25 posts · 2,738 views
EpiBeat is a new 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.
Kevin B.
25 posts
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- June 14, 2013
- 07:13 PM
- 61 views
Yet Another Reason to Thank Dad This Father’s Day! Evidence for Paternally-Inherited Epigenetic Modifications
Maternal health during gestation and prenatal conditions are well documented as having profound effects on health and development of a baby after birth. The mechanisms behind many of these effects are attributed to epigenetic changes that take place in utero. More recently, pre-fertilization maternal health has been also been implicated in affecting development of babies ...The post Yet Another Reason to Thank Dad This Father’s Day! Evidence for Paternally-Inherited Epigenetic Modifications a........ Read more »
Mychasiuk R, Harker A, Ilnytskyy S, & Gibb R. (2013) Paternal stress prior to conception alters DNA methylation and behaviour of developing rat offspring. Neuroscience, 100-5. PMID: 23531434
- June 10, 2013
- 05:42 PM
- 32 views
Old Dog, New Tricks? Cytosine Methylation in Long Non-Coding RNAs
Cytosine methylation (5-mC) in DNA is very common, and is generally associated with repression of gene expression. DNA methylation was the first discovered type of epigenetic modification and remains one of the most actively investigated epigenetic processes, especially with respect to its use as a valuable biomarker for cancer and other human diseases. The presence ...The post Old Dog, New Tricks? Cytosine Methylation in Long Non-Coding RNAs appeared first on .... Read more »
Amort T, Soulière MF, Wille A, Jia XY, Fiegl H, Wörle H, Micura R, & Lusser A. (2013) Long non-coding RNAs as targets for cytosine methylation. RNA biology, 10(6). PMID: 23595112
- May 30, 2013
- 08:43 PM
- 37 views
The Basics of Bisulfite Conversion for DNA Methylation Analysis
by Kevin B. and Ryan K. in EpiBeat
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
- May 24, 2013
- 03:26 PM
- 27 views
A State of Dis”array”: Two Recent Studies Highlight Common Problems Associated with Using Illumina’s 450k Array for Epigenetics Research
by Keith B. and Kevin B. in EpiBeat
Epigenetic analysis is one of the hottest areas in all of biological research. Covalent modifications to DNA, proteins, and RNA, without changing the primary sequence of these molecules, are known to epigenetically regulate numerous cellular processes and contribute to many important human disease phenotypes. One of the most intensely studied epigenetic modifications is DNA methylation ...... Read more »
Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S, Hudson TJ, & Weksberg R. (2013) Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics : official journal of the DNA Methylation Society, 8(2), 203-9. PMID: 23314698
Harper KN, Peters B, & Gamble MV. (2013) Batch Effects and Pathway Analysis: Two Potential Perils in Cancer Studies Involving DNA Methylation Array Analysis. Cancer epidemiology, biomarkers . PMID: 23629520
- May 16, 2013
- 05:02 PM
- 46 views
Does Loss of DNA Methylation and Hydroxymethylation in the Brain Lead to Loss of Memory?
