59 posts · 22,309 views
E3 is a social network for epigenetics experts, set up to facilitate progress in this frontier field. The E3 blog promotes discussions and collaborations in the community, and it helps experts--you--keep up with the latest epigenetics news, techniques, organizations, conferences and seminars.
New England Biolabs is well known for its extensive in house research programs - 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.... Read more »
Sun Z, Terragni J, Borgaro JG, Liu Y, Yu L, Guan S, Wang H, Sun D, Cheng X, Zhu Z.... (2013) High-resolution enzymatic mapping of genomic 5-hydroxymethylcytosine in mouse embryonic stem cells. Cell reports, 3(2), 567-76. PMID: 23352666
Recent news in cancer research points to the importance of epigenetics and cell signalling in the "war on cancer".... Read more »
Watson J. (2013) Oxidants, antioxidants and the current incurability of metastatic cancers. Open biology, 3(1), 120144. PMID: 23303309
Finally there’s research comparing the epigenetic marks of human brain neurons to those of other primates, and it’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?... Read more »
Shulha HP, Crisci JL, Reshetov D, Tushir JS, Cheung I, Bharadwaj R, Chou HJ, Houston IB, Peter CJ, Mitchell AC.... (2012) Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS biology, 10(11). PMID: 23185133
Epigenetic pathways among those ID'd as regulated by Sirtuin3 in mitochondria during calorie restriction reprogramming.... Read more »
Hebert AS, Dittenhafer-Reed KE, Yu W, Bailey DJ, Selen ES, Boersma MD, Carson JJ, Tonelli M, Balloon AJ, Higbee AJ.... (2012) Calorie Restriction and SIRT3 Trigger Global Reprogramming of the Mitochondrial Protein Acetylome. Molecular cell. PMID: 23201123
Epigenetic analysis shows new roles for restriction modification methyltransferases in developing pathogenic bacteria.... Read more »
Fang G, Munera D, Friedman DI, Mandlik A, Chao MC, Banerjee O, Feng Z, Losic B, Mahajan MC, Jabado OJ.... (2012) Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing. Nature biotechnology. PMID: 23138224
Research advance put forth by scientists from New England Biolabs & Pacific Biosciences™ demonstrates how the 3rd generation SMRT DNA sequencing system is used to explore bacterial methylomes.... Read more »
Hint: using their methylomes!... Read more »
Ruiz S, Diep D, Gore A, Panopoulos AD, Montserrat N, Plongthongkum N, Kumar S, Fung HL, Giorgetti A, Bilic J.... (2012) Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells. Proceedings of the National Academy of Sciences of the United States of America, 109(40), 16196-201. PMID: 22991473
New method invented to prioritize cancer SNPs to demonstrate those essential to disease profiles.... Read more »
Cowper-Sal Lari R, Zhang X, Wright JB, Bailey SD, Cole MD, Eeckhoute J, Moore JH, & Lupien M. (2012) Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nature genetics. PMID: 23001124
Researchers describe epigenetic and transcription factor relationships in cellular differentiation, in Nucleic Acids Research paper. ... Read more »
Sérandour AA, Avner S, Oger F, Bizot M, Percevault F, Lucchetti-Miganeh C, Palierne G, Gheeraert C, Barloy-Hubler F, Péron CL.... (2012) Dynamic hydroxymethylation of deoxyribonucleic acid marks differentiation-associated enhancers. Nucleic acids research. PMID: 22730288
World Anti-Doping Agency (WADA) currently uses the biological passport monitoring system. WADA also funds R&D of direct monitoring methods for gene doping, an emerging concern...including microRNA studies. ... Read more »
Ancient history breast cancer prognosis and a new method contributes epigenetics based biomarkers.... Read more »
ana Jeschke, Leander Van Neste, Sabine C. Glöckner, Mashaal Dhir, Marilia Freitas Calmon, Valérie Deregowski, Wim Van Criekinge, Ilse Vlassenbroeck, Alexander Koch, Timothy A. Chan.... (2012) Biomarkers for detection and prognosis of breast cancer identified by a functional hypermethylome screen. Epigenetics. DOI: 10.4161/epi.20445
A great interview with Manel Esteller, a leader in Epigenetics, regarding our methylomes and aging.... Read more »
Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, Diez J, Sanchez-Mut JV, Setien F, Carmona FJ.... (2012) Distinct DNA methylomes of newborns and centenarians. Proceedings of the National Academy of Sciences of the United States of America, 109(26), 10522-7. PMID: 22689993
Acute myeloid leukemia bone marrow samples analysed with an enhanced method of reduced representational bisulfite sequencing. Hoping this will translate into generating AML treatment plans.... Read more »
Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL.... (2012) Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS genetics, 8(6). PMID: 22737091
O-GlcNAcylation is part of the "histone code" and interacts with other epigenetic machinery, to link our diet to some diseases. Plus a Stephen Wright quote, just for fun.
