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Epigenetics profilling

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https://www.readbyqxmd.com/read/28343122/genetic-and-epigenetic-variation-of-transposable-elements-in-arabidopsis
#1
REVIEW
Charles J Underwood, Ian R Henderson, Robert A Martienssen
Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation...
March 23, 2017: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/28340001/early-life-origin-of-intestinal-inflammatory-disorders
#2
Delphine Ley, Jean-Luc Desseyn, Mona Mischke, Jan Knol, Dominique Turck, Frédéric Gottrand
A growing body of evidence supports the concept of perinatal programming through which the perinatal environment affects the development of the fetus and infant, thereby modifying the risk profile for disease later in life. Increasing attention is focusing on the role of the early environment in the development of chronic intestinal disorders. Epidemiological studies have highlighted the link between perinatal factors, such as breastfeeding, cesarean delivery, and antibiotic use, and an increased risk for inflammatory bowel disease and/or celiac disease...
March 7, 2017: Nutrition Reviews
https://www.readbyqxmd.com/read/28337194/il-1%C3%AE-il-8-and-matrix-metalloproteinases-1-2-and-10-are-enriched-upon-monocyte-breast-cancer-cell-cocultivation-in-a-matrigel-based-three-dimensional-system
#3
Nancy Adriana Espinoza-Sánchez, Gloria Karina Chimal-Ramírez, Alejandra Mantilla, Ezequiel Moisés Fuentes-Pananá
Breast cancer remains the first cancer-related cause of death in women worldwide, particularly in developing countries in which most cases are diagnosed in late stages. Although most cancer studies are based in the genetic or epigenetic changes of the tumor cells, immune cells within the tumor stroma often cooperate with cancer progression. Particularly, monocytes are attracted to the tumor primary site in which they are differentiated into tumor-associated macrophages that facilitate tumor cell invasion and metastasis...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28334937/dynamically-and-epigenetically-coordinated-gata-ets-sox-transcription-factor-expression-is-indispensable-for-endothelial-cell-differentiation
#4
Yasuharu Kanki, Ryo Nakaki, Teppei Shimamura, Taichi Matsunaga, Kohei Yamamizu, Shiori Katayama, Jun-Ichi Suehiro, Tsuyoshi Osawa, Hiroyuki Aburatani, Tatsuhiko Kodama, Youichiro Wada, Jun K Yamashita, Takashi Minami
Although studies of the differentiation from mouse embryonic stem (ES) cells to vascular endothelial cells (ECs) provide an excellent model for investigating the molecular mechanisms underlying vascular development, temporal dynamics of gene expression and chromatin modifications have not been well studied. Herein, using transcriptomic and epigenomic analyses based on H3K4me3 and H3K27me3 modifications at a genome-wide scale, we analysed the EC differentiation steps from ES cells and crucial epigenetic modifications unique to ECs...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28332701/the-epigenetic-landscape-related-to-reactive-oxygen-species-formation-in-the-cardiovascular-system
#5
REVIEW
Thomas Kietzmann, Andreas Petry, Antonina Shvetsova, Joachim M Gerhold, Agnes Görlach
Cardiovascular diseases are the leading cause of death worldwide. Reactive oxygen species (ROS) can act as damaging molecules but also represent central hubs in cellular signalling networks. Increasing evidence indicates that ROS play an important role in the pathogenesis of cardiovascular diseases, although the underlying mechanisms and consequences of pathophysiological elevated ROS in the cardiovascular system are still not completely resolved. More recently, alterations of the epigenetic landscape which can affect DNA methylation, post-translational histone modifications, ATP-dependent alterations to chromatin and non-coding RNA transcripts, have been considered to be of increasing importance in the pathogenesis of cardiovascular diseases...
