Editor-run page for the journal Epigenetics (published by T&F Group). Our goal is to establish Epigenetics as the lead journal in the field.
Epigenetics is the first peer-reviewed, Medline-indexed journal to focus exclusively in the fascinating field of epigenetics. As a multidisciplinary journal, Epigenetics publishes original research and scholarly review articles covering this scientific discipline in its broadest interpretation, providing a forum where epigenetics mechanisms involved in medical and biological processes can be discu
ssed. Published once a month, in print and online, Epigenetics strives to offer rapid turnaround times from submission through peer-review to publication.
Epigenetics is now only accepting manuscripts for Open Access Publication! Read more about it here! https://think.taylorandfrancis.com/epigenetics-journal/
Epigenetics publishes research into heritable changes in gene expression caused by mechanisms other than DNA sequence in biological systems.
New Open Access article out from Rocío Melissa Rivera's group on ART-induced large offspring syndrome DNA methylome.
(2022). Spontaneous and ART-induced large offspring syndrome: similarities and differences in DNA methylome. Epigenetics. Ahead of Print.
Some genes are rapidly methylated in domesticated fish changing them from "wild" to "farmed".
(2022). Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype. Epigenetics. Ahead of Print.
Even the areas of white matter that appear normal in MS patients, have highly altered glial methylomes.
(2022). DNA methylation changes in glial cells of the normal-appearing white matter in Multiple Sclerosis patients. Epigenetics. Ahead of Print.
Hypermethylation correlates with cisplatin resistance in testicular germ cell tumors (Fazal et al) https://www.tandfonline.com/doi/full/10.1080/15592294.2020.1834926
Hypermethylation and global remodeling of DNA methylation is associated with acquired cisplatin resistance in testicular germ cell tumors. Epigenetics. Accepted 29 September 2020.
Malousi et al demonstrate the role of cytosine hydroxymethylation in recognition of G-quadruplex/palindrome sequences and how the balance of these epigenetic elements is lost in hepatocellular carcinoma. https://doi.org/10.1080/15592294.2020.1805693
(2020). In silico structural analysis of sequences containing 5-hydroxymethylcytosine reveals its potential as binding regulator for development, ageing and cancer-related transcription factors. Epigenetics. Ahead of Print.
There have been many great reads posted recently (https://www.tandfonline.com/action/showAxaArticles?journalCode=kepi20), including this article about the activation of POTE genes in ovarian cancer from the Karpf lab (https://www.tandfonline.com/doi/full/10.1080/15592294.2019.1581590)!
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How do super enhancers compare to stretch enhancers when it comes to epigenetic and transcriptomic activity? Khan et al found that super enhancers really are super! Please take a look at their work in the latest issue of Epigenetics! https://www.tandfonline.com/doi/abs/10.1080/15592294.2018.1514231?journalCode=kepi20
(2018). Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers. Epigenetics: Vol. 13, No. 9, pp. 910-922.
In this installment of epigenetics does what?: An epigenetic mark-based system that predicts s*x in fish! Check it out!
https://www.tandfonline.com/doi/full/10.1080/15592294.2018.1529504
(2018). Dynamic epimarks in s*x-related genes predict g***d phenotype in the European sea bass, a fish with mixed genetic and environmental s*x determination. Epigenetics: Vol. 13, No. 9, pp. 988-1011.
How do the structures of sequences neighboring clock CpGs related to age-related methylation changes? Check this out: https://doi.org/10.1080/15592294.2018.1514232.
(2018). Age-dependent methylation in epigenetic clock CpGs is associated with G-quadruplex, co-transcriptionally formed RNA structures and tentative splice sites. Epigenetics: Vol. 13, No. 8, pp. 808-821.
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Analysis of DNA methylation helps to understand the effects of environmental exposures as well as the role of epigenetics in human health. Illumina, Inc. recently replaced the HumanMethylation450 BeadChip (450K) with the EPIC BeadChip, which nearly doubles the measured CpG sites to >850,000. Although the new chip uses the same underlying technology, it is important to establish if data between the two platforms are comparable within cohorts and for meta-analyses. This article recently published in Epigenetics does just that. https://tandfonline.com/doi/full/10.1080/15592294.2018.1497386
(2018). Comparison of DNA methylation measured by Illumina 450K and EPIC BeadChips in blood of newborns and 14-year-old children. Epigenetics. Ahead of Print.
