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Epigenetic regulation of chromosome

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https://www.readbyqxmd.com/read/29792221/sex-differences-in-cardiovascular-epigenetics-a-systematic-review
#1
REVIEW
Robin J G Hartman, Sarah E Huisman, Hester M den Ruijter
BACKGROUND: Differences in cardiovascular diseases are evident in men and women throughout life and are mainly attributed to the presence of sex hormones and chromosomes. Epigenetic mechanisms drive the regulation of the biological processes that may lead to CVD and are possibly influenced by sex. In order to gain an overview of the status quo on sex differences in cardiovascular epigenetics, we performed a systematic review. MATERIALS AND METHODS: A systematic search was performed on PubMed and Embase for studies mentioning cardiovascular disease, epigenetics, and anything related to sex differences...
May 23, 2018: Biology of Sex Differences
https://www.readbyqxmd.com/read/29784956/dynamics-and-function-of-dna-methylation-in-plants
#2
REVIEW
Huiming Zhang, Zhaobo Lang, Jian-Kang Zhu
DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so-called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions...
May 21, 2018: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29769286/targeted-inhibition-of-histone-h3k27-demethylation-is-effective-in-high-risk-neuroblastoma
#3
Timothy L Lochmann, Krista M Powell, Jungoh Ham, Konstantinos V Floros, Daniel A R Heisey, Richard I J Kurupi, Marissa L Calbert, Maninderjit S Ghotra, Patricia Greninger, Mikhail Dozmorov, Madhu Gowda, Andrew J Souers, C Patrick Reynolds, Cyril H Benes, Anthony C Faber
High-risk neuroblastoma is often distinguished by amplification of MYCN and loss of differentiation potential. We performed high-throughput drug screening of epigenetic-targeted therapies across a large and diverse tumor cell line panel and uncovered the hypersensitivity of neuroblastoma cells to GSK-J4, a small-molecule dual inhibitor of lysine 27 of histone 3 (H3K27) demethylases ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX), and histone demethylase Jumonji D3 (JMJD3). Mechanistically, GSK-J4 induced neuroblastoma differentiation and endoplasmic reticulum (ER) stress, with accompanying up-regulation of p53 up-regulated modulator of apoptosis (PUMA) and induction of cell death...
May 16, 2018: Science Translational Medicine
https://www.readbyqxmd.com/read/29765862/genomic-imprinting-and-the-regulation-of-postnatal-neurogenesis
#4
REVIEW
Anna Lozano-Ureña, Raquel Montalbán-Loro, Anne C Ferguson-Smith, Sacri R Ferrón
Most genes required for mammalian development are expressed from both maternally and paternally inherited chromosomal homologues. However, there are a small number of genes known as " imprinted genes " that only express a single allele from one parent, which is repressed on the gene from the other parent. Imprinted genes are dependent on epigenetic mechanisms such as DNA methylation and post-translational modifications of the DNA-associated histone proteins to establish and maintain their parental identity...
November 9, 2017: Brain Plasticity
https://www.readbyqxmd.com/read/29759441/nuclear-organization-mediates-cancer-compromised-genetic-and-epigenetic-control
#5
REVIEW
Sayyed K Zaidi, Andrew Fritz, Kirsten Tracy, Jonathan Gordon, Coralee Tye, Joseph Boyd, Andre Van Wijnen, Jeffrey Nickerson, Anthony Imbalzano, Jane Lian, Janet Stein, Gary Stein
Nuclear organization is functionally linked to genetic and epigenetic regulation of gene expression for biological control and is modified in cancer. Nuclear organization supports cell growth and phenotypic properties of normal and cancer cells by facilitating physiologically responsive interactions of chromosomes, genes and regulatory complexes at dynamic three-dimensional microenvironments. We will review nuclear structure/function relationships that include: 1. Epigenetic bookmarking of genes by phenotypic transcription factors to control fidelity and plasticity of gene expression as cells enter and exit mitosis; 2...
