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https://www.readbyqxmd.com/read/29679643/classification-and-experimental-identification-of-plant-long-non-coding-rnas
#1
Muneeza I Rai, Maheen Alam, David A Lightfoot, Priyatansh Gurha, Ahmed J Afzal
Our understanding of gene regulation is constantly evolving. It is now clear that the majority of cellular transcripts are non-coding RNAs. The spectrum of non-coding RNAs is diverse and includes short (<200 nt) and long non-coding RNAs (lncRNAs) (>200 nt). LncRNAs regulate gene expression through diverse mechanisms. In this review, we describe the emerging roles of lncRNA mediated plant gene regulation. We discuss the current classification of lncRNAs and their role in genome organization and gene regulation...
April 18, 2018: Genomics
https://www.readbyqxmd.com/read/29679612/protein-arginine-methyltransferase-5-promotes-lung-cancer-metastasis-via-the-epigenetic-regulation-of-mir-99-family-fgfr3-signaling
#2
Pengyu Jing, Nan Zhao, Mingxiang Ye, Yong Zhang, Zhipei Zhang, Jianyong Sun, Zhengxin Wang, Jian Zhang, Zhongping Gu
Protein arginine methyltransferase 5 (PRMT5) functions as a tumor initiator to regulate several cancer progressions, such as proliferation and apoptosis, by catalyzing the symmetrical dimethylation (me2s) of arginine residues within targeted molecules. However, the exact role of PRMT5-mediated metastasis in lung cancer is not fully understood. Here, we illustrated its potential effects in lung cancer metastasis in vivo and vitro. PRMT5 was frequently overexpressed in lung tumors, and its expression was positively related to tumor stages, lymphatic metastasis and poor outcome...
April 18, 2018: Cancer Letters
https://www.readbyqxmd.com/read/29679470/molecular-progression-to-cervical-precancer-epigenetic-switch-or-sequential-model
#3
Belinda Nedjai, Caroline Reuter, Amar Ahmad, Rawinder Banwait, Rhian Warman, James Carton, Sabrina Boer, Jack Cuzick, Attila Lorincz
The evolution of precancerous cervical lesions is poorly understood. A widely held model of cervical intraepithelial neoplasia grade 3 (CIN3) development is sequential progression from normal through CIN1 and CIN2 to CIN3. Another hypothesis, the "molecular switch" model, postulates that CIN3 can evolve directly from human papillomavirus (HPV)-infected normal epithelium without progressing through CIN1 and CIN2. To shed light on this process, we compared DNA methylation of selected human biomarkers and HPV types in two groups of CIN1: CIN1 that were near or adjacent to CIN3 (adjacent-CIN1) and CIN1 that were the principal lesions with no CIN3 detected (principal-CIN1)...
April 21, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29679395/placental-adaptations-to-micronutrient-dysregulation-in-the-programming-of-chronic-disease
#4
Pierre Hofstee, Daniel McKeating, Anthony V Perkins, James S M Cuffe
Poor nutrition during pregnancy is known to impair foetal development and increase the risk of chronic disease in offspring. Both macronutrients and micronutrients are required for a healthy pregnancy although significantly less is understood about the role of micronutrients in the programming of chronic disease. This is despite the fact that modern calorie rich diets are often also deficient in key micronutrients. The importance of micronutrients in gestational disorders is clearly understood but how they impact long term disease in humans requires further investigation...
April 21, 2018: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/29679205/changes-in-the-position-and-volume-of-inactive-x-chromosomes-during-the-g0-g1-transition
#5
Guoliang Lyu, Tan Tan, Yiting Guan, Lei Sun, Qianjin Liang, Wei Tao
In female mammals, each cell silences one X chromosome by converting it into transcriptionally inert heterochromatin. The inactivation is concomitant with epigenetic changes including methylation of specific histone residues and incorporation of macroH2A. Such epigenetic changes may exert influence on the positioning of the inactive X chromosome (Xi) within the nucleus beyond the level of chromatin structure. However, the dynamic positioning of the inactive X chromosome during cell cycle remains unclear. Here, we show that H3K27me3 is a cell-cycle-independent marker for the inactivated X chromosomes in WI38 cells...
