Search results for "epigenetics"
showing 10 items of 517 documents
Chances in the Brain Cells, From Epigenetic To the Future
2014
Copyright: © 2014 Valles SL. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Both oxidative damage and inflammation are elevated in brain from neurodegenerative patients [1], but their pathogenic significance remains unclear. Central nervous system has its own resident immune system, in which glial cells not only serve such as supportive and nutritive roles for neuron cells, also engage in several inflammatory processes that defend the central nervous system from pathogens and help it to recover from stres…
sevenC
2018
Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. This package uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events.
Immunotherapy With Human Gamma Delta T Cells—Synergistic Potential of Epigenetic Drugs?
2018
Epigenetics has emerged as one of the fastest growing concepts, adding more than 45 new publications every day, spreading through various fields ( 1). Conrad Waddington coined the term “epigenetics” in 1942; however, a multitude of definitions has been endorsed by different researchers. In essence, Waddington’s definition of “epigenetics” and its redefinition by Holiday is at the heart of cellular function. Hence, it is obvious that epigenetic regulation plays a central role also in the specification, differentiation, and functional plasticity of T lymphocytes ( 2). T-cell fate decision in progenitor cells, functional CD4 T-cell plasticity, CD8 T-cell differentiation, but also T-cell memory…
p53 is involved in regulation of the DNA repair gene O6-methylguanine-DNA methyltransferase (MGMT) by DNA damaging agents
1998
The DNA repair protein O6-methylguanine-DNA methyltransferase (MGMT) is inducible by genotoxic stress. MGMT induction results from transcriptional activation of the MGMT gene which is a specific response to DNA damage. A possible factor involved in triggering MGMT induction might be p53, because both p53 and MGMT are activated by DNA breaks. To study the effect of p53 on induction of the MGMT gene, we compared the presence of functional wild-type (wt) and mutant p53 with MGMT expression level in various mouse fibroblasts and rat hepatoma cell lines upon genotoxic treatment. Cells which responded to ionizing radiation (IR) by MGMT induction displayed functional p53, whereas in cells not expr…
Epigenetic Transcriptional Regulation of the Growth Arrest-Specific gene 1 (Gas1) in Hepatic Cell Proliferation at Mononucleosomal Resolution
2011
Background Gas1 (growth arrest-specific 1) gene is known to inhibit cell proliferation in a variety of models, but its possible implication in regulating quiescence in adult tissues has not been examined to date. The knowledge of how Gas1 is regulated in quiescence may contribute to understand the deregulation occurring in neoplastic diseases. Methodology/Principal Findings Gas1 expression has been studied in quiescent murine liver and during the naturally synchronized cell proliferation after partial hepatectomy. Chromatin immunoprecipitation at nucleosomal resolution (Nuc-ChIP) has been used to carry out the study preserving the in vivo conditions. Transcription has been assessed at real …
DNA methylation episignature testing improves molecular diagnosis of Mendelian chromatinopathies
2021
Abstract Purpose Chromatinopathies include more than 50 disorders caused by disease-causing variants of various components of chromatin structure and function. Many of these disorders exhibit unique genome-wide DNA methylation profiles, known as episignatures. In this study, the methylation profile of a large cohort of individuals with chromatinopathies was analyzed for episignature detection. Methods DNA methylation data was generated on extracted blood samples from 129 affected individuals with the Illumina Infinium EPIC arrays and analyzed using an established bioinformatic pipeline. Results The DNA methylation profiles matched and confirmed the sequence findings in both the discovery an…
Sequenom MassARRAY Technology for the Analysis of DNA Methylation
2016
Abstract DNA methylation is one of several epigenetic mechanisms that cells use to control gene expression and is involved in the development of different pathologies such as obesity, Alzheimer's, and cancer. In this chapter, we have analyzed in depth the Sequenom MassARRAY® technology for the analysis of DNA methylation with special emphasis on its applications in clinical practice. In recent years, the Sequenom EpiTYPER® system technology has emerged as a novel technique for methylation analysis that offers a high range of options with great performance and several advantages.
Epigenetics and precision medicine in lung cancer
2022
Abstract Lung cancer is one of the most common types of cancer and the leading cause of cancer-related deaths worldwide. A major factor related with the high mortality rate of lung cancer patients is the late diagnosis of the disease. So, the identification and characterization of new epigenetic marks and mechanisms may contribute to better diagnose and treat lung cancer. In this chapter we review the epigenetic mechanisms involved in lung cancer, including DNA methylation, histone posttranslational modification and noncoding RNAs. The chapter focuses on biomarkers for diagnostic, prognostic and response to treatment. Finally, thanks to the reversible nature of epigenetic marks, we provide …
CORENup: a combination of convolutional and recurrent deep neural networks for nucleosome positioning identification
2020
Abstract Background Nucleosomes wrap the DNA into the nucleus of the Eukaryote cell and regulate its transcription phase. Several studies indicate that nucleosomes are determined by the combined effects of several factors, including DNA sequence organization. Interestingly, the identification of nucleosomes on a genomic scale has been successfully performed by computational methods using DNA sequence as input data. Results In this work, we propose CORENup, a deep learning model for nucleosome identification. CORENup processes a DNA sequence as input using one-hot representation and combines in a parallel fashion a fully convolutional neural network and a recurrent layer. These two parallel …
Epigenetic profile of developmentally important genes in bovine oocytes
2011
Assisted reproductive technologies are associated with an increased incidence of epigenetic aberrations, specifically in imprinted genes. Here, we used the bovine oocyte as a model to determine putative epigenetic mutations at three imprinted gene loci caused by the type of maturation, either in vitro maturation (IVM) in Tissue Culture Medium 199 (TCM) or modified synthetic oviduct fluid (mSOF) medium, or in vivo maturation. We applied a limiting dilution approach and direct bisulfite sequencing to analyze the methylation profiles of individual alleles (DNA molecules) for H19/IGF2, PEG3, and SNRPN, which are each associated with imprinting defects in humans and/or the mouse model, and are k…