A Researcher’s Guide to Successful DNA Bisulfite Conversion

October 14, 2014 Milka Rodriguez

DNA bisulfite conversion is a unique tool used to discriminate between methylated and unmethylated cytosines for DNA methylation studies. Only bisulfite modification of DNA followed by sequencing yields reliable information on the methylation states of individual cytosines at single base resolution. The bisulfite modification technique uses bisulfite salt to deaminate cytosine residues on single-stranded DNA, converting them to uracil while leaving 5-methylcytosine unchanged (Figure 1). To effectively and efficiently prepare converted DNA for use in various downstream analyses, an ideal [more…]

Global DNA Methylation Analysis: The Best Assay You Haven’t Done Yet

July 24, 2014 Milka Rodriguez

Over the past decade significant advances have been made in methylation profiling technology allowing for highly specific and accurate information about the epigenome of various species. Because the 5mC and 5hmC modifications are widespread with possibly different functions, further insight into their distribution is important. Traditional methylation analysis methods such as mass spec, HPLC and TLC allow high accuracy but also require sophisticated equipment, are not high through-put and most importantly are expensive. Likewise more modern applications such as next [more…]

Eat Well, Exercise Regularly and Monitor Your Epigenome

April 11, 2014 Milka Rodriguez

Cardiometabolic disease (CMD) is a term used to define risk factors associated with the development of diabetes and cardiovascular disease.  One major characteristic which contributes to these risk factors is obesity. Worldwide, obesity has nearly doubled since 1980 and in 2008, more than 1.4 billion adults 20 and older were overweight (1).  Additionally more than 40 million children under the age of five were overweight in 2011 (1). Childhood obesity is associated with a higher chance of obesity, premature death [more…]

DNA Methylation Patterns May Be Associated With Birth Weight Outcomes

March 21, 2014 Milka Rodriguez

We are well aware that environmental factors such as smoking, drinking and diet can affect fetal development; however, we do not have a clear understanding of the epigenetic factors that may be involved in this process. A new study now shows that epigenetics may also be involved in fetal growth – in particular birth weight. The scientists at the University of North Carolina at Chapel Hill conducted a study which examined the relationship between CpG-specific cord blood DNA methylation and [more…]

New Hope for People Suffering from Kidney Fibrosis

March 3, 2014 Milka Rodriguez

Injury to tissue in major organs such as the kidney causes inflammation which can lead to cell damage or cell death in the affected area. The human body is programmed with a normal physiological wound repair process for the damaged tissue – similar to the formation of a scar when we injure or damage our skin. Normally, once the injury has been contained, the wound repair process stops. Fibrosis is a pathological process similar to normal tissue wound repair; however, [more…]

“I Am No Longer Haunted By That Awful Memory” – New Epigenetic Drug Treatment May Erase Painful Memories

January 27, 2014 Milka Rodriguez

 Is it possible for a drug to dampen a traumatic memory? It may be, as researchers are discovering that a fundamental epigenetic mechanism is responsible for long-term fear memory. Neuroplasticity, also called brain plasticity, refers to the changes in neural connections such as synapses and neural pathways as a result of changes in behavior, environmental exposure and neural processes (1,2).  While it was once believed that the brain is a physiologically static organ and its networks were fixed, research over [more…]

Book Review: Epigenetics by Lyle Armstrong

January 13, 2014 Milka Rodriguez

The study of epigenetics has been around for some time, but to many it is still a relatively new field of research. Not that much is written about it or easy to reference on the web. That’s why we were thrilled when Garland Science announced its newest publication, Epigenetics by Lyle Armstrong, PhD, Newcastle University. This easy to follow and well-written scientific textbook brings together the structure and machinery of epigenetic modification, how epigenetic modification controls cellular functions, and the [more…]

Stem/Early Progenitor Cell Commitment is Directed by Hydroxymethylation at Gene Regulatory Regions During Erythropoiesis

January 7, 2014 Milka Rodriguez

Hematopoietic stem cells (HSCs) are rare bone marrow cells that have self-renewal capability and are multipotent. Upon differentiation, HSCs become progressively lineage-committed and give rise to different mature blood cells. This process involves extrinsic and intrinsic signals that are strongly influenced by the stem cell microenvironment.  Furthermore, differentiation involves silencing of self-renewal genes and induction of a specific transcriptional program. It is not known how epigenetic modifications influences stem cell differentiation and commitment and what specific role these modifications may [more…]

mRNA Stability Is Regulated By Dynamic m6A RNA Methylation

December 18, 2013 Milka Rodriguez

Messenger RNA (mRNA) is a single-stranded RNA molecule that is essential in mediating the transfer of genetic information from DNA by serving as a template for protein synthesis. There are several mechanisms involved in regulating the stability of messenger RNA to influence the level and timing of protein production.  Such mechanisms include regulatory elements such as sequence elements or structural motifs that can target mRNA for degradation. Furthermore, post-transcriptional modifications such as dynamic methylation of mRNA could also be involved [more…]

Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis Revealed by High-Resolution Mapping

December 4, 2013 Milka Rodriguez

In eukaryotic RNA, the methylation of adenosine at the N6 position to form N6-methyladenosine (m6A) is the most common and abundant postsynthesis modification known. Until recently, the biological significance of this RNA modification has remained unclear due to technical and experimental limitation. These include: detection methods that are mostly limited to immunoprecipitation; low resolution mapping of m6A around methylation sites which cause precise locations to be unclear; and the lack of an experimental model for depletion of the methylation complex [more…]

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