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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.
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
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
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
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
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
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
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 »
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
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
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
Autism Spectrum Disorder (ASD) encompasses a broad range of social and developmental delays with onset before three years of age. Characteristics of children with ASD include restricted and repetitive behavior, communication deficits, and social impairments. ASD is the result of neurodevelopmental disorders, but genetics cannot fully explain the onset. Although some cases have been linked ...... Read more »
Kong SW, Collins CD, Shimizu-Motohashi Y, Holm IA, Campbell MG, Lee IH, Brewster SJ, Hanson E, Harris HK, Lowe KR.... (2012) Characteristics and predictive value of blood transcriptome signature in males with autism spectrum disorders. PloS one, 7(12). PMID: 23227143
The role of DNA methylation in healthy embryonic and postnatal neurological development has been well established in recent years. In addition to 5-methylcytosine (5-mC), high levels of 5-hydroxymethylcystosine (5-hmC) have also been detected in brain and other neurological tissue. Several studies have shown that defects in the ten-eleven translocation (TET) proteins, which catalyze the conversion ...... Read more »
Wang T, Pan Q, Lin L, Szulwach KE, Song CX, He C, Wu H, Warren ST, Jin P, Duan R.... (2012) Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum. Human molecular genetics, 21(26), 5500-10. PMID: 23042784
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
Histone tails that are exposed at the nucleosomal surface are targets for a multitude of covalent modifications, such as acetylation, methylation, and phosphorylation. These post-translational modifications have been shown to function as a ‘histone code’ that coordinates the recruitment of effector proteins and regulates chromatin structure, gene expression, and genome stability. DNA methylation of CpG ...... Read more »
Rothbart SB, Krajewski K, Nady N, Tempel W, Xue S, Badeaux AI, Barsyte-Lovejoy D, Martinez JY, Bedford MT, Fuchs SM.... (2012) Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation. Nature structural , 19(11), 1155-60. PMID: 23022729
The chemotherapeutic drug decitabine (DAC) and its analog azacitidine (AZA) are FDA approved to treat cancers of the blood, such as myelodysplastic syndromes and certain types of leukemias. In high concentrations, DAC and AZA cause acute DNA damage followed by cell death. Currently, both drugs are limited to treatment of blood cancers, since the high ...... Read more »
Tsai HC, Li H, Van Neste L, Cai Y, Robert C, Rassool FV, Shin JJ, Harbom KM, Beaty R, Pappou E.... (2012) Transient low doses of DNA-demethylating agents exert durable antitumor effects on hematological and epithelial tumor cells. Cancer cell, 21(3), 430-46. PMID: 22439938
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