Epigenomes, Vol. 3, Pages 12: Polycomb Assemblies Multitask to Regulate Transcription Epigenomes doi: 10.3390/epigenomes3020012 Authors: Miguel Vidal The Polycomb system is made of an evolutionary ancient group of proteins, present throughout plants and animals. Known initially from developmental studies with the fly Drosophila melanogaster, they were associated with stable sustainment of gene repression and maintenance of cell identity. Acting as multiprotein assemblies with an ability...
Thu Jun 20, 2019 03:00
Epigenomes, Vol. 3, Pages 11: Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors
Epigenomes, Vol. 3, Pages 11: Disruption of Broad Epigenetic Domains in PDAC Cells by HAT Inhibitors Epigenomes doi: 10.3390/epigenomes3020011 Authors: Diana L. Gerrard Joseph R. Boyd Gary S. Stein Victor X. Jin Seth Frietze The spreading of epigenetic domains has emerged as a distinguishing epigenomic phenotype for diverse cell types. In particular, clusters of H3K27ac- and H3K4me3-marked elements, referred to as super-enhancers, and broad H3K4me3 domains, respectively,...
Sun Jun 02, 2019 03:00
Epigenomes, Vol. 3, Pages 10: Integrating Signals from Sperm Methylome Analysis and Genome-Wide Association Study for a Better Understanding of Male Fertility in Cattle Epigenomes doi: 10.3390/epigenomes3020010 Authors: Lingzhao Fang Yang Zhou Shuli Liu Jicai Jiang Derek M. Bickhart Daniel J. Null Bingjie Li Steven G. Schroeder Benjamin D. Rosen John B. Cole Curtis P. Van Tassell Li Ma George E. Liu Decreased male fertility is a big concern in both...
Thu May 16, 2019 03:00
Epigenomes, Vol. 3, Pages 9: 5-Methylcytosine and 5-Hydroxymethylcytosine Signatures Underlying Pediatric Cancers Epigenomes doi: 10.3390/epigenomes3020009 Authors: Shalu Jhanwar Ajinkya Deogade In addition to the genetic variations, recent evidence has shown that DNA methylation of both 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) underlies the pathogenesis of pediatric cancer. Given the high mortality rate, there is an urgent need to study the mechanisms...
Thu May 09, 2019 03:00
Epigenomes, Vol. 3, Pages 8: Global DNA Methylation in the Limbic System of Cattle Epigenomes doi: 10.3390/epigenomes3020008 Authors: Bonnie Cantrell Hannah Lachance Brenda Murdoch Julia Sjoquist Richard Funston Robert Weaber Stephanie McKay To elucidate the extent to which DNA methylation varies across multiple tissues in the brain and between animals, we have quantified global DNA methylation in tissues comprising the limbic system for six Red Angus x Simmental steers....
Sun May 05, 2019 03:00
Epigenomes, Vol. 3, Pages 7: An Orphan CpG Island Drives Expression of a let-7 miRNA Precursor with an Important Role in Mouse Development Epigenomes doi: 10.3390/epigenomes3010007 Authors: Martha V. Koerner Kashyap Chhatbar Shaun Webb Justyna Cholewa-Waclaw Jim Selfridge Dina De Sousa Bill Skarnes Barry Rosen Mark Thomas Joanna Bottomley Ramiro Ramirez-Solis Christopher Lelliott David J. Adams Adrian Bird Most human genes are associated with promoters...
Wed Mar 13, 2019 02:00
Epigenomes, Vol. 3, Pages 6: The Relevance of Gender in Tumor-Influencing Epigenetic Traits Epigenomes doi: 10.3390/epigenomes3010006 Authors: Victoria Sarne Sandrina Braunmueller Lisa Rakob Rita Seeboeck Tumorigenesis as well as the molecular orchestration of cancer progression are very complex mechanisms that comprise numerous elements of influence and regulation. Today, many of the major concepts are well described and a basic understanding of a tumor’s fine-tuning...
Mon Jan 28, 2019 02:00
Epigenomes, Vol. 3, Pages 5: Epigenomics of Pancreatic Cancer: A Critical Role for Epigenome-Wide Studies Epigenomes doi: 10.3390/epigenomes3010005 Authors: Rahul R. Singh Katie M. Reindl Rick J. Jansen Several challenges present themselves when discussing current approaches to the prevention or treatment of pancreatic cancer. Up to 45% of the risk of pancreatic cancer is attributed to unknown causes, making effective prevention programs difficult to design. The most common type...
