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EpiBeat is an epigenetics resource and community for you to stay up-to-date and join the conversation on the rapidly expanding field of epigenetics. Here, you can read and discuss summaries of some of our favorite new epigenetic publications, each presented succinctly so you can keep current with the literature without having to read every paper in detail. It’s a simple way to keep with the beat in epigenetics! We also make it easy to learn more about epigenetics, get tips & tricks from the industry, ask questions about your research and get answers from other scientists. EpiBeat was created for scientists by scientists and is hosted by Zymo Research, The Epigenetics Company.
Global cytosine hypomethylation and promoter hypermethylation are characteristic in cancer, but how DNA methylation targets biological pathways and gene sets is unclear. It is hypothesized that during tumorigenesis certain pathways and gene sets are commonly dysregulated via DNA methylation across cancer types. A logistic regression-based gene set enrichment method called LRpath was established to identify ...... Read more »
Kim JH, Karnovsky A, Mahavisno V, Weymouth T, Pande M, Dolinoy DC, Rozek LS, & Sartor MA. (2012) LRpath analysis reveals common pathways dysregulated via DNA methylation across cancer types. BMC genomics, 526. PMID: 23033966
Genetic and lifestyle factors both play important roles in controlling our weight, and epigenetics has recently emerged as a powerful new tool to study the effects of lifestyle on obesity. Epigenetic mechanisms regulate heritable patterns of gene expression without changes in the DNA sequence through numerous processes, including DNA methylation and histone modification. Adolescence is ...The post Want To Lose More Weight With Less Effort? Epigenetics Can Help. appeared first on EpiBeat.... Read more »
Moleres A, Campión J, Milagro FI, Marcos A, Campoy C, Garagorri JM, Gómez-Martínez S, Martínez JA, Azcona-Sanjulián MC, & Martí A. (2013) Differential DNA methylation patterns between high and low responders to a weight loss intervention in overweight or obese adolescents: the EVASYON study. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 27(6), 2504-12. PMID: 23475851
The mitochondria, often referred to as the “power-house” of the cell, provide a platform for energy production through glucose metabolism. As a bi-product of this, they also are the major producer of reactive oxidative species. Mitochondria also play other important physiological roles, such as calcium homeostasis and aid in the regulation of cell death through ...
The post The Mitochondrial Epigenetic Revolution: A New Avenue for Potential Research appeared first on EpiBeat.
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Chestnut BA, Chang Q, Price A, Lesuisse C, Wong M, & Martin LJ. (2011) Epigenetic regulation of motor neuron cell death through DNA methylation. The Journal of neuroscience : the official journal of the Society for Neuroscience, 31(46), 16619-36. PMID: 22090490
Manev H, Dzitoyeva S, & Chen H. (2012) Mitochondrial DNA: A Blind Spot in Neuroepigenetics. Biomolecular concepts, 3(2), 107-115. PMID: 22639700
Shock LS, Thakkar PV, Peterson EJ, Moran RG, & Taylor SM. (2011) DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proceedings of the National Academy of Sciences of the United States of America, 108(9), 3630-5. PMID: 21321201