March 23, 2017: British Journal of Pharmacology
https://www.readbyqxmd.com/read/28330812/molecular-evidence-for-differential-long-term-outcomes-of-early-life-severe-acute-malnutrition
#6
Allan Sheppard, Sherry Ngo, Xiaoling Li, Michael Boyne, Debbie Thompson, Anthony Pleasants, Peter Gluckman, Terrence Forrester
BACKGROUND: Severe acute malnutrition (SAM) in infants may present as one of two distinct syndromic forms: non-edematous (marasmus), with severe wasting and no nutritional edema; or edematous (kwashiorkor) with moderately severe wasting. These differences may be related to developmental changes prior to the exposure to SAM and phenotypic changes appear to persist into adulthood with differences between the two groups. We examined whether the different response to SAM and subsequent trajectories may be explained by developmentally-induced epigenetic differences...
March 8, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28328153/behavioral-transcriptomic-and-epigenetic-responses-to-social-challenge-in-honey-bees
#7
Hagai Y Shpigler, Michael C Saul, Emma E Murdoch, Amy C Cash-Ahmed, Christopher H Seward, Laura Sloofman, Sriram Chandrasekaran, Saurabh Sinha, Lisa J Stubbs, Gene E Robinson
Understanding how social experiences are represented in the brain and shape future responses is a major challenge in the study of behavior. We addressed this problem by studying behavioral, transcriptomic and epigenetic responses to intrusion in honey bees. Previous research showed that initial exposure to an intruder provokes an immediate attack; we now show that this also leads to longer-term changes in behavior in the response to a second intruder, with increases in the probability of responding aggressively and the intensity of aggression lasting two and one hours, respectively...
March 22, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28324113/microrna-expression-patterns-involved-in-amyloid-beta-induced-retinal-degeneration
#8
Peirong Huang, Junran Sun, Fenghua Wang, Xueting Luo, Jingyang Feng, Qing Gu, Te Liu, Xiaodong Sun
Purpose: Dry age-related macular degeneration (AMD) is characterized by the accumulation of drusen under Bruch's membrane, and amyloid beta (Aβ) is speculated to be one of the key pathologic factors. While the detrimental effects of Aβ on retinas have been widely explored, Aβ-induced epigenetic regulatory changes have yet to be fully investigated. We therefore aimed to identify the microRNA (miRNA) expression profiles in an Aβ-induced mouse model of retinal degeneration. Methods: C57BL/6 mice were intravitreally injected with Aβ1-40 or PBS and the eye tissues were collected for hematoxylin and eosin (H&E) staining, apoptosis immunofluorescence staining, and miRNA profiling...
March 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28321510/dna-methylation-patterns-of-behavior-related-gene-promoter-regions-dissect-the-gray-wolf-from-domestic-dog-breeds
#9
Zsofia Banlaki, Giulia Cimarelli, Zsofia Viranyi, Eniko Kubinyi, Maria Sasvari-Szekely, Zsolt Ronai
A growing body of evidence highlights the relationship between epigenetics, especially DNA methylation, and population divergence as well as speciation. However, little is known about how general the phenomenon of epigenetics-wise separation of different populations is, or whether population assignment is, possible based on solely epigenetic marks. In the present study, we compared DNA methylation profiles between four different canine populations: three domestic dog breeds and their ancestor the gray wolf...
March 21, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28320934/allele-specific-non-cg-dna-methylation-marks-domains-of-active-chromatin-in-female-mouse-brain
#10
Christopher L Keown, Joel B Berletch, Rosa Castanon, Joseph R Nery, Christine M Disteche, Joseph R Ecker, Eran A Mukamel
DNA methylation at gene promoters in a CG context is associated with transcriptional repression, including at genes silenced on the inactive X chromosome in females. Non-CG methylation (mCH) is a distinct feature of the neuronal epigenome that is differentially distributed between males and females on the X chromosome. However, little is known about differences in mCH on the active (Xa) and inactive (Xi) X chromosomes because stochastic X-chromosome inactivation (XCI) confounds allele-specific epigenomic profiling...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28320365/systematic-review-of-lung-function-and-copd-with-peripheral-blood-dna-methylation-in-population-based-studies
#11
Matthew Machin, André F S Amaral, Matthias Wielscher, Faisal I Rezwan, Medea Imboden, Marjo-Riitta Jarvelin, Ian M Adcock, Nicole Probst-Hensch, John W Holloway, Deborah L Jarvis
BACKGROUND: Epigenetic variations in peripheral blood have potential as biomarkers for disease. This systematic review assesses the association of lung function and chronic obstructive pulmonary disease (COPD) with DNA methylation profiles in peripheral blood from population-based studies. METHODS: Online databases Medline, Embase, and Web of Science were searched. Google Scholar was searched to identify grey literature. After removing duplicate articles, 1155 articles were independently screened by two investigators...