5-methylcytosine (5-mC) and 5-hydroxymethycytosine (5-hmC) are two major epigenetic modifications of DNA. Dynamic changes in 5-mC and 5-hmC levels are tightly regulated and impact neural cell development, differentiation, and other biological functions. Deregulation of 5-mC and 5-hmC has also been implicated in various human diseases. However, whether 5-mC and 5-hmC are involved in aging-related neurodegenerative ...... Read more »
Chouliaras L, Mastroeni D, Delvaux E, Grover A, Kenis G, Hof PR, Steinbusch HW, Coleman PD, Rutten BP, & van den Hove DL. (2013) Consistent decrease in global DNA methylation and hydroxymethylation in the hippocampus of Alzheimer's disease patients. Neurobiology of aging. PMID: 23582657
Mastroeni D, McKee A, Grover A, Rogers J, & Coleman PD. (2009) Epigenetic differences in cortical neurons from a pair of monozygotic twins discordant for Alzheimer's disease. PloS one, 4(8). PMID: 19672297
- May 10, 2013
- 07:49 PM
- 60 views
Digging for Answers: The Potential of Curcumin as an Epigenetic Therapeutic Drug to Treat Cancer
by Karolyn G. in EpiBeat
The brilliant golden powder of turmeric is best known as the main spice in curry, but has also been widely used for many years in Eastern traditional medicines as an anti-inflammatory agent. Turmeric has been used as an alleviator for arthritis, stomach pain, and cancer, among many other health issues. The healing properties of turmeric ...... Read more »
Link A, Balaguer F, Shen Y, Lozano JJ, Leung HC, Boland CR, & Goel A. (2013) Curcumin modulates DNA methylation in colorectal cancer cells. PloS one, 8(2). PMID: 23460897
- May 3, 2013
- 05:33 PM
- 58 views
Chop It While It’s Hot! An Enzyme-Free Alternative to Hydroxymethylated DNA Detection
by Xueguang S. in EpiBeat
5-hydroxymethylcytosine (5-hmC) has been widely studied in many biological contexts, but the precise mechanistic functions of this epigenetic modification remain largely unknown. Some evidence suggests that 5-hmC may be an intermediate in the process of DNA demethylation because it can be further oxidized to form 5-formylcytosine (5-fC) and 5-carboxylcytosine (5-caC), which are recognized and eliminated ...... Read more »
Mao W, Hu J, Hong T, Xing X, Wang S, Chen X, & Zhou X. (2013) A convenient method for selective detection of 5-hydroxymethylcytosine and 5-formylcytosine sites in DNA sequences. Organic . PMID: 23629475
- May 1, 2013
- 05:21 PM
- 56 views
Cut It Out! Characterization of PvuRts1I Homologues and Hydroxymethylated DNA Digestion
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
- April 30, 2013
- 01:32 PM
- 83 views
Down the Drain? 1MNA Acts as a Potent ‘Methylation Sink’ in Cancer Cells
The cancer field consistently proves to be one of the most critical areas for investigations into mechanisms governing tight epigenetic regulation, as nearly all types of cancers demonstrate misregulated epigenetic patterns. Most studies focus on the final epigenomic landscape in terms of histone and DNA modifications and methylomes; relatively few, however, have placed as much ...... Read more »
Ulanovskaya OA, Zuhl AM, & Cravatt BF. (2013) NNMT promotes epigenetic remodeling in cancer by creating a metabolic methylation sink. Nature chemical biology, 9(5), 300-6. PMID: 23455543
- April 26, 2013
- 08:20 PM
- 96 views
Patenting Genes: Human Invention or Product of Nature?
Leading up to the debate on gene patenting, this week marks the 60th anniversary of the discovery of the DNA double helix. On April 25th, 1953 the work of James Watson, Francis Crick, Maurice Wilkins, Rosalind Franklin and other colleagues on the structure of DNA was published in Nature. Without this milestone achievement, we wouldn’t ...... Read more »
Hall JM, Lee MK, Newman B, Morrow JE, Anderson LA, Huey B, & King MC. (1990) Linkage of early-onset familial breast cancer to chromosome 17q21. Science (New York, N.Y.), 250(4988), 1684-9. PMID: 2270482
WATSON JD, & CRICK FH. (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature, 171(4356), 737-8. PMID: 13054692
- April 17, 2013
- 03:18 PM
- 98 views
Put down that water bottle! BPA Exposure Alters Epigenetic Profile in Neurons
by YAP C.C., PH.D in EpiBeat
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
- April 9, 2013
- 07:42 PM
- 95 views
You can take a gene out of context, but can you take context out of a gene?