Sat Jan 19, 2019 02:00
Epigenomes, Vol. 3, Pages 4: Uncovering Differentially Methylated Regions (DMRs) in a Salt-Tolerant Rice Variety under Stress: One Step towards New Regulatory Regions for Enhanced Salt Tolerance Epigenomes doi: 10.3390/epigenomes3010004 Authors: Liliana J. Ferreira Mark T. A. Donoghue Pedro Barros Nelson J. Saibo Ana Paula Santos M. Margarida Oliveira Chromatin structure, DNA methylation, and histone modifications act in a concerted manner to influence gene expression...
Fri Jan 18, 2019 02:00
Epigenomes, Vol. 3, Pages 3: Biotic Stress-Induced Priming and De-Priming of Transcriptional Memory in Arabidopsis and Apple Epigenomes doi: 10.3390/epigenomes3010003 Authors: Kay Gully Jean-Marc Celton Alexandre Degrave Sandra Pelletier Marie-Noelle Brisset Etienne Bucher Under natural growth conditions, plants experience various and repetitive biotic and abiotic stresses. Salicylic acid (SA) is a key phytohormone involved in the response to biotic challenges. Application...
Mon Jan 14, 2019 02:00
Epigenomes, Vol. 3, Pages 2: Acknowledgement to Reviewers of Epigenomes in 2018 Epigenomes doi: 10.3390/epigenomes3010002 Authors: Epigenomes Editorial Office Rigorous peer-review is the corner-stone of high-quality academic publishing [...]
Fri Jan 11, 2019 02:00
Epigenomes, Vol. 3, Pages 1: Epigenetic Regulation of EMT (Epithelial to Mesenchymal Transition) and Tumor Aggressiveness: A View on Paradoxical Roles of KDM6B and EZH2 Epigenomes doi: 10.3390/epigenomes3010001 Authors: Camille Lachat Michaël Boyer-Guittaut Paul Peixoto Eric Hervouet EMT (epithelial to mesenchymal transition) is a plastic phenomenon involved in metastasis formation. Its plasticity is conferred in a great part by its epigenetic regulation. It has been reported...
Thu Dec 20, 2018 02:00
Epigenomes, Vol. 2, Pages 22: Non-CpG Methylation Revised Epigenomes doi: 10.3390/epigenomes2040022 Authors: Andrea Fuso Textbook and scientific papers addressing DNA methylation usually still cite “DNA methylation occurs at CpG cytosines”. Methylation at cytosines outside the CpG nucleotide, the so-called “non-CpG methylation”, is usually considered a minor and not biologically relevant process. However, the technical improvements and additional...
Wed Dec 12, 2018 02:00
Epigenomes, Vol. 2, Pages 21: How to Design a Whole-Genome Bisulfite Sequencing Experiment Epigenomes doi: 10.3390/epigenomes2040021 Authors: Claudius Grehl Markus Kuhlmann Claude Becker Bruno Glaser Ivo Grosse Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of adenine bases....
Tue Dec 11, 2018 02:00
Epigenomes, Vol. 2, Pages 20: On the Cooperation between Epigenetics and Transcription Factor Networks in the Specification of Tissue Stem Cells Epigenomes doi: 10.3390/epigenomes2040020 Authors: Torsten Thalheim Lydia Hopp Hans Binder Gabriela Aust Joerg Galle It is generally accepted that epigenetic modifications, such as DNA and histone methylations, affect transcription and that a gene’s transcription feeds back on its epigenetic profile. Depending on the epigenetic...
Tue Oct 23, 2018 03:00
Epigenomes, Vol. 2, Pages 19: Genetic and Epigenetic Regulation of Zebrafish Intestinal Development Epigenomes doi: 10.3390/epigenomes2040019 Authors: Bilge San Marco Aben Dei M. Elurbe Kai Voeltzke Marjo J. Den Broeder Julien Rougeot Juliette Legler Leonie M. Kamminga Many regulatory pathways are conserved in the zebrafish intestine compared to mammals, rendering it a strong model to study intestinal development. However, the (epi)genetic regulation of zebrafish...
