Category Archives: Sodium Bisulfite Sequencing

Reading the Effect of Tea Leaves…and Beating Genetic Fatalism in Breast Cancer

Posted on June 6, 2013 by Nicole Kelesoglu

The recent news about Angelina Jolie getting a prophylactic double mastectomy is both sad and encouraging. Women, and their physicians, are becoming more aware of individual breast cancer risk. They are willing to use any available treatments to reduce that risk, and promote health. Tamoxifen is a breast cancer drug success story. It works by competing with estradiol for estrogen receptor protein. Thereby inhibiting the Erα (estrogen receptor). See http://www.drugs.com/pro/tamoxifen.html Tamoxifen 1st significantly improves survival.  2nd reduces recurrence.  3rd reduces the incidence of breast cancer in high risk women. The drawback is that the tumors need to be overexpressing estrogen receptor, or ER+. Cancer that is “estrogen receptor negative”, or ER- now has a comparably worse prognosis. This is because … Continue reading →

Posted in Acetylation, Breast cancer, Cell Culture Models, DNA Methylation, Histone Modifications, Hydroxymethylation, Methyltransferases, Oncology, Sodium Bisulfite Sequencing, chIP | Tagged , , , , , , | Leave a comment

Canada Joins the International Human Epigenome Consortium – Q&A with Tomi Pastinen of Génome Québec

Posted on October 31, 2012 by Chris Womack

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 … Continue reading →

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

The Epigenetics of Real-Life Stress and Serotonin

Posted on October 10, 2012 by Chris Womack

Sure, M.D.s often suffer a lot of pressure. But as I learned in a brief hospital job, nurses really bear the brunt of all the biological clean-up, red tape, weird hours, patient complaints, and snippy doctors’ demands. So this new study in PLoS One on stress-related epigenetic changes in shift-working female nurses really caught my attention, and seemed like a good followup that post on situational stress and epigenetics. Nurses under high stress appear to have their gene expression epigenetically regulated in a way that may decrease serotonin in the brain’s synapses. It seems a bit like the reverse of Prozac, and it bears a passing resemblance to what might happen at the beginning of depression. By interfering with serotonin … Continue reading →

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Will Epigenetics Help Overcome Cisplatin Resistance in Ovarian Cancers?

Posted on January 10, 2012 by Nicole Kelesoglu

Hello Epiexperts! There are a couple recent open access papers to point out to you this week. Both relate to ovarian cancer progression and desensitization to the chemotherapy, Cisplatin. Cisplatin resistance is the primary obstacle to surviving ovarian cancer. These cancers are rare thankfully, but the 5 year survival rate is only 15-20%. Epigentics researchers are actively engaged in confronting this challenging disease. There are several Phase II clinical trials in progress for individual and combinational therapies using DNA methylation inhibitors and histone deacetlase (HDAC) inhibitors. Until those epigenetics based therapy trial results are available, as things stand, the current outlook is bleak. Please see this piece by Donna Trussell, in the Washington Post. She writes from her personal perspective … Continue reading →

Posted in Bioinformatics, Biomarkers, Clinical Studies, DNA Methylation, Databases, Genetics, Genomewide Methylation Profiling, History & Trends, Methylated DNA Capture, Next Gen Sequencing, Oncology, Real-time PCR, Sodium Bisulfite Sequencing, Transcriptome microarray | Tagged , , , , | Leave a comment

Smoking and Placental Transcription–an Epigenetic Route to Low Birth Weight?

Posted on December 2, 2011 by Chris Womack

In an interesting little study published last month in the journal Epigenetics, researchers at Baylor College of Medicine compared transcriptomes and methylomes of placentas from 18 smokers and 18 non-smokers — checking for mRNA expression changes that matched methylations (or demethylations) in nearby promoters or enhancers. (Nearby the up- or down-regulated gene, that is.) It’s a new approach because no one’s ever related maternal smoking with transcriptome-wide altered expression and methylation changes at 27,000 CpG sites. That wide search netted 622 genes that showed significantly different expression patterns between the two groups, and 1,024 CpG sites that showed significant methylation differences. And after clearing away the … uh … statistical smoke, the BCM scientists discovered that at least six CpG … Continue reading →

Posted in DNA Methylation, Developmental Biology, Gene Regulation, Genomewide Methylation Profiling, In Utero, Sodium Bisulfite Sequencing, Transcriptome microarray | Tagged , , , | 1 Comment