Human tumors undergo massive changes in DNA methylation. Recent studies showed that site-specific methylation of CpG sites is determined by the DNA sequence context surrounding the CpG site, which alludes to a possible mechanism for site-specific aberrant DNA methylation in cancer through DNA-binding proteins. In this paper, DNA methylation data and RNA-Seq data of breast tumors and normal tissues in the database of The Cancer Genome Atlas (TCGA) were integrated with information of DNA motifs in seven databases to find DNA-binding proteins and their binding motifs that were involved in aberrant DNA methylation in breast cancer. https://tandfonline.com/doi/full/10.1080/15592294.2018.1469894
(2018). Identification of epigenetic modulators in human breast cancer by integrated analysis of DNA methylation and RNA-Seq data. Epigenetics. Ahead of Print.
The glioma stem cell and glioblastoma subtype–specific DNA methylation signatures described in this study could be useful for refining glioblastoma sub-classification, improving prognostic accuracy and making therapeutic decisions. https://tandfonline.com/doi/full/10.1080/15592294.2018.1469892?scroll=top&needAccess=true
(2018). Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma. Epigenetics. Ahead of Print.
Evolving evidence links maternal stress exposure to changes in placental DNA methylation of specific genes regulating placental function that may have implications for the programming of a host of chronic disorders. Brunst et al. have implemented an epigenome-wide approach to investigate placental DNA methylation in relation to maternal experiences of traumatic and non-traumatic stressors. They found that maternal lifetime stress/trauma is associated with changes in the epigenome-wide methylation status of multiple loci in genes that have key roles in cellular processes and metabolism. https://tandfonline.com/doi/full/10.1080/15592294.2018.1497387
(2018). Cumulative lifetime maternal stress and epigenome-wide placental DNA methylation in the PRISM cohort. Epigenetics. Ahead of Print.
Did you know that fetal s*x is associated with the risk of several specific pregnancy complications related to placental function? In this article, Gong et al. studied the association between fetal s*x and placental DNA methylation by carrying out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Among other interesting findings, the authors show that the gene body of an autosomal gene, CSMD1, is differentially methylated in a s*x- and placental-specific manner, displaying s*x-specific differences in placental transcript abundance. https://tandfonline.com/doi/full/10.1080/15592294.2018.1429857
(2018). Genome-wide oxidative bisulfite sequencing identifies s*x-specific methylation differences in the human placenta. Epigenetics: Vol. 13, No. 3, pp. 228-239.
Genomic imprinting is the process of epigenetic modification whereby genes are expressed in a parent-of-origin dependent manner; it plays an important role in normal growth and development. Parthenogenetic embryos contain only the maternal genome. Parthenogenetic embryonic stem cells could be useful for studying imprinted genes. In this article human parthenogenetic induced pluripotent stem cell lines were established and their global methylation status was compared to that of biparental human induced pluripotent stem cells. This analysis is useful for identifying imprinted genes and investigating their roles in human development and diseases.
https://tandfonline.com/doi/full/10.1080/15592294.2018.1460033
(2018). Novel imprinted single CpG sites found by global DNA methylation analysis in human parthenogenetic induced pluripotent stem cells. Epigenetics. Ahead of Print.
This article presents a robust classification approach that predicts the gene-specific regulation through DNA methylation in colorectal cancer tissues with possible transition to different cancer entities. Check it out https://tandfonline.com/doi/full/10.1080/15592294.2018.1460034
Contaminated marine food, DNA methylation, and chronic disease.
The authors of this recently published article identify key environmental chemicals in cord blood associated with DNA methylation changes in a population with elevated exposure to chemical mixtures. The significant enrichment of specific X-chromosome sites in males implies potential s*x-specific epigenome responses to prenatal chemical exposures. https://www.tandfonline.com/doi/full/10.1080/15592294.2018.1445901
(2018). Identification of s*x-specific DNA methylation changes driven by specific chemicals in cord blood in a Faroese birth cohort. Epigenetics. Ahead of Print.
