., New England Biolab’s Chief Scientific Officer, and senior author on the paper, commented: “DNA methylation is widespread in bacteria where it can protect against restriction enzymes and also regulate gene expression. Until the advent of SMRT sequencing it was not possible to examine the complete methylome of any bacterium. Now it has become simple and we are awash in fascinating new data. Understanding the biological significance of these methylation patterns represents a welcome new challenge for microbiologists.”

I’m sure all you Epiexperts are just as keen to see how the data on microbe gene expression, controlling functions like adaptability and disease pathology, plays out.

Murray IA, Clark TA, Morgan RD, Boitano M, Anton BP, Luong K, Fomenkov A, Turner SW, Korlach J, & Roberts RJ (2012). The methylomes of six bacteria. Nucleic acids research PMID: 23034806

Posted in Applications, Bioinformatics, DNA Methylation, Genomewide Methylation Profiling, Microbial Epigenetics, New Lab Methods, Next Gen Sequencing, Software | Tagged , , , , | Leave a comment

In an ambitious project investigating the interplay of environment, disease, and epigenetics, Canada is funneling $41 million into epigenomics research. It’s a multi-pronged effort to scrutinize a variety of tissue samples, disease states, and responses to environmental insults, so I called up Tomi Pastinen, the Canada research chair in human genetics, to learn more about the project. Here’s a lightly edited transcript of our conversation.

But first, more about the project itself. It’s Canada’s entrée into the International Human Epigenome Consortium, and its announcement last week follows closely on the heels of last year’s launch of a European IHEC effort, BLUEPRINT (see our interview with the project’s Henk Stunnenberg here). While BLUEPRINT focused on blood epigenomes, which is common in epigenomic research, the Canadian project is hoping for a wide variety of tissues—and crucially, it includes an effort to find out just how comparable blood epigenomes are to epigenomes observed in tissues collected from the same individuals.

Each IHEC effort is funded by agencies that have contributed at least $10 million for producing reference epigenomes, which are intended to give future researchers a set of standards to which they can compare new epigenetic findings. The overarching IHEC goal is to produce 1,000 such epigenomes.

Government agencies in Germany, Italy, South Korea, and Japan are currently taking part in projects, while agencies in France, Australia, and the United Kingdom have signaled interest. The U.S. effort, overseen by the U.S. National Institutes of Health, is known as the Roadmap Epigenomics Mapping Consortium.

The Canadian version’s funding comes from a variety of sources, including the Japan Science and Technology Agency and Fonds de Recherche Sante Québec, but the Canadian Institute of Health Research is distributing it all through a two-phase bundle of institutional funding and research grants.

The first phase will provide a total of $15 million to fuel work at Genome Sciences Center in British Colombia and Genome Québec Innovation Center—known as the Epigenome Mapping Center at McGill University—for a five-year effort to produce 100 full human epigenomes that will be publicly available for researchers to access online. It also pays for two data coordination centers at each institution.

An earlier portion of that first-phase funding paid for about $2 million in seed funding—divvied out in April as $100,000, one-year “catalyst grants”—for tools and technologies that may not pan out.

The second, $25 million funding phase pays for “team grants” that will be awarded in January to support research using reference epigenomes in disease-related studies, such as measuring the epigenetic impact of environmental insults in the epigenomes of animals—and even some humans—who belong to certain disease cohorts. The ultimate goal is to produce new drugs, diagnostics, and even health care policy recommendations.

This sounds like a very exciting project. I’m really looking forward to seeing what happens.

I think the whole field is quite excited about it. Every time we talk to people coming slightly from left-field in biomedicine, they get pretty excited about the potential. And it’s tremendous how much more potential there is now than there was two years ago, just because of how sequencing technologies have evolved.
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Posted in Animal Models, Applications, DNA Methylation, Epigenome, Gene Regulation, Genomewide Methylation Profiling, Histone Modifications, Metabolism, Neuroscience, Next Gen Sequencing, Sodium Bisulfite Sequencing, Transcriptome | Tagged , , , , , , , , , , , , , | Leave a comment