Tue Oct 23, 2018 03:00
Epigenomes, Vol. 2, Pages 18: The Role of the Prader-Willi Syndrome Critical Interval for Epigenetic Regulation, Transcription and Phenotype Epigenomes doi: 10.3390/epigenomes2040018 Authors: Simona Zahova Anthony R. Isles Prader-Willi Syndrome (PWS) is a neurodevelopmental disorder caused by loss of expression of the paternally inherited genes on chromosome 15q11.2-q13. However, the core features of PWS have been attributed to a critical interval (PWS-cr) within the 15q11.2-q13 imprinted...
Thu Oct 18, 2018 03:00
Epigenomes, Vol. 2, Pages 17: The Cytoplasm Affects the Epigenome in Drosophila melanogaster Epigenomes doi: 10.3390/epigenomes2030017 Authors: Christoph Grunau Susanne Voigt Ralph Dobler Damian K. Dowling Klaus Reinhardt Cytoplasmic components and their interactions with the nuclear genome may mediate patterns of phenotypic expression to form a joint inheritance system. However, proximate mechanisms underpinning these interactions remain elusive. To independently assess...
Sun Sep 09, 2018 03:00
Epigenomes, Vol. 2, Pages 16: Targeting EZH2 in Multiple Myeloma—Multifaceted Anti-Tumor Activity Epigenomes doi: 10.3390/epigenomes2030016 Authors: Mohammad Alzrigat Helena Jernberg-Wiklund Jonathan D. Licht The enhancer of zeste homolog 2 (EZH2) is the enzymatic subunit of the polycomb repressive complex 2 (PRC2) that exerts important functions during normal development as well as disease. PRC2 through EZH2 tri-methylates histone H3 lysine tail residue 27 (H3K27me3), a modification...
Mon Sep 03, 2018 03:00
Epigenomes, Vol. 2, Pages 15: Nuclear Envelope Regulation of Oncogenic Processes: Roles in Pancreatic Cancer Epigenomes doi: 10.3390/epigenomes2030015 Authors: Claudia C. Preston Randolph S. Faustino Pancreatic cancer is an aggressive and intractable malignancy with high mortality. This is due in part to a high resistance to chemotherapeutics and radiation treatment conferred by diverse regulatory mechanisms. Among these, constituents of the nuclear envelope play a significant role...
Sun Sep 02, 2018 03:00
Epigenomes, Vol. 2, Pages 14: Dynamics of the Methylome and Transcriptome during the Regeneration of Rice Epigenomes doi: 10.3390/epigenomes2030014 Authors: Fei-Man Hsu Moloya Gohain Archana Allishe Yan-Jiun Huang Jo-Ling Liao Lin-Yun Kuang Pao-Yang Chen Oryza sativa indica (cv. IR64) and Oryza sativa japonica (cv. TNG67) vary in their regeneration efficiency. Such variation may occur in response to cultural environments that induce somaclonal variation. Somaclonal...
Sat Jul 21, 2018 03:00
Epigenomes, Vol. 2, Pages 13: Cancer Risks Linked to the Bad Luck Hypothesis and Epigenomic Mutational Signatures Epigenomes doi: 10.3390/epigenomes2030013 Authors: José E. Belizário Exposure to pathogen infection, and occupational and environmental agents, contributes to induction of most types of cancer through different mechanisms. Cancer is defined and characterized by accumulation of mutations and epimutations that lead to changes in the cellular genome and epigenome. According...
Fri Jul 20, 2018 03:00
Epigenomes, Vol. 2, Pages 12: Salt Stress Induces Non-CG Methylation in Coding Regions of Barley Seedlings (Hordeum vulgare) Epigenomes doi: 10.3390/epigenomes2020012 Authors: Moumouni Konate Michael J. Wilkinson Benjamin T. Mayne Stephen M. Pederson Eileen S. Scott Bettina Berger Carlos M. Rodriguez Lopez Salinity can negatively impact crop growth and yield. Changes in DNA methylation are known to occur when plants are challenged by stress and have been associated...
Wed Jun 20, 2018 03:00
Epigenomes, Vol. 2, Pages 11: Recent Advances in Chromatin Mechanisms Controlling Pancreatic Carcinogenesis Epigenomes doi: 10.3390/epigenomes2020011 Authors: Thomas Hank Andrew S. Liss Pancreatic ductal adenocarcinoma has a heterogeneous genetic landscape, marked by frequent mutation of KRAS, CDKN2A, TP53, and SMAD4, resulting in poor responses to conventional therapeutic regimens. Over the past decade, increased understanding of the genetic underpinnings of this lethal cancer has...
