methylation
« Previous EntriesEpigenetic Natural Variation in Arabidopsis thaliana
Tuesday, June 19th, 2007A new research paper appearing today in PLoS Biology provides new insight into the DNA methylation patterns in the plant Araabidopsis thaliana:
Cytosine methylation of repetitive sequences is widespread in plant genomes, occurring in both symmetric (CpG and CpNpG) as well as asymmetric sequence contexts. We used the methylation-dependent restriction enzyme McrBC to profile methylated DNA [...]
CpG Methylation Targeted to Transcription Units in an Invertebrate Genome
Thursday, June 14th, 2007I just came across an interesting research paper by Suzuki et al. in a recent issue of Genome Research: CpG methylation is targeted to transcription units in an invertebrate genome.
DNA is methylated at the dinucleotide CpG in genomes of a wide range of plants and animals. Among animals, variable patterns of genomic CpG methylation have [...]
DNA Methylation Affects Nuclear Organization and Histone Modifications
Wednesday, May 16th, 2007In a paper recently published in the Journal of Cell Biology, Gilbert et. al. use mutant mouse embryonic stem cells lacking DNA methylation to show that DNA methylation affects nuclear organization and nucleosome structure, but not chromatin compaction.
DNA methylation has been implicated in chromatin condensation and nuclear organization, especially at sites of constitutive heterochromatin. How [...]
Moving Towards Better Mapping of CpG Islands
Friday, May 4th, 2007A new research paper available as an early online release in the journal PLoS Compitational Biology helps provide some new insight into how the definition and mapping of CpG islands could be improved.
CpG islands were originally identified by epigenetic and functional properties, namely absence of DNA methylation and frequent promoter association. However, this concept was [...]
Illumina Launches Custom Methylation Application
Monday, April 16th, 2007Today Illumina, Inc. (NASDAQ:ILMN) launched a custom-content methylation product that allows researchers to perform methylation profiling specific to individual CpG sites. From the press release:
Joining Illumina’s GoldenGate Methylation Cancer Panel I, the Company’s first standard methylation product launched in January 2007, investigators now have the option to select their favorite genes or gene regions to [...]
Epigenetics in Focus at Nature Reviews Genetics
Monday, March 26th, 2007Following closely on the heels of the special issue of Cell on epigenetics, Nature Reviews Genetics today published its own focus issue on epigenetics (April 2007), with reviews from some of the most prominent experts in several sub-disciplines within epigenetics, including stem cell research, cancer epigenomics, and environmental epigenetics. The editors of the journal open [...]
DNA Methylation Involved in Memory Formation
Wednesday, March 14th, 2007Researchers at the University of Alabama at Birmingham have published new research supporting their hypothesis that DNA methylation plays a role in forming memories (1). The link between methylation and memory formation came about from the observation that methylation was disregulated in people suffering from brain disorders such as autism and schizophrenia.
In their experiments, the [...]
Liposuctioned Fat as a Source of Stem Cells
Friday, March 9th, 2007
In 2004, members of the American Society of Plastic Surgerons performed over 320,000 liposuction procedures (1). Who knew that the extracted fat was a potential source of stem cells for research or therapeutics.
Dr. Philipe Collas at the University os Oslo in Norway is conducting research to identify the stem cells among liposuctioned fat cells that [...]
Gadd45a Promotes Epigenetic Gene Activation by Repair-Mediated DNA Demethylation
Monday, March 5th, 2007Nature has published a letter from researchers at the German Cancer Research Center involving their implication of the gene Gadd45a in one of the black boxes of epigenetic mechanisms: demethylation.
DNA methylation is an epigenetic modification that is essential for gene silencing and genome stability in many organisms. Although methyltransferases that promote DNA methylation are well [...]
Cell Reviews Epigenetics and Chromatin Organization
Monday, February 26th, 2007The 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 [...]
Unmethylated Promoter-Proximal Region Required for Transcription
Friday, February 16th, 2007A 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 [...]
Optimizing Annealing Temperature in Bisulfite Methylation Analysis
Wednesday, February 7th, 2007Sodium 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 [...]
Histone Modifications Regulate Pluripotency in the Early Mouse Embryo
Tuesday, February 6th, 2007Earlier 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 [...]
Transgenerational Epigenetic Modification with Nutritional Supplementation
Monday, February 5th, 2007Reader 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 [...]
Epigenetic Control of Regulatory T Cells
Wednesday, January 31st, 2007New research published this week in PLoS Biology shows the importance of epigenetic modifications in regulatory T cells.
Regulatory T cells play a pivotal role in the maintenance of self-tolerance within the immune system by preventing autoimmunity or excessive activation of the T cells that respond to pathogens (naïve and effector T cells). They differentiate within [...]
