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	<title>Epigenetics Experts Blog</title>
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	<link>http://epiexperts.com/blog</link>
	<description>Engaging Ideas</description>
	<lastBuildDate>Tue, 12 Mar 2013 20:16:08 +0000</lastBuildDate>
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		<title>Tet1 Enzyme Based Enrichment Method for Methylome Sequencing: TamC-Seq</title>
		<link>http://epiexperts.com/blog/tet1-enzyme-based-enrichment-method-for-methylome-sequencing-tamc-seq/</link>
		<comments>http://epiexperts.com/blog/tet1-enzyme-based-enrichment-method-for-methylome-sequencing-tamc-seq/#comments</comments>
		<pubDate>Tue, 12 Mar 2013 20:16:08 +0000</pubDate>
		<dc:creator>Nicole Kelesoglu</dc:creator>
				<category><![CDATA[Applications]]></category>
		<category><![CDATA[DNA Methylation]]></category>
		<category><![CDATA[Genomewide Methylation Profiling]]></category>
		<category><![CDATA[Glycosylases]]></category>
		<category><![CDATA[Hydroxymethylation]]></category>
		<category><![CDATA[Methylation]]></category>
		<category><![CDATA[New Lab Methods]]></category>
		<category><![CDATA[Next Gen Sequencing]]></category>
		<category><![CDATA[Epigenetics]]></category>
		<category><![CDATA[methylome]]></category>
		<category><![CDATA[Sequencing]]></category>
		<category><![CDATA[TamC-Seq]]></category>
		<category><![CDATA[Tet1]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2252</guid>
		<description><![CDATA[Here&#8217;s another great advance in methylome sequencing. You all know about bisulfite sequencing, the “gold standard” method. Unfortunately it&#8217;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 &#8230; <a href="http://epiexperts.com/blog/tet1-enzyme-based-enrichment-method-for-methylome-sequencing-tamc-seq/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
		<wfw:commentRss>http://epiexperts.com/blog/tet1-enzyme-based-enrichment-method-for-methylome-sequencing-tamc-seq/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Introducing Aba-seq for Enzyme Based High-Res Mapping of Mammalian Hydroxymethylomes</title>
		<link>http://epiexperts.com/blog/introducing-aba-seq-for-enzyme-based-high-res-mapping-of-mammalian-hydroxymethylomes/</link>
		<comments>http://epiexperts.com/blog/introducing-aba-seq-for-enzyme-based-high-res-mapping-of-mammalian-hydroxymethylomes/#comments</comments>
		<pubDate>Fri, 22 Feb 2013 02:31:53 +0000</pubDate>
		<dc:creator>Nicole Kelesoglu</dc:creator>
				<category><![CDATA[Applications]]></category>
		<category><![CDATA[Biomarkers]]></category>
		<category><![CDATA[DNA Methylation]]></category>
		<category><![CDATA[Enzymology]]></category>
		<category><![CDATA[Genomewide Methylation Profiling]]></category>
		<category><![CDATA[Hydroxymethylation]]></category>
		<category><![CDATA[Methylation Sensitive Restriction Enzymes]]></category>
		<category><![CDATA[New Lab Methods]]></category>
		<category><![CDATA[Oncology]]></category>
		<category><![CDATA[Stem Cells]]></category>
		<category><![CDATA[5hmC]]></category>
		<category><![CDATA[Aba-seq]]></category>
		<category><![CDATA[Epigenetics]]></category>
		<category><![CDATA[epigenome]]></category>
		<category><![CDATA[hydroxymethylation]]></category>
		<category><![CDATA[New England Biolabs]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2233</guid>
		<description><![CDATA[New England Biolabs is well known for its extensive in house research programs &#8211; 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 &#8230; <a href="http://epiexperts.com/blog/introducing-aba-seq-for-enzyme-based-high-res-mapping-of-mammalian-hydroxymethylomes/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
		<wfw:commentRss>http://epiexperts.com/blog/introducing-aba-seq-for-enzyme-based-high-res-mapping-of-mammalian-hydroxymethylomes/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
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		<title>Methylome Data in Lethal Prostate Cancer Supports Personalized Medicine</title>
		<link>http://epiexperts.com/blog/methylomes-in-lethal-prostate-cancer-support-personalized-medicine/</link>