May 9, 2018: Advances in Biological Regulation
https://www.readbyqxmd.com/read/29750270/peripheral-re-localization-of-constitutive-heterochromatin-advances-its-replication-timing-and-impairs-maintenance-of-silencing-marks
#6
Kathrin S Heinz, Corella S Casas-Delucchi, Timea Török, Dusan Cmarko, Alexander Rapp, Ivan Raska, M Cristina Cardoso
The replication of the genome is a highly organized process, both spatially and temporally. Although a lot is known on the composition of the basic replication machinery, how its activity is regulated is mostly unknown. Several chromatin properties have been proposed as regulators, but a potential role of the nuclear DNA position remains unclear. We made use of the prominent structure and well-defined heterochromatic landscape of mouse pericentric chromosome domains as a well-studied example of late replicating constitutive heterochromatin...
May 10, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29745967/expression-and-clinical-relations-of-protein-tyrosine-phosphatase-receptor-type-s-in-esophageal-squamous-cell-carcinoma
#7
Guoliang Zhang, Xinyang Liu, Jingjing Wu, Qikun Zhu, Hui Zeng, Tao Wang, Rui Wang
Protein tyrosine phosphatase receptor type S is a tumor suppressor gene, located at chromosome 19p13.3, frequently inactivated through deletions or epigenetic mechanisms in many types of cancers. In this study, we investigate protein tyrosine phosphatase receptor S (PTPRS) expression level, clinicopathological and prognostic significance in 205 cases of esophageal squamous cell carcinoma (ESCC). Paraffin embedded tissue with immunohistochemistry methods was adopted to exam PTPRS expression in ESCC and paired normal esophageal mucosa tissues on Tissue Microarrays (TMAs)...
May 10, 2018: Histology and Histopathology
https://www.readbyqxmd.com/read/29739320/mobilization-of-retrotransposons-as-a-cause-of-chromosomal-diversification-and-rapid-speciation-the-case-for-the-antarctic-teleost-genus-trematomus
#8
J Auvinet, P Graça, L Belkadi, L Petit, E Bonnivard, A Dettaï, W H Detrich, C Ozouf-Costaz, D Higuet
BACKGROUND: The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative analyses on complete taxonomic groups. To help overcome this problem, we have focused on the Antarctic teleost genus Trematomus (Notothenioidei: Nototheniidae), as they experienced rapid speciation accompanied by dramatic chromosomal diversity...
May 9, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29729188/atopic-asthma-after-rhinovirus-induced-wheezing-is-associated-with-dna-methylation-change-in-the-smad3-gene-promoter
#9
Riikka J Lund, Maria Osmala, Maia Malonzo, Minna Lukkarinen, Annamari Leino, Jussi Salmi, Sanna Vuorikoski, Riitta Turunen, Tytti Vuorinen, Cezmi Akdis, Harri Lähdesmäki, Riitta Lahesmaa, Tuomas Jartti
Children with rhinovirus-induced severe early wheezing have an increased risk of developing asthma later in life. The exact molecular mechanisms for this association are still mostly unknown. To identify potential changes in the transcriptional and epigenetic regulation in rhinovirus-associated atopic or non-atopic asthma we analyzed a cohort of 5-year-old children (n = 45) according to the virus etiology of the first severe wheezing episode at the mean age of 13 months and to five-year asthma outcome. The development of atopic asthma in children with early rhinovirus-induced wheezing was associated with DNA methylation changes at several genomic sites in chromosomal regions previously linked to asthma...
May 5, 2018: Allergy
https://www.readbyqxmd.com/read/29724885/a-simple-method-for-visualization-of-locus-specific-h4k20me1-modifications-in-living-caenorhabditis-elegans-single-cells
#10
Yoichi Shinkai, Masahiro Kuramochi, Motomichi Doi
Recently, advances in next-generation sequencing technologies have enabled genome-wide analyses of epigenetic modifications; however, it remains difficult to analyze the states of histone modifications at a single-cell resolution in living multicellular organisms because of the heterogeneity within cellular populations. Here we describe a simple method to visualize histone modifications on the specific sequence of target locus at a single-cell resolution in living Caenorhabditis elegans , by combining the LacO/LacI system and a genetically-encoded H4K20me1-specific probe, "mintbody"...