March 20, 2017: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/28319850/methylation-of-hpa-axis-related-genes-in-men-with-hypersexual-disorder
#12
Jussi Jokinen, Adrian E Boström, Andreas Chatzittofis, Diana M Ciuculete, Katarina Görts Öberg, John N Flanagan, Stefan Arver, Helgi B Schiöth
Hypersexual Disorder (HD) defined as non-paraphilic sexual desire disorder with components of compulsivity, impulsivity and behavioral addiction, and proposed as a diagnosis in the DSM 5, shares some overlapping features with substance use disorder including common neurotransmitter systems and dysregulated hypothalamic-pituitary-adrenal (HPA) axis function. In this study, comprising 67 HD male patients and 39 male healthy volunteers, we aimed to identify HPA-axis coupled CpG-sites, in which modifications of the epigenetic profile are associated with hypersexuality...
March 10, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28319609/developmental-alterations-in-huntington-s-disease-neural-cells-and-pharmacological-rescue-in-cells-and-mice
#13
(no author information available yet)
Neural cultures derived from Huntington's disease (HD) patient-derived induced pluripotent stem cells were used for 'omics' analyses to identify mechanisms underlying neurodegeneration. RNA-seq analysis identified genes in glutamate and GABA signaling, axonal guidance and calcium influx whose expression was decreased in HD cultures. One-third of gene changes were in pathways regulating neuronal development and maturation. When mapped to stages of mouse striatal development, the profiles aligned with earlier embryonic stages of neuronal differentiation...
March 20, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28315775/assessment-of-histone-tail-modifications-and-transcriptional-profiling-during-colon-cancer-progression-reveals-a-global-decrease-in-h3k4me3-activity
#14
Karen Triff, Mathew W McLean, Kranti Konganti, Jiahui Pang, Evelyn Callaway, Beiyan Zhou, Ivan Ivanov, Robert S Chapkin
During colon cancer, epigenetic alterations contribute to the dysregulation of major cellular functions and signaling pathways. Modifications in chromatin signatures such as H3K4me3 and H3K9ac, which are associated with transcriptionally active genes, can lead to genomic instability and perturb the expression of gene sets associated with oncogenic processes. In order to further elucidate early pre-tumorigenic epigenetic molecular events driving CRC, we integrated diverse, genome-wide, epigenetic inputs (by high throughput sequencing of RNA, H3K4me3, and H3K9ac) and compared differentially expressed transcripts (DE) and enriched regions (DER) in an in-vivo rat colon cancer progression model...
March 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28314692/identification-of-an-atypical-etiological-head-and-neck-squamous-carcinoma-subtype-featuring-the-cpg-island-methylator-phenotype
#15
K Brennan, J L Koenig, A J Gentles, J B Sunwoo, O Gevaert
Head and neck squamous cell carcinoma (HNSCC) is broadly classified into HNSCC associated with human papilloma virus (HPV) infection, and HPV negative HNSCC, which is typically smoking-related. A subset of HPV negative HNSCCs occur in patients without smoking history, however, and these etiologically 'atypical' HNSCCs disproportionately occur in the oral cavity, and in female patients, suggesting a distinct etiology. To investigate the determinants of clinical and molecular heterogeneity, we performed unsupervised clustering to classify 528 HNSCC patients from The Cancer Genome Atlas (TCGA) into putative intrinsic subtypes based on their profiles of epigenetically (DNA methylation) deregulated genes...