... Read more »
Hanover, J., Krause, M., & Love, D. (2012) Post-translational modifications: Bittersweet memories: linking metabolism to epigenetics through O-GlcNAcylation. Nature Reviews Molecular Cell Biology, 13(5), 312-321. DOI: 10.1038/nrm3334
Facinating PNAS paper describing an epigenetic phenotype requiring both embryonic exposure to the crop fungicide Vinclozolin,and adolescent exposure to stress. This work was a collaborative effort between the Michael Skinner and David Crews groups. ... Read more »
Crews, D., Gillette, R., Scarpino, S., Manikkam, M., Savenkova, M., & Skinner, M. (2012) Epigenetic transgenerational inheritance of altered stress responses. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1118514109
Sure, single-cell sorting devices are cool and useful and all, but Harold Craighead’s lab at the Cornell University Department of Biomedical Engineering is developing a microfluidic device that can separate individual methylated DNA fragments from a single cell’s total genetic content. In a lab test reported in their recent open-access paper (pdf) in Proceedings of the National Academy of Sciences, the team used the device to separate methylated plasmids from among 11 femtograms of m........ Read more »
Cipriany, B., Murphy, P., Hagarman, J., Cerf, A., Latulippe, D., Levy, S., Benitez, J., Tan, C., Topolancik, J., Soloway, P.... (2012) Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1117549109
A team out of the Chinese Academy of Sciences has reported both a new dual-fluorescent reporter system, and an insight on a suspected general phenomenon of functionally matched viral and cellular microRNA in viral-host interactions. ... Read more »
You X, Zhang Z, Fan J, Cui Z, & Zhang XE. (2012) Functionally Orthologous Viral and Cellular MicroRNAs Studied by a Novel Dual-Fluorescent Reporter System. PloS one, 7(4). PMID: 22558366
Genomewide single nucleotide resolution of hydroxymethylation is now possible, with an innovative method added to bisulfite sequencing! Also, Epigenetic plasticity, is the 5hmC mark a "pause button"? ... Read more »
Booth, M., Branco, M., Ficz, G., Oxley, D., Krueger, F., Reik, W., & Balasubramanian, S. (2012) Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution. Science. DOI: 10.1126/science.1220671
No kidding. Roberto Ferrari and colleagues at UCLA are studying DNA viruses that can change the epigenetic landscape of infected cells to make them more like cancer and less like their old selves. Adenovirus e1a introduces “small e1a oncoprotein” to change fibroblast histone marks — at least, in culture. The virus erases a cell’s previous identity, and apparently alters the cell cycle for repeated cell divisions.... Read more »
Ferrari, R., Su, T., Li, B., Bonora, G., Oberai, A., Sasidharan, R., Chan, Y., Berk, A., Pellegrini, M., & Kurdistani, S. (2012) Reorganization of the host epigenome by a viral oncogene. Genome Research. DOI: 10.1101/gr.132308.111
An example of how twin studies provide unique epigenetic research opportunies...with Austism research in mind.... Read more »
Gao Y, He Z, Wang Z, Luo Y, Sun H, Zhou Y, Huang L, Li M, Fang Q, & Jiang S. (2012) Increased Expression and Altered Methylation of HERVWE1 in the Human Placentas of Smaller Fetuses from Monozygotic, Dichorionic, Discordant Twins. PloS one, 7(3). PMID: 22457770
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