Wed Jun 20, 2018 03:00
Epigenomes, Vol. 2, Pages 10: The Epigenetic Landscape of Pancreatic Cancer Stem Cells Epigenomes doi: 10.3390/epigenomes2020010 Authors: Sladjana Zagorac Laura Garcia-Bermejo Bruno Sainz Data now indicates that in addition to genetic alterations/mutations, human cancer cells exhibit important changes in their epigenome. In the context of this review, we define the epigenome as the chemical compounds and/or proteins that can interact with nuclear DNA to direct the specific and...
Thu Jun 14, 2018 03:00
Epigenomes, Vol. 2, Pages 9: On the Relationships between LncRNAs and Other Orchestrating Regulators: Role of the Circadian System Epigenomes doi: 10.3390/epigenomes2020009 Authors: Rüdiger Hardeland Numerous lncRNAs exhibit circadian rhythms, sometimes with high amplitudes. Therefore, they are controlled by cellular circadian oscillators. However, they also seem to influence circadian clocks, as shown by the important core oscillator gene Per2, at which antiphasic rhythms of Per2 mRNA...
Thu May 31, 2018 03:00
Epigenomes, Vol. 2, Pages 7: DNA Methylation Suppression by Bhendi Yellow Vein Mosaic Virus Epigenomes doi: 10.3390/epigenomes2020007 Authors: Kandhalu Sagadevan Dinesh Babu Ashirbad Guria Jeyalakshmi Karanthamalai Nagesh Srikakulam Kamlesh Kumari Priyanka Sharma Sam Aldrin Chandran Anburaj Daniel Barnabas Jebasingh Tennyson Gopal Pandi Bhendi yellow vein mosaic virus (BYVMV) belongs to the monopartite begomovirus associated with the β satellite. As...
Thu May 31, 2018 03:00
Epigenomes, Vol. 2, Pages 8: Epigenetic Targeting of Aberrant Transcriptional Modulation in Pancreatic Cancer Epigenomes doi: 10.3390/epigenomes2020008 Authors: Feda H. Hamdan Steven A. Johnsen While the mortality rates of cancer are generally declining, pancreatic cancer persists to be an exception with a 5-year-survival rate of less than 7%. Late diagnosis and resistance to conventional therapies contribute to high mortality rates in spite of the remarkable recent advances in cancer...
Thu May 31, 2018 03:00
Epigenomes, Vol. 2, Pages 6: Epigenomics of Plant Responses to Environmental Stress Epigenomes doi: 10.3390/epigenomes2010006 Authors: Suresh Kumar Genome-wide epigenetic changes in plants are being reported during development and environmental stresses, which are often correlated with gene expression at the transcriptional level. The sum total of the biochemical changes in nuclear DNA, post-translational modifications in histone proteins and variations in the biogenesis of non-coding...
Fri Mar 16, 2018 02:00
Epigenomes, Vol. 2, Pages 5: Panobinostat Potentiates Temozolomide Effects and Reverses Epithelial–Mesenchymal Transition in Glioblastoma Cells Epigenomes doi: 10.3390/epigenomes2010005 Authors: Alejandro Urdiciain Bárbara Meléndez Juan Rey Miguel Idoate Javier Castresana Glioblastoma is the most common form of glioma, as well as the most aggressive. Patients suffering from this disease have a very poor prognosis. Surgery, radiotherapy, and temozolomide are the only approved...
Mon Feb 19, 2018 02:00
Epigenomes, Vol. 2, Pages 4: From Flies to Mice: The Emerging Role of Non-Canonical PRC1 Members in Mammalian Development Epigenomes doi: 10.3390/epigenomes2010004 Authors: Izabella Bajusz Gergő Kovács Melinda Pirity Originally two types of Polycomb Repressive Complexes (PRCs) were described, canonical PRC1 (cPRC1) and PRC2. Recently, a versatile set of complexes were identified and brought up several dilemmas in PRC mediated repression. These new class of complexes were named...