Identical Twins are Not Identically Imprinted : Epigenome in Context of the Genome

Posted on October 28, 2011 by Nicole Kelesoglu

As is the case with their fingerprints, imprinted genes are NOT identical in identical twins. In fact, methylation levels vary notably, yet randomly, in localized imprinted regulatory regions, between MZ twins. Even cooler, a new epigenetics clue came out of demonstrating this imprinting variability. This month in PloS one, the collaborators from the Garvin Institute, the University of Nijmegen Medical Centre, the Queensland Institute of Medical Research and St. Vincent’s Clinical School, University of NSW, produced the paper Impact of the Genome on the Epigenome Is Manifested in DNA Methylation Patterns of Imprinted Regions in Monozygotic and Dizygotic Twins. by Marcel W. Coolen et al. Blood samples from 128 pairs of identical, and 128 pairs of fraternal teen aged twins, … Continue reading →

Posted in Autism, Bioinformatics, DNA Methylation, Developmental Biology, Divergent Transcription, Gene Regulation, Gene Silencing, Genomewide Methylation Profiling, In Utero, Mass Spec, Methylation Specific PCR, Next Gen Sequencing, Sodium Bisulfite Sequencing, Transcriptome microarray | Tagged , , , | Leave a comment

Q&A with BLUEPRINT’s Henk Stunnenberg on the New Leukemia, Blood Epigenome Project

Posted on October 7, 2011 by Chris Womack

The European Union’s $53.5 million, 4-year BLUEPRINT project launched this week with the ambitious goal of cataloging the epigenomes of 100 different cell types, with a focus on hematopoietic cells and leukemia disease states. The project is only the second such effort associated with the International Human Epigenome Consortium—the first being the U.S. National Institutes of Health’s Roadmap Epigenomics Mapping Consortium—and it’s composed of 41 research entities, including university labs, research institutes, and drug and diagnostics companies. BLUEPRINT coordinator Henk Stunnenberg, a professor of molecular biology at the Radboud University Nijmegen in the Netherlands, says the project may publish early work as soon as a year from now, and that the epigenomes it uncovers have the potential to generate diagnostics … Continue reading →

Posted in Applications, Biomarkers, Chromatin Structure, DNA Methylation, Diagnostics, Gene Regulation, Histone Modifications, New Lab Methods, Next Gen Sequencing, Sodium Bisulfite Sequencing, Translational Research | Tagged , , , , , , , , | 1 Comment

No Promoter is an Island: Methylation Affects Transcription Even Without CpG Clusters

Posted on August 26, 2011 by Chris Womack

Last week I stumbled on an interesting finding–or so it seems to me. Even genes whose promoters aren’t near CpG islands can be regulated by DNA methylation. Previous research seemed to point to the idea that CpG islands–short DNA stretches containing lots of two-nucleotide cytosine-guanosine sequences–were necessary for controlling nearby transcriptional promoters. Methylating a CpG island turns a gene off–shutting down RNA transcription from that site–while demethylating the island turns a gene on. And methylating CpGs in a CpG-poor promoter seemed to have little or no effect. About half of promoter sequences don’t have nearby CpG islands, which seems a little strange, since many of these promoters control genes that’re important only for specific tissues. After all, methylation is one … Continue reading →

Posted in DNA Methylation, Gene Regulation, Gene Silencing, Sodium Bisulfite Sequencing | Tagged , , | Leave a comment

Can Epigenetics Improve Forensic Science? : “Matters of Life, Liberty & Death”

Posted on July 8, 2011 by Nicole Kelesoglu

With the Casey Anthony case verdict, and recent capture of Whitey Bulger in the news, my attention is drawn to the important service forensic scientists do to society – promoting justice.  The National Academy of Sciences put out a report in 2009, Strengthening Forensic Science in the United States: A Path Forward. The report details the challenges faced in forensic science, and makes recommendations, which aim for universal standards and establishing best practice. The major challenge for forensic scientists analyzing DNA from a crime scene, is getting useful data from limited and poor quality samples. There are several research avenues where epigenetics can aid forensic science. While genetic information identifies an individual, the epigenetic information can add informative layers to … Continue reading →

Posted in Applications, DNA Methylation, Forensic genetics, Methylation Specific PCR, Next Gen Sequencing, Sodium Bisulfite Sequencing | 3 Comments