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Cell Line Development
Published in Wei-Shou Hu, Cell Culture Bioprocess Engineering, 2020
Some genome segments are transcriptionally more active than others, or are considered to be ‘hot spots’ because of their high accessibility to transcription factors. The genome regions that have an abundance of such highly accessible segments are considered to be super-enhancer regions. Although data is still lacking, it is possible that the insertion of the GOI into such a highly accessible region will facilitate high transcription of the GOI. Local context may negatively affect transcription. The genome consists of euchromatin regions and heterochromatin regions. In heterochromatin regions, DNA is densely packed, making it less accessible to transcription factors. Super-enhancer and heterochromatin regions are both lineage-specific and are inherited in cell division. However, variation does occur and the boundary of a heterochromatin region may extend, causing a decrease in transcription of nearby genes.
Genes and Genomics
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2020
Chromatin is the complex combination of DNA, RNA, and protein that makes up chromosomes. It is found inside the nuclei in eukaryotic cells, and within the nucleoid in prokaryotic cells. It is divided between heterochromatin (condensed) and euchromatin (extended) forms. The major components of chromatin are DNA and histone proteins, although many other chromosomal proteins have prominent roles too. The functions of chromatin are to package DNA into a smaller volume to fit in the cell, to strengthen the DNA to allow mitosis and meiosis, and to serve as a mechanism to control expression and DNA replication. Chromatin contains genetic material instructions to direct cell functions. Changes in chromatin structure are affected by chemical modifications of histone proteins such as methylation (DNA and proteins) and acetylation (proteins), and by non-histone DNA-binding proteins.
Epigenetic Landscape–Modifying Nanoparticles
Published in Pradipta Ranjan Rauta, Yugal Kishore Mohanta, Debasis Nayak, Nanotechnology in Biology and Medicine, 2019
The histone core itself is not enough to sustain the pattern of chromatin configuration. Chromatin modifier–arbitrated histone tail modifications are the main driver of the genetic regulation. Vincent Allfrey, in his studies in the 1960s, first showed that histones are post-translationally modified (Allfrey, Faulkner et al. 1964). In later years, it has been proven that there are a huge number of different histone post-translational modifications (PTMs). In 1997, the high-resolution X-ray structure of the nucleosome showed that PTMs could affect chromatin structure (Luger, Mader et al. 1997). The cell possesses various chromatin remodeling activities that can transform histones or move nucleosomes (Cole, Cui et al. 2016). From birth to death, a cell passes through a large genetic expression profile which is regulated by DNA and histone modifications. There are two types of chromatin in the genome, silent heterochromatin and active euchromatin. Each of these chromatin patterns associates with various sets of chromatin marks, tagged on DNA and histones where miRNAs also participate. In the early stages of embryo development in mammals, changes occur in genome-wide DNA methylation and histone modification patterns. Development of the embryo is controlled by Hox gene expression, which is involved in transcriptional regulation that maintains cell proliferation, and differentiation in the stem and progenitor cells is strictly regulated by Trithorax group (TrxG) and Polycomb group (PcG) proteins (Ringrose and Paro 2004).
Epigenotoxicity: a danger to the future life
Published in Journal of Environmental Science and Health, Part A, 2023
Farzaneh Kefayati, Atoosa Karimi Babaahmadi, Taraneh Mousavi, Mahshid Hodjat, Mohammad Abdollahi
Epigenetic mechanisms are divided into DNA modifications, chromatin modifications, non-coding RNAs and RNA modifications, which produce a set of potential hereditary changes in gene expression;[2] thus, epigenetic markers can persevere throughout growth and likely pass from offspring to offspring. For example, the open state of chromatin is caused by chemical changes in histone proteins that facilitate gene expression by interacting with transcription factors and enzymes with DNA, or the closed state of heterochromatin, which prevents the initiation of transcription and suppresses gene expression. Although epigenetic markers are stable and regulate gene expression, environmental factors can act as stimuli; thus, altered epigenetic patterns may change phenotypic responses via different pathways and disruption of epigenetic modifiers.[3] These factors include air pollution, metals, pesticides, and electrical waste (E-waste), which have become more prevalent following urbanization and the expansion of industries. The role of environmental stimuli on epigenetic changes can be clearly understood in the case of identical twins. Although they have the same DNA sequence, epigenetic mechanisms such as DNA methylation and histone modification have led to phenotypic differences resulting from different exposure to environmental factors.[1]
Re-Analysis of Non-Small Cell Lung Cancer and Drug Resistance Microarray Datasets with Machine Learning
Published in Cybernetics and Systems, 2023
Çiğdem Erol, Tchare Adnaane Bawa, Yalçın Özkan
All genes obtained as a result of the analyzes and their distribution according to frequencies are shared in the findings section (Tables 2 and 3). It is thought that genes with high frequency in the same data set should also be considered as potential candidates. As a result; ELOVL7, HMGA2, SAT1, RRM1, IER3, SLC7A11, and U2AF1 genes were found in at least 2 different datasets. Pathways for 7 genes obtained as a result of our research and their links are given in parentheses; ELOVL7 (Synthesis of very long-chain fatty acyl-CoAs), HMGA2 (Formation of Senescence-Associated Heterochromatin Foci), SAT1 (Interconversion of polyamines, Arginine and Proline metabolism), RRM1 (Glutathione metabolism, Pyrimidine metabolism, Purine metabolism, Mitochondrial DNA Depletion Syndrome-3), IER3 (PI5P, PP2A, and IER3 Regulate PI3K/AKT Signaling, Gastrin_CCK2R_240212), SLC7A11 (Amino acid transport across the plasma membrane, Basigin interactions, Transport of inorganic cations/anions and amino acids/oligopeptides), U2AF1 (Transport of Mature mRNA derived from an Intron-Containing Transcript, pre-mRNA splicing, RNA Polymerase II Transcription Termination, mRNA 3′-end processing).
Inter-retrotransposon amplified polymorphism markers revealed long terminal repeat retrotransposon insertion polymorphism in flax cultivated on the experimental fields around Chernobyl
Published in Journal of Environmental Science and Health, Part A, 2020
Veronika Lancíková, Jana Žiarovská
Hypermethylation is considered as one of the most important manifestations of plant stress response on the genome level. In general, epigenetics controls genome stability and allows adaptation to irradiation. However, when the effect of stress factor is alleviated, DNA methylation returns back to its original state.[51] Also, in terms of radiation stress, it has been shown that the progeny of radiation exposed plants can respond by genome wide DNA methylation loss. Loss of methylation and changed level of DNA methyltransferases can lead to the activation of transposons.[2,52] Stress factors can lead to the rearrangement of genome. Copy number variation of genes can lead to the variability on the genetic and phenotypic level.[53] However, Pecinka et al. observed that the DNA methylation loss is not necessarily needed while heterochromatin decondensation can result into activation of transposable elements.[54]