		<comments>http://epiexperts.com/blog/methylomes-in-lethal-prostate-cancer-support-personalized-medicine/#comments</comments>
		<pubDate>Wed, 30 Jan 2013 19:21:23 +0000</pubDate>
		<dc:creator>Nicole Kelesoglu</dc:creator>
				<category><![CDATA[Biomarkers]]></category>
		<category><![CDATA[Epigenome]]></category>
		<category><![CDATA[Methylated DNA Capture]]></category>
		<category><![CDATA[Microarray]]></category>
		<category><![CDATA[Oncology]]></category>
		<category><![CDATA[Epigenetics]]></category>
		<category><![CDATA[MBD]]></category>
		<category><![CDATA[methylation]]></category>
		<category><![CDATA[Prostate cancer]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2213</guid>
		<description><![CDATA[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 &#8230; <a href="http://epiexperts.com/blog/methylomes-in-lethal-prostate-cancer-support-personalized-medicine/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
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		<slash:comments>0</slash:comments>
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		<title>New Years Resolution, Reflection on Cancer Research</title>
		<link>http://epiexperts.com/blog/new-years-resolution-reflection-on-cancer-research/</link>
		<comments>http://epiexperts.com/blog/new-years-resolution-reflection-on-cancer-research/#comments</comments>
		<pubDate>Mon, 14 Jan 2013 17:34:53 +0000</pubDate>
		<dc:creator>Nicole Kelesoglu</dc:creator>
				<category><![CDATA[Epigenome]]></category>
		<category><![CDATA[Genetics]]></category>
		<category><![CDATA[History & Trends]]></category>
		<category><![CDATA[Oncology]]></category>
		<category><![CDATA[Cancer]]></category>
		<category><![CDATA[Epigenetics]]></category>
		<category><![CDATA[Metastatic]]></category>
		<category><![CDATA[oncology]]></category>
		<category><![CDATA[Watson]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2196</guid>
		<description><![CDATA[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&#8217;t change. Rather their expression &#8230; <a href="http://epiexperts.com/blog/new-years-resolution-reflection-on-cancer-research/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
		<wfw:commentRss>http://epiexperts.com/blog/new-years-resolution-reflection-on-cancer-research/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
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		<title>Did Epigenetics Make Us Smart?</title>
		<link>http://epiexperts.com/blog/did-epigenetics-make-us-smart/</link>
		<comments>http://epiexperts.com/blog/did-epigenetics-make-us-smart/#comments</comments>
		<pubDate>Wed, 19 Dec 2012 16:10:45 +0000</pubDate>
		<dc:creator>Chris Womack</dc:creator>
				<category><![CDATA[Applications]]></category>
		<category><![CDATA[Chromatin Structure]]></category>
		<category><![CDATA[Chromosome conformation capture]]></category>
		<category><![CDATA[Conformation Capture]]></category>
		<category><![CDATA[Divergent Transcription]]></category>
		<category><![CDATA[Evolutionary Epigenetics]]></category>
		<category><![CDATA[Gene Regulation]]></category>
		<category><![CDATA[Histone Modifications]]></category>
		<category><![CDATA[Neuroscience]]></category>
		<category><![CDATA[anti-sense RNA]]></category>
		<category><![CDATA[Epigenetics]]></category>
		<category><![CDATA[Evolution]]></category>
		<category><![CDATA[H3K4me3]]></category>
		<category><![CDATA[histone methylation]]></category>
		<category><![CDATA[transcription regulation]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2183</guid>
		<description><![CDATA[Finally there&#8217;s research comparing the epigenetic marks of human brain neurons to those of other primates, and it&#8217;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&#8217;m not a gambler, but since primate neuron-specific genes don&#8217;t show a whole lot of difference from one another in their protein-coding sequences, that&#8217;s where I&#8217;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 &#8230; <a href="http://epiexperts.com/blog/did-epigenetics-make-us-smart/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
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		<slash:comments>0</slash:comments>