Wong M, Gertz B, Chestnut BA, & Martin LJ. (2013) Mitochondrial DNMT3A and DNA methylation in skeletal muscle and CNS of transgenic mouse models of ALS. Frontiers in cellular neuroscience, 279. PMID: 24399935
Cigarette smoking leads to some of the most preventable causes of death and illness in the world. The Centers for Disease Control (CDC) in the United States has reported that there are approximately 440,000 deaths due to smoking each year, and an additional 49,000 deaths due to secondhand smoke. Roughly 600 chemicals are found in ...The post Cigarette Smoking and Epigenetics: DNA Methylation Differences Between Ethnic Groups appeared first on EpiBeat.... Read more »
Elliott HR, Tillin T, McArdle WL, Ho K, Duggirala A, Frayling TM, Davey Smith G, Hughes AD, Chaturvedi N, & Relton CL. (2014) Differences in smoking associated DNA methylation patterns in South Asians and Europeans. Clinical epigenetics, 6(1), 4. PMID: 24485148
The field of epigenetics plays a key role in multiple developmental diseases and processes. When dealing with infertility issues, DNA methylation should be looked at as a potential factor. Approximately 1% of infertile couples experience Recurrent Spontaneous Abortion (RSA), defined as the miscarriage of two or more pregnancies before 20 weeks of gestation. Limited studies ...... Read more »
Rotondo JC, Bosi S, Bazzan E, Di Domenico M, De Mattei M, Selvatici R, Patella A, Marci R, Tognon M, & Martini F. (2012) Methylenetetrahydrofolate reductase gene promoter hypermethylation in semen samples of infertile couples correlates with recurrent spontaneous abortion. Human reproduction (Oxford, England), 27(12), 3632-8. PMID: 23010533
The discovery of induced pluripotent stem cells (iPSCs) and the creation of clinically relevant cell types derived from them, have been great leaps toward the implementation of stem cell based therapies and disease models. But in recent years, concerns have risen about iPSCs “remembering” their original cell types and favoring differentiation towards their origins. This ...The post iPSC Epigenetic Memory: One more Roadblock for Regenerative Medicine? appeared first on EpiBeat.... Read more »
Roessler R, Smallwood SA, Veenvliet JV, Pechlivanoglou P, Peng SP, Chakrabarty K, Groot-Koerkamp MJ, Pasterkamp RJ, Wesseling E, Kelsey G.... (2014) Detailed Analysis of the Genetic and Epigenetic Signatures of iPSC-Derived Mesodiencephalic Dopaminergic Neurons. Stem cell reports, 2(4), 520-33. PMID: 24749075
Bisulfite conversion is one of the most popular and powerful methods available to study cytosine methylation in DNA (also known as 5-methylcytosine or 5-mC). The use of sodium bisulfite to convert unmethylated cytosines to uracil was first reported in 1970 by two groups independently, Shapiro et al. at New York University and Hayatsu et al. ...... Read more »
Hayatsu H, Wataya Y, & Kazushige K. (1970) The addition of sodium bisulfite to uracil and to cytosine. Journal of the American Chemical Society, 92(3), 724-6. PMID: 5411063
Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, & Paul CL. (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proceedings of the National Academy of Sciences of the United States of America, 89(5), 1827-31. PMID: 1542678
Gerhard A. Coetzee, Wange Lu, Peggy Farnham USC Genome-wide association studies (GWAS) have revealed numerous single-nucleotide polymorphisms (SNPs) where allelic frequencies differ between cases and controls of many complex diseases (NHGRI GWA Catalog). In the last decade 6,696 genetic associations of 598 traits have been reported in 16,770 papers (up to 2013). Despite these impressive ...