May 3, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29723955/the-methylome-of-vertebrate-sex-chromosomes
#11
REVIEW
Shafagh A Waters, Alexander Capraro, Kim L McIntyre, Jennifer A Marshall Graves, Paul D Waters
DNA methylation is a key epigenetic modification in vertebrate genomes known to be involved in the regulation of gene expression, X chromosome inactivation, genomic imprinting, chromatin structure, and control of transposable elements. DNA methylation is common to all eukaryote genomes, but we still lack a complete understanding of the variation in DNA methylation patterns on sex chromosomes and between the sexes in diverse species. To better understand sex chromosome DNA methylation patterns between different amniote vertebrates, we review literature that has analyzed the genome-wide distribution of DNA methylation in mammals and birds...
May 1, 2018: Genes
https://www.readbyqxmd.com/read/29712868/-insulin-promoter-in-human-pancreatic-%C3%AE-cells-contacts-diabetes-susceptibility-loci-and-regulates-genes-affecting-insulin-metabolism
#12
Xing Jian, Gary Felsenfeld
Both type 1 and type 2 diabetes involve a complex interplay between genetic, epigenetic, and environmental factors. Our laboratory has been interested in the physical interactions, in nuclei of human pancreatic β cells, between the insulin ( INS) gene and other genes that are involved in insulin metabolism. We have identified, using Circularized Chromosome Conformation Capture (4C), many physical contacts in a human pancreatic β cell line between the INS promoter on chromosome 11 and sites on most other chromosomes...
April 30, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29697370/ldsplitdb-a-database-for-studies-of-meiotic-recombination-hotspots-in-mhc-using-human-genomic-data
#13
Jing Guo, Hao Chen, Peng Yang, Yew Ti Lee, Min Wu, Teresa M Przytycka, Chee Keong Kwoh, Jie Zheng
BACKGROUND: Meiotic recombination happens during the process of meiosis when chromosomes inherited from two parents exchange genetic materials to generate chromosomes in the gamete cells. The recombination events tend to occur in narrow genomic regions called recombination hotspots. Its dysregulation could lead to serious human diseases such as birth defects. Although the regulatory mechanism of recombination events is still unclear, DNA sequence polymorphisms have been found to play crucial roles in the regulation of recombination hotspots...
April 20, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/29691407/long-ncrna-a-rod-activates-its-target-gene-dkk1-at-its-release-from-chromatin
#14
Evgenia Ntini, Annita Louloupi, Julia Liz, Jose M Muino, Annalisa Marsico, Ulf Andersson Vang Ørom
Long ncRNAs are often enriched in the nucleus and at chromatin, but whether their dissociation from chromatin is important for their role in transcription regulation is unclear. Here, we group long ncRNAs using epigenetic marks, expression and strength of chromosomal interactions; we find that long ncRNAs transcribed from loci engaged in strong long-range chromosomal interactions are less abundant at chromatin, suggesting the release from chromatin as a crucial functional aspect of long ncRNAs in transcription regulation of their target genes...
April 24, 2018: Nature Communications
https://www.readbyqxmd.com/read/29668306/dosage-compensation-of-the-x-chromosome-a-complex-epigenetic-assignment-involving-chromatin-regulators-and-long-noncoding-rnas
#15
Maria Samata, Asifa Akhtar
X chromosome regulation represents a prime example of an epigenetic phenomenon where coordinated regulation of a whole chromosome is required. In flies, this is achieved by transcriptional upregulation of X chromosomal genes in males to equalize the gene dosage differences in females. Chromatin-bound proteins and long noncoding RNAs (lncRNAs) constituting a ribonucleoprotein complex known as the male-specific lethal (MSL) complex or the dosage compensation complex mediate this process. MSL complex members decorate the male X chromosome, and their absence leads to male lethality...