Mon Feb 05, 2018 02:00
Epigenomes, Vol. 2, Pages 3: 5-Hydroxymethylcytosine (5hmC), or How to Identify Your Favorite Cell Epigenomes doi: 10.3390/epigenomes2010003 Authors: Szilvia Ecsedi Jesús Rodríguez-Aguilera Héctor Hernandez-Vargas Recently described as the sixth base of the DNA macromolecule, the precise role of 5-hydroxymethylcytosine (5hmC) is the subject of debate. Early studies indicate that it is functionally distinct from cytosine DNA methylation (5mC), and there is evidence for 5hmC being...
Tue Jan 30, 2018 02:00
Epigenomes, Vol. 2, Pages 2: Acknowledgement to Reviewers of Epigenomes in 2017 Epigenomes doi: 10.3390/epigenomes2010002 Authors: Epigenomes Editorial Office Peer review is an essential part in the publication process, ensuring that Epigenomes maintains high quality standards for its published papers. [...]
Sat Jan 27, 2018 02:00
Epigenomes, Vol. 2, Pages 1: Drosophila DNA-Binding Proteins in Polycomb Repression Epigenomes doi: 10.3390/epigenomes2010001 Authors: Maksim Erokhin Pavel Georgiev Darya Chetverina The formation of individual gene expression patterns in different cell types is required during differentiation and development of multicellular organisms. Polycomb group (PcG) proteins are key epigenetic regulators responsible for gene repression, and dysregulation of their activities leads to developmental...
Tue Jan 16, 2018 02:00
Epigenomes, Vol. 1, Pages 24: Large-Scale Integrative Analysis of Epigenetic Modifications Induced by Isotretinoin, Doxycycline and Metronidazole in Murine Colonic Intestinal Epithelial Cells Epigenomes doi: 10.3390/epigenomes1030024 Authors: Eugenia Becker Susan Bengs Sirisha Aluri Lennart Opitz Kirstin Atrott Felix Rost Irina Leonardi Claudia Stanzel Tina Raselli Stephanie Kasper Pedro Ruiz Gerhard Rogler Environmental factors are playing a central...
Mon Dec 18, 2017 02:00
Epigenomes, Vol. 1, Pages 23: The Genome-Wide DNA Methylation Profile of Peripheral Blood Is Not Systematically Changed by Short-Time Storage at Room Temperature Epigenomes doi: 10.3390/epigenomes1030023 Authors: Nicklas Heine Staunstrup Anna Starnawska Mette Nyegaard Anders Lade Nielsen Anders Dupont Børglum Ole Mors Background: Epigenetic epidemiology has proven an important research discipline in the delineation of diseases of complex etiology. The approach, in such...
Fri Dec 15, 2017 02:00
Epigenomes, Vol. 1, Pages 22: PRC1 Prevents Replication Stress during Chondrogenic Transit Amplification Epigenomes doi: 10.3390/epigenomes1030022 Authors: Frank Spaapen Lars M. T. Eijssen Michiel E. Adriaens Tim J. Welting Peggy Prickaerts Juliette Salvaing Vivian E. H. Dahlmans Donald A. M. Surtel Frans Kruitz Roel Kuijer Yoshihiro Takihara Hendrik Marks Hendrik G. Stunnenberg Bradly G. Wouters Miguel Vidal Jan Willem Voncken Transit amplification...
Mon Dec 11, 2017 02:00
Epigenomes, Vol. 1, Pages 21: Switch-Like Roles for Polycomb Proteins from Neurodevelopment to Neurodegeneration Epigenomes doi: 10.3390/epigenomes1030021 Authors: Anke Hoffmann Vincenza Sportelli Michael Ziller Dietmar Spengler Polycomb Group (PcG) proteins are best-known for maintaining repressive or active chromatin states that are passed on across multiple cell divisions, and thus sustain long-term memory of gene expression. PcG proteins engage different, partly gene- and/or...
Fri Dec 01, 2017 02:00
Epigenomes, Vol. 1, Pages 20: Genome-Wide Epigenetic Studies in Chicken: A Review Epigenomes doi: 10.3390/epigenomes1030020 Authors: Sarah-Anne David Marjorie Mersch Sylvain Foissac Anne Collin Frédérique Pitel Vincent Coustham Over the years, farmed birds have been selected on various performance traits mainly through genetic selection. However, many studies have shown that genetics may not be the sole contributor to phenotypic plasticity. Gene expression programs can...
Thu Nov 23, 2017 02:00
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