DNA methylation is recognized as one of several epigenetic regulators of gene expression and as potential driver of carcinogenesis through gene-silencing of tumor suppressors and activation of oncogenes. However, abnormal methylation, even of promoter regions, does not necessarily alter gene expression levels, especially if the gene is already silenced, leaving the exact mechanisms of methylation unanswered. Klett el al. here present a robust classification approach that predicts the gene-specific regulation through DNA methylation in colorectal cancer tissues with possible transition to different cancer entities.
(2018). Robust prediction of gene regulation in colorectal cancer tissues from DNA methylation profiles. Epigenetics. Ahead of Print.
Stress is something we are all too familiar with. When it comes down to a stressful situation, it seems that there are almost two types of people: those stricken by anxiety and depression, and those who keep on walking on as if nothing has happened. But what shapes such a distinction between people? One contributing factor is early-life maternal care. With over five decades of evidence, rodent models have served as an important proxy for humans, where licking and grooming of a pup by their mother mirrors the contact that a human mother provides to her baby.
Take a look at this Epigenie commentary on this recently published Epigenetics article.
Integrative analysis of DNA methylation with miRNA and gene expression reveals a genome-wide epigenomic profile in the brains of rat pups that received extra maternal care
Long noncoding RNAs (lncRNAs) are critical regulators of cell biology whose alteration can lead to the development of diseases such as cancer. The potential role of lncRNAs and their epigenetic regulation in response to platinum treatment are largely unknown. Vera et al. analyzed four paired cisplatin-sensitive/resistant non-small cell lung cancer and ovarian cancer cell lines and determined the epigenetic landscape of overlapping and cis-acting lncRNAs. Differential expression in response to therapy was observed more frequently in cis-acting than in overlapping lncRNAs, while significantly altered methylation profiles were more commonly associated with overlapping lncRNAs. These and other novel findings provide new insights into epigenetic mechanisms and acquired resistance to cisplatin that highlight specific lncRNAs, some with unknown function, that may signal strategies in epigenetic therapies. https://tandfonline.com/doi/full/10.1080/15592294.2018.1436364
(2018). An epigenomic approach to identifying differential overlapping and cis-acting lncRNAs in cisplatin-resistant cancer cells. Epigenetics. Ahead of Print.
We just passed 10K likes. Thank you for your continuous support of our journal! Let's keep spreading epigenetics knowledge! Check out recently published content online: https://tandfonline.com/toc/kepi20/0/0
Editor-run page for the journal Epigenetics (published by T&F Group).
Very interesting study showing that it is possible to reprogram a human cancer DNA methylome by expression of a plant DNA demethylase. https://tandfonline.com/doi/full/10.1080/15592294.2017.1414128?scroll=top&needAccess=true
(2018). DNA methylation reprogramming of human cancer cells by expression of a plant 5-methylcytosine DNA glycosylase. Epigenetics: Vol. 13, No. 1, pp. 95-107.
The CRISPR-Cas9 system has revolutionized genome engineering, allowing precise modification of DNA in various organisms. The most popular method for conducting CRISPR-based functional screens involves the use of pooled lentiviral libraries in selection screens coupled with next-generation sequencing. Henser-Brownhill et al. have generated a focused small-guide (sg)RNA library targeting 450 epigenetic regulators with multiple sgRNAs in human cells. This sgRNA library can be used for both selection and high-content screens, as well as for targeted investigation of selected proteins without requiring isolation of knock-out clones. The library is suitable for both in vitro and in vivo applications, representing a unique resource to study epigenetic mechanisms in physiological and pathological conditions.
https://tandfonline.com/doi/full/10.1080/15592294.2017.1395121?scroll=top&needAccess=true
(2017). Generation of an arrayed CRISPR-Cas9 library targeting epigenetic regulators: from high-content screens to in vivo assays. Epigenetics: Vol. 12, No. 12, pp. 1065-1075.
Have you seen the recent publication on how SLC9B1 methylation predicts fetal intolerance of labor? Check it out at https://www.tandfonline.com/doi/full/10.1080/15592294.2017.1411444?scroll=top&needAccess=true
(2018). SLC9B1 methylation predicts fetal intolerance of labor. Epigenetics: Vol. 13, No. 1, pp. 33-39.
