Cell Reviews Epigenetics and Chromatin Organization


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The journal Cell has released a special review issue, “Epigenetics and Chromatin Organization.” The issue contains 11 review articles, beginning with a review of one of the most exciting aspects of epigenetics: its effect on evolution.

According to classical evolutionary theory, phenotypic variation originates from random mutations that are independent of selective pressure. However, recent findings suggest that organisms have evolved mechanisms to influence the timing or genomic location of heritable variability. Hypervariable contingency loci and epigenetic switches increase the variability of specific phenotypes; error-prone DNA replicases produce bursts of variability in times of stress. Interestingly, these mechanisms seem to tune the variability of a given phenotype to match the variability of the acting selective pressure. Although these observations do not undermine Darwin’s theory, they suggest that selection and variability are less independent than once thought. Link

A nice summary of this review article is available at Gene Expression.

Cell

The other review articles include:

This special review issue from Cell is a clear indication of the role that epigenetics is playing in changing the scope and direction of scientific research in many different areas. My hope is that epigenetics will continue to inspire more articles in the press and will become well known among both those in science and the general public. Link

New Sponsor: Ion Channel Media


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The latest sponsor of Epigenetics News is Ion Channel Media, who has purchased a text link across every page of the site for US$40. Ion Channel Media has a network of 43 science portals that provide feeds of the latest published research in a wide range of scientific disciplines, including bioinformatics, apoptosis, cell cycle, transgenics, and their newest portal, epigenetics.

The epigenetics portal has some very interesting features, including a list of epigenetics research authors and their related score ranked by number of times their articles have been cited. There is a list of upcoming books with epigenetics in the title, and a listing of job openings that contain epigenetics in the description.

I would like to thank Ion Channel Media for their sponsorship and support. Link

Just Science Wrap-Up: Better Late Than Never


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In my view, the Just Science week was a success. Yeah, we didn’t really meet the challenge. Mr. Rekow and I were able to cover a few epigenetics research articles, and then the inevitable hit: preparation for three exams. On the same day.

To be honest, I was impressed that Rekow and I were able to generate the posts that we did and still come out (mostly) unscathed after the exams were final. I was hoping to get more accomplished in preparation for the event, but the blog has to take a back seat to a lot of things, including my classes and my work. It’s a difficult balancing act.

I would like to give a lot of credit to all of the blogs that participated in the effort and produced a lot of great content. The organizers of Just Science Week have promised to do it again next year, and we’ll probably give it a go again. Until then, all of the content written for Just Science will be available for your viewing pleasure.

Link

Unmethylated Promoter-Proximal Region Required for Transcription


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A new paper published this week in PLoS Genetics provides evidence that an unmethylated region extending several hundred base pairs from the promoter of a gene is required for activation of transcription.

Genes, the functional units of heredity, are made up of DNA, which is packaged inside the nuclei of eukaryotic cells in association with a number of proteins in a structure called chromatin. In order for transcription, the process of transferring genetic information from DNA to RNA, to take place, chromatin must be decondensed to allow the transcription machinery to bind the genes that are to be transcribed. In mammals, promoters, the starting position of genes, are frequently embedded in “CpG islands,” regions with a relatively high density of the CpG dinucleotide. Paradoxically, while cytosines in the context of the CpG dinucleotide are generally methylated, CpGs flanking the start sites of genes typically remain methylation-free. As CpG methylation is associated with condensed chromatin, it is generally believed that promoter regions must remain free of methylation to allow for binding of the transcription machinery. Here, using a novel method for introducing methylated DNA into a defined genomic site, we demonstrate that DNA methylation in the promoter-proximal region of a gene is sufficient to block transcription via the generation of a chromatin structure that inhibits binding of the transcription machinery. Thus, methylation may inhibit transcription even when present outside the promoter region.

PLoS Genetics is an open access journal with free access to full text articles. Link

Optimizing Annealing Temperature in Bisulfite Methylation Analysis


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Sodium bisulfite treatment of DNA is widely used by researchers to analyze the DNA methylation patterns of DNA regions of interest. With bisulfite treatment of DNA, researchers are able to quantitatively determine if a 5′ cytosine is methylated. If a cytosine (C) is methylated, bisulfite treatment will leave the cytosine untouched. If the cytosine is unmethylated, bisulfite treatment will convert the C to a uracil (U). Researchers can then sequence a region of interest after bisulfite treatment to determine the 5′ cytosines that are methylated and unmethylated.

A new paper in the January 2007 issue of BioTechniques shows that PCR bias can be reduced by optimizing the annealing temperature in PCR methylation analysis (1).

The main concern for PCR-based quantitative DNA methylation analysis is PCR bias, which is due to the fact that methylated and unmethylated DNA molecules sometimes amplify with greatly differing efficiencies.

After analysis of several variables in the PCR reaction mixture that could contribute to this variability, the authors concluded that increasing annealing temperature in the PCR reaction resulted in a higher level of methylation detected.

It is clear from the results that regardless of the primer system, there is a strong bias toward the amplification of unmethylated DNA, and increasing annealing temperature for PCR improved the amplification toward methylated DNA.

References:

1. Shen L, Guo Y, Ahmed S, Issa JJ. 2007. Optimizing annealing temperature overcomes bias in bisulfite PCR methylation analysis. BioTechniques 42(1):48-58.