April 18, 2018: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/29667298/distinct-chromatin-structures-at-the-monoamine-oxidase-a-maoa-promoter-correlate-with-allele-specific-expression-in-sh-sy5y-cells
#16
M Manca, V Pessoa, P Myers, A Pickles, J Hill, H Sharp, C Murgatroyd, V J Bubb, J P Quinn
Monoamine oxidase-A (MAOA) metabolises monoamines and is implicated in the pathophysiology of psychiatric disorders. A polymorphic repetitive DNA domain, termed the uVNTR (upstream variable number tandem repeat), located at the promoter of the MAOA gene is a risk factor for many of these disorders. MAOA is on the X chromosome suggesting gender could play a role in regulation. We analysed MAOA regulation in the human female cell line, SH-SY5Y, which is polymorphic for the uVNTR. This heterozygosity allowed us to correlate allele specific gene expression with allele specific transcription factor binding and epigenetic marks for MAOA...
April 18, 2018: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29662485/our-environment-shapes-us-the-importance-of-environment-and-sex-differences-in-regulation-of-autoantibody-production
#17
REVIEW
Michael Edwards, Rujuan Dai, S Ansar Ahmed
Consequential differences exist between the male and female immune systems' ability to respond to pathogens, environmental insults or self-antigens, and subsequent effects on immunoregulation. In general, females when compared with their male counterparts, respond to pathogenic stimuli and vaccines more robustly, with heightened production of antibodies, pro-inflammatory cytokines, and chemokines. While the precise reasons for sex differences in immune response to different stimuli are not yet well understood, females are more resistant to infectious diseases and much more likely to develop autoimmune diseases...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/29661849/feedback-regulation-by-antagonistic-epigenetic-factors-potentially-maintains-homeostasis-in-drosophila
#18
Devendran A Sadasivam, Der-Hwa Huang
Polycomb group (PcG) repressors confer epigenetically heritable silencing on key regulatory genes through histone H3 trimethylation on lysine 27 (H3K27me3). How the silencing state withstands antagonistic activities from co-expressed trithorax group (trxG) activators is unclear. Using overexpression of Trx H3K4 methylase to perturb the silenced state, we find a dynamic process triggered in a stepwise fashion to neutralize the inductive impacts from excess Trx. Shortly after Trx overexpression, there are global increases in H3K4 trimethylation and RNA polymerase II phosphorylation, marking active transcription...
April 16, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29651155/epigenetic-activation-during-t-helper-17-cell-differentiation-is-mediated-by-tripartite-motif-containing-28
#19
Yu Jiang, Ying Liu, Huiping Lu, Shao-Cong Sun, Wei Jin, Xiaohu Wang, Chen Dong
Epigenetic regulation is important for T-cell fate decision. Although STAT3 is known to initiate Th17 differentiation program, the downstream mechanism is unclear. Here we show that Tripartite motif containing 28 (Trim28) expression in Th17 cells is required for Th17-mediated cytokine production and experimental autoimmune diseases. Genome-wide occupancy analysis reveals that TRIM28-bound regions overlap with almost all Th17-specific super-enhancers (SE), and that those SEs are impaired by the deficiency of STAT3 or TRIM28, but not of RORγt...
April 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29649500/cancer-development-and-therapy-resistance-spotlights-on-the-dark-side-of-the-genome
#20
REVIEW
Eleonora Leucci
Cancer research has been focusing so far on genetic alterations in protein-coding genes. However, mounting evidence underlines the importance of epigenetic and post-transcriptional events in cancer progression and therapy resistance. Moreover, recent genome-wide studies show that disease-causing mutations and chromosome rearrangements often span areas of the genome that do not contain any known protein-coding gene. This finding is not surprising, considering that even though the vast majority of the human genome is transcribed, only a minor portion (accounting for less than 2%) encodes for proteins...
April 9, 2018: Pharmacology & Therapeutics
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