DNA methylation is an important regulator of gene function. Fetal s*x is associated with the risk of several specific pregnancy complications related to placental function. Gong et al. carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies. They showed that the gene body of an autosomal gene, CSMD1, is differentially methylated in a s*x- and placental-specific manner, displaying s*x-specific differences in placental transcript abundance. Take a look at this recent publication in Epigenetics: https://tandfonline.com/doi/full/10.1080/15592294.2018.1429857
(2018). Genome-wide oxidative bisulfite sequencing identifies s*x-specific methylation differences in the human placenta. Epigenetics. Ahead of Print.
Smoking during pregnancy influences fetal development and may compromise the offspring's health during childhood, but also later in life. In this article, Meyer at al. compare the effect of prenatal smoke exposure in female versus male offspring, followed by similar but s*x-dependent comparisons in lung versus liver.
UBE3A Networks with Other Imprinted Genes to Shape Neurodevelopment and Autism
(read full
commentary @ Epigenie) Networking shapes our brains in many ways; whether it be in a professional, social, or genomically imprinted fashion. Linking us into the latter, new findings from the lab of Janine LaSalle at the University of California, Davis, uncover a hub in an imprinted gene network critical to neurodevelopment. The imprinted 15q11-q13 locus is involved in neurodevelopmental disorders such as Angelman, Prader-Willi, and Dup15q syndromes. Dup15q is an autism spectrum disorder (ASD) with a known genetic cause. Within the complex 15q11-q13 locus lies Ube3a, a ubiquitin ligase that is maternally expressed in neurons. Ube3a targets Ring1b, another ubiquitin ligase that is a member of the polycomb repressive 1 complex (PRC1), which monoubiquitinates the histone variant H2A.Z. Previously, the LaSalle lab has demonstrated that post-mortem Dup15q brains and a Dup15q cell culture exhibit global DNA hypomethylation and altered H2A.Z positioing at genes used for neuronal signaling, which are also ASD candidate genes. To dig deeper into the epigenomic functions of Ube3a, the talented team employed siRNA to knockdown Ube3a in a human neuroblastoma cell line (SH-SY5Y) and a Dup15q model cell line known as SH(15M). Here’s what they discovered when they applied whole-genome bisulfite sequencing, ChIP-seq, and RNA-seq to examine DNA methylation, H2A.Z & H3K4me3, and gene expression: DNA methylation, H2A.Z positioning, and H3K4me3 maintain a tight relationship following alterations to Ube3a; however, altered transcription does not typically reflect epigenomic differences. The team hypothesizes that the epigenomic differences represent a fingerprint of past developmental events, while the transcriptional changes are transient Either a gain or loss of Ube3a alters DNA methylation at genes involved in neurodevelopment and transcriptional regulation, which are associated with ASD related behaviors Knockdown of Ube3a alters the methylation of half of all known imprinted genes, thus uncovering an imprinted gene network in the brain associated with ASD First author S. Jesse Lopez shares, “I would say that imprinted gene networks are yet another layer of regulation in neurodevelopment. Imprinting is a complex epigenetic process where certain genes are turned on and off at different developmental stages and even different brain regions and the idea that they are controlled in networks highlights the delicate balance of brain development.” Senior author Janine LaSalle concludes, “Imprinted genes and imprinted human neurodevelopmental disorders such as Angelman syndrome were what originally got me interested in epigenetic mechanisms back in the 90’s in my postdoc years. But I was surprised to see that imprinted genes were selectively enriched in this unbiased analysis of the transcriptome and epigenome in human neurons when UBE3A levels were altered. Clearly, we have more work to do to further understand the implications of an imprinted gene network in neurons mediated by UBE3A and the relevance of other imprinted genes to autism.” Go peel away at the layers of this network over at Epigenetics, September 2017
http://epigenie.com/ube3a-networks-imprinted-genes-shape-neurodevelopment-autism/
Histone Variant H2A.Z Represses Memories and Accumulates with Age
A comparison of learning in young and aged mice uncovers a dynamic role for the histone variant H2A.Z in suppressing memory formation, which changes with age
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