The post SNP-SNP here, SNP-SNP there, everywhere a SNP-SNP, old McDonald had a GWAS…… appeared first o........ Read more »
Hazelett DJ, Rhie SK, Gaddis M, Yan C, Lakeland DL, Coetzee SG, Ellipse/GAME-ON consortium, Practical consortium, Henderson BE, Noushmehr H.... (2014) Comprehensive functional annotation of 77 prostate cancer risk loci. PLoS genetics, 10(1). PMID: 24497837
Eeles RA, Olama AA, Benlloch S, Saunders EJ, Leongamornlert DA, Tymrakiewicz M, Ghoussaini M, Luccarini C, Dennis J, Jugurnauth-Little S.... (2013) Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. Nature genetics, 45(4), 385. PMID: 23535732
Coetzee SG, Rhie SK, Berman BP, Coetzee GA, & Noushmehr H. (2012) FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic acids research, 40(18). PMID: 22684628
1 in 5. That is the statistic for Iraq and Afghanistan war veterans that have been diagnosed with Post-Traumatic Stress Disorder (PTSD), according to the Department of Veteran Affairs. PTSD is a severe psychological condition that can develop after witnessing traumatic events, and its symptoms include disturbing flashbacks, anxiety, distress, and numbing of the memory ...The post Connecting Epigenetics and Memory to PTSD appeared first on EpiBeat.... Read more »
Rudenko A, Dawlaty MM, Seo J, Cheng AW, Meng J, Le T, Faull KF, Jaenisch R, & Tsai LH. (2013) Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron, 79(6), 1109-22. PMID: 24050401
There is now mounting evidence that diet and other environmental factors can have widespread and long-lasting influences on a developing fetus. Historically, folic acid supplementation is recommended to pregnant mothers as a means to prevent developmental disorders and birth defects. However, there is still no clear understanding how such supplementation may influence a developing child’s ...The post Maternal Diet Affects DNA Methylation Patterns in Offspring appeared first on EpiBeat.... Read more »
Barua S, Kuizon S, Chadman KK, Flory MJ, Brown WT, & Junaid MA. (2014) Single-base resolution of mouse offspring brain methylome reveals epigenome modifications caused by gestational folic acid. Epigenetics , 7(1), 3. PMID: 24484737
Many scientists are hopeful that studying aberrant epigenetic patterns will help us find promising biomarkers for early diagnosis and prognosis of carcinogenesis. Among such markers, there has recently been heightened interest in 5-hydroxymethylcytosine (5-hmC), which is an enzymatically-modified form of 5-methylcytosine (5-mC). A group of researchers in Europe investigated changes in 5-mC as well as ...The post DNA Hydroxymethylation as an Up-and-Coming Epigenetic Biomarker for Liver Cancer........ Read more »
Thomson JP, Hunter JM, Lempiäinen H, Müller A, Terranova R, Moggs JG, & Meehan RR. (2013) Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver. Nucleic acids research, 41(11), 5639-54. PMID: 23598998
MicroRNAs (miRNAs) are single-stranded RNA molecules 18-24 bases in length that are important for the regulation of many biological processes by posttranscriptionally interfering with gene expression. MiRNAs generally regulate gene expression by either facilitating mRNA degradation or repressing translation. Generation of the mature and active form of miRNAs requires the cleavage of pre-miRNA molecules by ...... Read more »
Xhemalce B, Robson SC, & Kouzarides T. (2012) Human RNA methyltransferase BCDIN3D regulates microRNA processing. Cell, 151(2), 278-88. PMID: 23063121
During an adaptive immune response, naive CD8 T cells differentiate into antigen-specific effector cells that release cytotoxic proteins and rapidly proliferate to kill infected cells. When the pathogen has cleared, the majority of effector cells undergo apoptosis while a selected pool becomes memory cells. The differentiation process from naive to memory cells is known to ...The post DNA Methylation Regulates Differentiation of Naive Immune Cells into Effector Cells appeared first on EpiBeat.... Read more »
Scharer CD, Barwick BG, Youngblood BA, Ahmed R, & Boss JM. (2013) Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function. Journal of immunology (Baltimore, Md. : 1950). PMID: 23956425
Itching of the eyes and nose, nasal congestion, sneezing, and runny nose are some symptoms of Allergic Rhinitis, better known as hay fever or seasonal allergies, which affects ~30% of people worldwide. In a recent PLOS Genetics publication, scientists from Sweden and the US investigated genome-wide DNA methylation and gene expression changes in CD4+ T-cells ...The post New Year, New Hay Fever Season, and New Role for Epigenetics in Allergies appeared first on EpiBeat.... Read more »