March 1, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28314271/identification-of-methylation-profiles-of-cancer-related-genes-in-circulating-tumor-cells-population
#16
Anna Lyberopoulou, Michail Galanopoulos, Gerasimos Aravantinos, George E Theodoropoulos, Evangelos Marinos, Efstathios P Efstathopoulos, Maria Gazouli
BACKGROUND: We performed an epigenetic analysis of the first exon of the hVIM gene and the SFRP2 in circulating tumor cells (CTCs) and correlation with the corresponding primary colorectal cancer (CRC) tissue. PATIENTS AND METHODS: CTCs detection in 52 colorectal cancer patients was managed by a multi-marker immunomagnetic method with the use of quantum dots (QDs). To determine methylation levels we used high-resolution melting (HRM) technology. RESULTS: In the case of VIM we found 76...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28302063/epigenetic-and-genetic-alterations-and-their-influence-on-gene-regulation-in-chronic-lymphocytic-leukemia
#17
Di Huang, Ivan Ovcharenko
BACKGROUND: To understand the changes of gene regulation in carcinogenesis, we explored signals of DNA methylation - a stable epigenetic mark of gene regulatory elements - and designed a computational model to profile loss and gain of regulatory elements (REs) during carcinogenesis. We also utilized sequencing data to analyze the allele frequency of single nucleotide polymorphisms (SNPs) and detected the cancer-associated SNPs, i.e., the SNPs displaying the significant allele frequency difference between cancer and normal samples...
March 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28302031/hif1a-is-overexpressed-in-medulloblastoma-and-its-inhibition-reduces-proliferation-and-increases-epas1-and-atg16l1-methylation
#18
Gustavo Alencastro Veiga Cruzeiro, Maristella Bergamo Dos Reis, Vanessa Silva Silveira, Régia Caroline Peixoto Lira, Carlos Gilberto Carlotti, Luciano Neder, Ricardo Santos Oliveira, José Andres Yunes, Silvia Regina Brandalise, Simone Aguiar, Agda Karina Eterovic, Luiz Gonzaga Tone, Carlos Alberto Scrideli, Elvis Terci Valera
BACKGROUND: Genetic and epigenetic modifications are closely related to tumor initiation and progression and can provide guidance for understanding tumor functioning, potentially leading to the discovery of new therapies. Studies have associated hypoxia-related genes to tumor progression and chemo/radioresistance in brain tumors. Information on the expression profile of hypoxia-related genes in pediatric medulloblastoma, although scarce, may reveal relevant information that could support treatment decisions...
March 15, 2017: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/28301567/integrated-analysis-of-promoter-mutation-methylation-and-expression-of-akt1-gene-in-chinese-breast-cancer-patients
#19
Jianfu Heng, Xinwu Guo, Wenhan Wu, Yue Wang, Guoli Li, Ming Chen, Limin Peng, Shouman Wang, Lizhong Dai, Lili Tang, Jun Wang
BACKGROUND: As downstream mediators of PI3K /PTEN /AKT /mTORC1 pathway, the AKT isoforms play critical roles in tumorgenesis. Although the pleiotropic effects of AKT1 in breast cancer have been reported, the genetic and epigenetic characteristics of AKT1 promoter region in breast cancer remains to be identified. In this study we aimed to investigate the promoter mutation spectrum, methylation and gene expression pattern of AKT1 and their relationship with breast cancer. METHODS: By using PCR target sequence enrichment and next-generation sequencing technology, we sequenced AKT1 promoter region in pairs of breast tumor and normal tissues from 95 unselected Chinese breast cancer patients...
2017: PloS One
https://www.readbyqxmd.com/read/28298930/predicting-the-remaining-lifespan-and-cultivation-related-loss-of-osteogenic-capacity-of-bone-marrow-multipotential-stromal-cells-applicable-across-a-broad-donor-age-range
#20
Sarah M Churchman, Sally A Boxall, Dennis McGonagle, Elena A Jones
Background and Objectives. Culture expanded multipotential stromal cells (MSCs) have considerable potential for bone regeneration therapy but their wider use is constrained by the lack of simple and predictive assays of functional potency. Extended passaging leads to loss of multipotency but speed of decline depends on MSC donor age. The aim of this study was to develop an assay predictive of MSC culture longevity applicable to a broad donor age range. Materials and Methods. Bone marrow (BM, n = 7) was obtained from a diverse range (2-72 years) of healthy donors...
2017: Stem Cells International
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