Histone Modifications Regulate Pluripotency in the Early Mouse Embryo


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Earlier this year, a group affiliated with Cambridge University at the Wellcome Trust/Cancer Research UK Gordon Institute reported in Nature that epigenetics, specifically methylation of certain arginine residues of histone H3, directly contribute to cell fate and success in the four-cell stage embryo in the mouse model. These findings confront the widely accepted paradigm that mammalian embryos begin development with similar, if not identical, cell types which differ only when inside and outside cells form. Furthermore, the findings solidify that epigenetic modifications influence cell direction and determination.

By investigating the belief that epigenetic mechanisms are utilized to support pluripotency, the researchers provided evidence that arginine methylation of histone H3 is at its highest in four-cell blastomeres which contribute to the inner cell mass (ICM), polar trophectoderm and fully develop when joined with chimaeras. Inversely, arginine methylation of histone H3 is lowest in cell progeny which contribute primarily to mural trophectoderm which exhibit abnormal development when joined with chimaeras. This finding indicates that maximal levels of arginine methylation of histone H3 influence blastomeres’ contribution to pluripotent cells of the inner cell mass. Furthermore, over-expression of the histone H3 arginine methyltransferase gene CARM1 in blastomeres resulted in direction of subsequent progeny cells to the ICM – solidifying the theory that “specific histone modifications are the earliest known epigenetic marker contributing to development of ICM” and precede formation of inside and outside cells.

References:

Torres-Padilla ME, Parfitt DE, Kouzarides T, Zernicka-Goetz M. 2007. Histone arginine methylation regulates pluripotency in the early mouse embryo. Nature 445:214-218.
doi:10.1038/nature05458

Transgenerational Epigenetic Modification with Nutritional Supplementation


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Reader Israel Barrantes recently commented on what he considered to be the “most memorable epigenetic moment of the year” for 2006, which was a groundbreaking paper by Cropley et al. that appeared in Proceedings of the National Academy of Science in November (1). I couldn’t argue with that nomination, so I decided to write about the paper to kick off the week of Just Science.

The paper, titled “Germ-line epigenetic modification of the murine Avy allele by nutritional supplementation,” uses a mutant mouse strain known as viable yellow agouti, or Avy. As shown previously, mice carrying the viable yellow agouti allele exhibit yellow fur, obesity, type II diabetes, and predisposition to tumors. Those that carry one Avy allele and one normal allele (referred to as Avy/a) exhibit varying degrees of the Avy phenotype, ranging from fully yellow and obese to lean and fully agouti. In previous studies, it has been shown that pregnant Avy females that receive a diet supplementation containing folate, choline, betaine, and vitamin B12 from two weeks prior to gestation to birth produce Avy offspring that are shifted toward the agouti phenotype. This shift was also highly correlated with an increase in cytosine methylation. In other words, nutritional supplementation during gestation seemed to cause an epigenetic alteration in phenotypes of offspring.

The picture below shows samples of the varying degrees of the yellow to agouti mice and their corresponding scores. The scores are used in this study as a quantitative way of determining the degree of tranmission of the Avy allele, comparing results when the mutant allele is contributed by the male (sire) or female (dam). The authors found that the previously mentioned shift to the agouti phenotype occurred only when the Avy allele was contributed by the sire, which provides evidence that the male germ line may play a role in transgenerational epigenetic alterations.

Agouti Mice

The authors then used this evidence of male-specific transmission of the Avy allele to propose that the altered phenotype could be passed to a subsequent generation without further diet supplementation. Further, they wanted to determine if diet supplementation was required throughout gestation to induce the epigenetic alteration. The authors proposed that supplementation was only critical during the period encompassing the point at which primordial germ cells differentiate and reset epigenetic marks. Therefore, the period of supplementation for pregnant a/a dams mated to Avy/a sires was set at E8.5 (embryonic day 8.5, or 8.5 days past conception) to E15.5. (Gestation in mice is about 21 days.) Interestingly, this midgestation exposure was very similar to the timepoint used in another study identifying a transgenerational epigenetic effect in mammals (2).

The authors found that when the F1 generation whose mothers received diet supplementation during gestation were mated, the F2 generation exhibited a similar shift in color score as the F1 generation. It is worth emphasizing that the F2 generation embryos were not directly exposed in utero to diet supplementation as the F1 generation embryos were, but the germ line of F2 animals was affected by the diet supplementation given to the previous generation.

This study was groundbreaking in that it provides the first direct evidence of a mechanism in a transgenerational, epigenetic alteration. However, it would be interesting to see if the shift to the agouti phenotype would continue into the F3 and F4 generations, as would be expected if the epigenetic germ line was permanently reprogrammed.

References:

1. Cropley JE, Suter CM, Beckman KB, Martin DIK.
2006. Germ-line epigenetic modification of the murine Avy allele by nutritional supplementation. Proc Natl Acad Sci USA 103:17308-17312.
doi:10.1073/pnas.0607090103
2. Anway MD, Cupp AS, Uzumcu M, Skinner MK. 2005. Epigenetic Transgenerational Actions of Endocrine Disruptors and Male Fertility. Science 308:1466-1469.
doi:10.1126/science.1108190