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		<title>Sirtuin3 Reprograms Mitochondrial Epigenetic Pathways: How Diet Affects Age</title>
		<link>http://epiexperts.com/blog/sirtuin3-reprograms-mitochondrial-epigenetic-pathways-how-diet-affects-age/</link>
		<comments>http://epiexperts.com/blog/sirtuin3-reprograms-mitochondrial-epigenetic-pathways-how-diet-affects-age/#comments</comments>
		<pubDate>Tue, 11 Dec 2012 19:30:59 +0000</pubDate>
		<dc:creator>Nicole Kelesoglu</dc:creator>
				<category><![CDATA[Animal Models]]></category>
		<category><![CDATA[Mass Spec]]></category>
		<category><![CDATA[Regenerative Medicine]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2157</guid>
		<description><![CDATA[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 &#8230; <a href="http://epiexperts.com/blog/sirtuin3-reprograms-mitochondrial-epigenetic-pathways-how-diet-affects-age/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
		<wfw:commentRss>http://epiexperts.com/blog/sirtuin3-reprograms-mitochondrial-epigenetic-pathways-how-diet-affects-age/feed/</wfw:commentRss>
		<slash:comments>1</slash:comments>
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		<title>SMRT Sequencing Studies Methyltransferease Driven Virulence in E.coli (0104:H4)</title>
		<link>http://epiexperts.com/blog/smrt-sequencing-studies-methyltransferease-driven-virulence-in-e-coli-0104h4/</link>
		<comments>http://epiexperts.com/blog/smrt-sequencing-studies-methyltransferease-driven-virulence-in-e-coli-0104h4/#comments</comments>
		<pubDate>Mon, 26 Nov 2012 18:10:10 +0000</pubDate>
		<dc:creator>Nicole Kelesoglu</dc:creator>
				<category><![CDATA[DNA Methylation]]></category>
		<category><![CDATA[Genomewide Methylation Profiling]]></category>
		<category><![CDATA[Methyltransferases]]></category>
		<category><![CDATA[Microbial Epigenetics]]></category>
		<category><![CDATA[New Lab Methods]]></category>
		<category><![CDATA[Next Gen Sequencing]]></category>
		<category><![CDATA[E.coli]]></category>
		<category><![CDATA[Epigenetics]]></category>
		<category><![CDATA[microbiology]]></category>
		<category><![CDATA[New England Biolabs]]></category>
		<category><![CDATA[SMRT]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2137</guid>
		<description><![CDATA[Microbiologists rushed to respond to the 2011 pathogenic E.coli (0104:H4) outbreak in Europe. The new strain&#8217;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 &#8230; <a href="http://epiexperts.com/blog/smrt-sequencing-studies-methyltransferease-driven-virulence-in-e-coli-0104h4/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
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		<title>Epigenetics and Fat &#8212; Not Just Girth</title>
		<link>http://epiexperts.com/blog/epigenetics-and-fat-not-just-girth/</link>
		<comments>http://epiexperts.com/blog/epigenetics-and-fat-not-just-girth/#comments</comments>
		<pubDate>Tue, 20 Nov 2012 17:52:00 +0000</pubDate>
		<dc:creator>Chris Womack</dc:creator>
				<category><![CDATA[DNA Methylation]]></category>
		<category><![CDATA[Metabolism]]></category>
		<category><![CDATA[diet]]></category>
		<category><![CDATA[DNA methylation]]></category>
		<category><![CDATA[environmental factors]]></category>
		<category><![CDATA[transcription regulation]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2088</guid>
		<description><![CDATA[In honor of the U.S. national day of gustatory indulgence, I thought I&#8217;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&#8217;s diet affects the polyunsaturated fats in her offspring&#8217;s cells and plasma, as well as how that diet may accomplish that feat &#8212; 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&#8217;s bracing, &#8230; <a href="http://epiexperts.com/blog/epigenetics-and-fat-not-just-girth/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
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		<slash:comments>0</slash:comments>
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		<item>
		<title>The Easy Way to Study Microbe Methylomes&#8230; use SMRT sequencing!</title>
		<link>http://epiexperts.com/blog/the-easy-way-to-study-microbe-methylomes-use-smrt-sequencing/</link>