Nestor CE, Barrenäs F, Wang H, Lentini A, Zhang H, Bruhn S, Jörnsten R, Langston MA, Rogers G, Gustafsson M.... (2014) DNA Methylation Changes Separate Allergic Patients from Healthy Controls and May Reflect Altered CD4( ) T-Cell Population Structure. PLoS genetics, 10(1). PMID: 24391521
While most of us will be hopping on the scale and hoping for a relatively low weight this holiday season, poultry farmers will be weighing their birds hoping for just the opposite. Chickens are the most commonly eaten poultry in the world and those bred for consumption are categorized as fryers, broilers, or roasters. They ...The post Chicken Little Can Blame It On Her Epigenetics! appeared first on EpiBeat.... Read more »
Hu Y, Xu H, Li Z, Zheng X, Jia X, Nie Q, & Zhang X. (2013) Comparison of the genome-wide DNA methylation profiles between fast-growing and slow-growing broilers. PloS one, 8(2). PMID: 23441189
As an organism ages, cells and tissues differentiate and change. These changes can include accumulation of DNA mutations, alterations to telomeres, decay of cellular and tissue structures, and changes in gene expression. Both differentiation of tissues and age effects are at least partially caused by epigenetic modifications of the genome, including DNA methylation, which is ...The post Wanna Be Forever 21? It May Be Possible By Resetting Your DNA Methylation Age Clock appeared first on EpiBeat......... Read more »
Horvath S. (2013) DNA methylation age of human tissues and cell types. Genome biology, 14(10). PMID: 24138928
The potential use of induced pluripotent stem cells in medicine has the power to completely revolutionize the way physicians treat human diseases. Imagine the possibility of treating diseased or damaged tissue by taking a patient’s own cells from an unaffected tissue, and turning them into healthy cells to replace the bad ones. This idea has ...The post Somatic Cells Turned Pluripotent by Acid Treatment – Major Breakthrough, Or Too Good To Be True? appeared first on EpiBeat.... Read more »
Obokata H, Wakayama T, Sasai Y, Kojima K, Vacanti MP, Niwa H, Yamato M, & Vacanti CA. (2014) Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature, 505(7485), 641-7. PMID: 24476887
Bisphenol A (BPA) is an industrial chemical that is present in many consumer products, including plastic bottles and other food and beverage containers. Although BPA has been used routinely since the 1960s, exposure to BPA has recently gained a lot of attention due to its proposed effect on brain development. Previous studies have reported that ...... Read more »
Yeo M, Berglund K, Hanna M, Guo JU, Kittur J, Torres MD, Abramowitz J, Busciglio J, Gao Y, Birnbaumer L.... (2013) Bisphenol A delays the perinatal chloride shift in cortical neurons by epigenetic effects on the Kcc2 promoter. Proceedings of the National Academy of Sciences of the United States of America, 110(11), 4315-20. PMID: 23440186
Restriction enzymes are critical tools that have aided researchers in making scientific breakthroughs for decades. The discovery and characterization of the 5-methylcytosine (5-mC) DNA modification also resulted in the unearthing of 5-mC-sensitive or -dependent restriction enzymes, however these enzymes are generally not capable of distinguishing 5-mC from 5-hydroxymethylcytosine (5-hmC). Although the biological function of 5-hmC ...... Read more »
Borgaro JG, & Zhu Z. (2013) Characterization of the 5-hydroxymethylcytosine-specific DNA restriction endonucleases. Nucleic acids research, 41(7), 4198-206. PMID: 23482393
Ah the fall…the leaves are changing color, you can feel a chill in the air, the days are getting shorter, and your libido is decreasing…wait, what?!? Well, maybe not in humans, but seasonal changes that affect the length of day, or photoperiod, can have a profound effect on reproductive behavior and hormone expression in seasonal ...The post Fall is in the Air: DNA Methylation Regulates Seasonal Hormonal Changes in Hamsters. appeared first on EpiBeat.... Read more »
Stevenson TJ, & Prendergast BJ. (2013) Reversible DNA methylation regulates seasonal photoperiodic time measurement. Proceedings of the National Academy of Sciences of the United States of America, 110(41), 16651-6. PMID: 24067648
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