A gene’s precise chromatin context profoundly affects its regulation. For example, genes located near nucleosomes containing acetylated histones are generally actively transcribed. By contrast, genes located near nucleosomes containing histones methylated at specific lysine residues are usually transcriptionally repressed. But is the opposite also true? Do specific gene sequences affect the surrounding epigenetic landscape when ...... Read more »
Chen M, Licon K, Otsuka R, Pillus L, & Ideker T. (2013) Decoupling epigenetic and genetic effects through systematic analysis of gene position. Cell reports, 3(1), 128-37. PMID: 23291096
- April 2, 2013
- 04:56 PM
- 210 views
Epigenetics of Cocaine Addiction: Your Brain on Drugs
The dramatic behavioral changes induced by cocaine, such as hyperactivity, are accompanied by post-translational modifications (PTMs) of histones. These modifications result in altered gene expression in the area of the brain known as the nucleus accumbens (NAc), which is associated with pleasure. Past research pointed to the use of histone deacetylase (HDAC) inhibitors as a ...... Read more »
Kennedy PJ, Feng J, Robison AJ, Maze I, Badimon A, Mouzon E, Chaudhury D, Damez-Werno DM, Haggarty SJ, Han MH.... (2013) Class I HDAC inhibition blocks cocaine-induced plasticity by targeted changes in histone methylation. Nature neuroscience, 16(4), 434-40. PMID: 23475113
- March 11, 2013
- 07:30 PM
- 196 views
Dietary Epigenetics, Chemoprevention, and Green Tea Cupcakes
EpiBeat is excited to have Nikki write this guest post for us! Nikki started her blog Scientifically Delicious about a year ago to write about the intersection between two of her passions: science and cooking. She uses her background in biology to explain recent news and findings about food and specific ingredients in a fun ...... Read more »
Fang MZ, Wang Y, Ai N, Hou Z, Sun Y, Lu H, Welsh W, & Yang CS. (2003) Tea polyphenol (-)-epigallocatechin-3-gallate inhibits DNA methyltransferase and reactivates methylation-silenced genes in cancer cell lines. Cancer research, 63(22), 7563-70. PMID: 14633667
- March 7, 2013
- 06:37 PM
- 180 views
Soaking up the Competition – Circular RNAs as Molecular Sponges for miRNAs
Numerous families of non-coding RNAs have been identified in mammalian cells, including lncRNA, miRNA, siRNA, and piRNA. Another type of RNA called circular RNA (circRNA) has remained a mysterious class, as the exact function of these molecules has not been described. Usually, circRNAs result from spicing events and have been identified in plants, animals, and ...... Read more »
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M.... (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. PMID: 23446348
- February 27, 2013
- 03:15 PM
- 150 views
Starting from Scratch: DNA Methylation Marks Erased Through 5-hmC in Primordial Germ Cells
A growing body of evidence indicates that ancestral environmental factors can influence the physiology and behavior of the offspring, a process known as epigenetic inheritance. However, in each generation the epigenetically inherited modifications are thought to be erased in cells called primordial germ cells (PGCs), the precursors to sperm and eggs, leaving scientists to question ...... Read more »
Hackett JA, Sengupta R, Zylicz JJ, Murakami K, Lee C, Down TA, & Surani MA. (2013) Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science (New York, N.Y.), 339(6118), 448-52. PMID: 23223451
- February 1, 2013
- 12:47 PM
- 81 views
Reviewing the Roles of Long noncoding RNAs in Epigenetic Processes
Although RNA has traditionally been thought to act primarily as an intermediate between DNA and protein in the central dogma of molecular biology, these important molecules have received more attention in the last few years for their ability to carry out a wide variety of biological processes, including epigenetic regulation of gene expression. Recent studies ...... Read more »
Lee JT. (2012) Epigenetic regulation by long noncoding RNAs. Science (New York, N.Y.), 338(6113), 1435-9. PMID: 23239728
- January 25, 2013
- 06:46 PM
- 96 views
A new web-based tool for high-throughput DNA methylation pathway analysis of multiple cancer types
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
- January 16, 2013
- 04:37 PM
- 141 views
The Importance of Epigenetic Modification of RNA in miRNA Maturation and Breast Cancer
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
- January 11, 2013
- 01:46 PM
- 179 views
Does defective binding of 5-hmC by MeCP2 contribute to Rett syndrome?
DNA methylation is an epigenetic modification that plays an important role in gene expression. Aberrant changes of DNA methylation in the genome are associated with many epigenetic-related neurological disorders. However, the mechanism by which DNA methylation affects chromatin structure and gene expression is not completely understood. Methyl-CpG-binding protein 2, (MeCP2), was first identified by its ...... Read more »
Mellén M, Ayata P, Dewell S, Kriaucionis S, & Heintz N. (2012) MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System. Cell, 151(7), 1417-30. PMID: 23260135
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