		<comments>http://epiexperts.com/blog/the-easy-way-to-study-microbe-methylomes-use-smrt-sequencing/#comments</comments>
		<pubDate>Mon, 05 Nov 2012 02:56:37 +0000</pubDate>
		<dc:creator>Nicole Kelesoglu</dc:creator>
				<category><![CDATA[Applications]]></category>
		<category><![CDATA[Bioinformatics]]></category>
		<category><![CDATA[DNA Methylation]]></category>
		<category><![CDATA[Genomewide Methylation Profiling]]></category>
		<category><![CDATA[Microbial Epigenetics]]></category>
		<category><![CDATA[New Lab Methods]]></category>
		<category><![CDATA[Next Gen Sequencing]]></category>
		<category><![CDATA[Software]]></category>
		<category><![CDATA[Epigenetics]]></category>
		<category><![CDATA[methylome]]></category>
		<category><![CDATA[microbiology]]></category>
		<category><![CDATA[New England Biolabs]]></category>
		<category><![CDATA[SMRT]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2058</guid>
		<description><![CDATA[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) &#38; 5-methylcytosine (5-mC). Single-molecule, real-time sequencing, &#8230; <a href="http://epiexperts.com/blog/the-easy-way-to-study-microbe-methylomes-use-smrt-sequencing/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
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		<title>Canada Joins the International Human Epigenome Consortium &#8211; Q&amp;A with Tomi Pastinen of Génome Québec</title>
		<link>http://epiexperts.com/blog/canada-joins-the-international-human-epigenome-consortium-qa-with-tomi-pastinen-of-genome-quebec/</link>
		<comments>http://epiexperts.com/blog/canada-joins-the-international-human-epigenome-consortium-qa-with-tomi-pastinen-of-genome-quebec/#comments</comments>
		<pubDate>Wed, 31 Oct 2012 00:13:07 +0000</pubDate>
		<dc:creator>Chris Womack</dc:creator>
				<category><![CDATA[Animal Models]]></category>
		<category><![CDATA[Applications]]></category>
		<category><![CDATA[DNA Methylation]]></category>
		<category><![CDATA[Epigenome]]></category>
		<category><![CDATA[Gene Regulation]]></category>
		<category><![CDATA[Genomewide Methylation Profiling]]></category>
		<category><![CDATA[Histone Modifications]]></category>
		<category><![CDATA[Metabolism]]></category>
		<category><![CDATA[Neuroscience]]></category>
		<category><![CDATA[Next Gen Sequencing]]></category>
		<category><![CDATA[Sodium Bisulfite Sequencing]]></category>
		<category><![CDATA[Transcriptome]]></category>
		<category><![CDATA[Cancer]]></category>
		<category><![CDATA[chronic disease]]></category>
		<category><![CDATA[diagnostics]]></category>
		<category><![CDATA[diet]]></category>
		<category><![CDATA[DNA methylation]]></category>
		<category><![CDATA[environmental factors]]></category>
		<category><![CDATA[epigenome]]></category>
		<category><![CDATA[histone acetylation]]></category>
		<category><![CDATA[histone ubiquination]]></category>
		<category><![CDATA[In Utero]]></category>
		<category><![CDATA[International Human Epigenome Consortium]]></category>
		<category><![CDATA[methylation]]></category>
		<category><![CDATA[transcription regulation]]></category>
		<category><![CDATA[Translational research]]></category>

		<guid isPermaLink="false">http://epiexperts.com/blog/?p=2047</guid>
		<description><![CDATA[In an ambitious project investigating the interplay of environment, disease, and epigenetics, Canada is funneling $41 million into epigenomics research. It&#8217;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&#8217;s a lightly edited transcript of our conversation. But first, more about the project itself. It&#8217;s Canada&#8217;s entrée into the International Human Epigenome Consortium, and its announcement last week follows closely on the heels of last year&#8217;s launch of a European IHEC effort, BLUEPRINT (see our interview with the project&#8217;s Henk Stunnenberg here). While BLUEPRINT focused on blood epigenomes, which is common in &#8230; <a href="http://epiexperts.com/blog/canada-joins-the-international-human-epigenome-consortium-qa-with-tomi-pastinen-of-genome-quebec/">Continue reading <span class="meta-nav">&#8594;</span></a>]]></description>
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