April 21, 2018: Chromosome Research
https://www.readbyqxmd.com/read/29679055/towards-annotating-the-plant-epigenome-the-arabidopsis-thaliana-small-rna-locus-map
#6
Thomas J Hardcastle, Sebastian Y Müller, David C Baulcombe
Based on 98 public and internal small RNA high throughput sequencing libraries, we mapped small RNAs to the genome of the model organism Arabidopsis thaliana and defined loci based on their expression using an empirical Bayesian approach. The resulting loci were subsequently classified based on their genetic and epigenetic context as well as their expression properties. We present the results of this classification, which broadly conforms to previously reported divisions between transcriptional and post-transcriptional gene silencing small RNAs, and to PolIV and PolV dependencies...
April 20, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29678955/studying-x-chromosome-inactivation-in-the-single-cell-genomic-era
#7
REVIEW
Andrew Keniry, Marnie E Blewitt
Single-cell genomics is set to revolutionise our understanding of how epigenetic silencing works; by studying specific epigenetic marks or chromatin conformations in single cells, it is possible to ask whether they cause transcriptional silencing or are instead a consequence of the silent state. Here, we review what single-cell genomics has revealed about X chromosome inactivation, perhaps the best characterised mammalian epigenetic process, highlighting the novel findings and important differences between mouse and human X inactivation uncovered through these studies...
April 20, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29678824/metabolic-karma-the-atherogenic-legacy-of-diabetes-the-2017-edwin-bierman-award-lecture
#8
Mark Emmanuel Cooper, Assam El-Osta, Terri Jean Allen, Anna Margareta Dorothea Watson, Merlin Christopher Thomas, Karin Agnes Maria Jandeleit-Dahm
Cardiovascular disease, despite all the recent advances in treatment of the various risk factors, remains the major cause of mortality in both type 1 and type 2 diabetes. Experimental models of diabetes-associated atherosclerosis, despite their limitations in recapitulating the human context, have assisted in the elucidation of molecular and cellular pathways implicated in the development and progression of macrovascular injury in diabetes. Our own studies have emphasized the role of oxidative stress and advanced glycation and identified potential targets for vasoprotective therapies in the setting of diabetes...
May 2018: Diabetes
https://www.readbyqxmd.com/read/29677477/systems-immunology-learning-the-rules-of-the-immune-system
#9
Alexandra-Chloé Villani, Siranush Sarkizova, Nir Hacohen
Given the many cell types and molecular components of the human immune system, along with vast variations across individuals, how should we go about developing causal and predictive explanations of immunity? A central strategy in human studies is to leverage natural variation to find relationships among variables, including DNA variants, epigenetic states, immune phenotypes, clinical descriptors, and others. Here, we focus on how natural variation is used to find patterns, infer principles, and develop predictive models for two areas: (a) immune cell activation-how single-cell profiling boosts our ability to discover immune cell types and states-and (b) antigen presentation and recognition-how models can be generated to predict presentation of antigens on MHC molecules and their detection by T cell receptors...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29677476/cd4-helper-and-cd8-cytotoxic-t-cell-differentiation
#10
Ichiro Taniuchi
A fundamental question in developmental immunology is how bipotential thymocyte precursors generate both CD4+ helper and CD8+ cytotoxic T cell lineages. The MHC specificity of αβ T cell receptors (TCRs) on precursors is closely correlated with cell fate-determining processes, prompting studies to characterize how variations in TCR signaling are linked with genetic programs establishing lineage-specific gene expression signatures, such as exclusive CD4 or CD8 expression. The key transcription factors ThPOK and Runx3 have been identified as mediating development of helper and cytotoxic T cell lineages, respectively...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29677472/translating-immunology-into-therapeutic-concepts-for-inflammatory-bowel-disease
#11
Holm H Uhlig, Fiona Powrie
Inflammatory bowel disease (IBD) defines a spectrum of complex disorders. Understanding how environmental risk factors, alterations of the intestinal microbiota, and polygenetic and epigenetic susceptibility impact on immune pathways is key for developing targeted therapies. Mechanistic understanding of polygenic IBD is complemented by Mendelian disorders that present with IBD, pharmacological interventions that cause colitis, autoimmunity, and multiple animal models. Collectively, this multifactorial pathogenesis supports a concept of immune checkpoints that control microbial-host interactions in the gut by modulating innate and adaptive immunity, as well as epithelial and mesenchymal cell responses...
April 26, 2018: Annual Review of Immunology
https://www.readbyqxmd.com/read/29676998/an-epigenetic-biomarker-of-aging-for-lifespan-and-healthspan
#12
Morgan E Levine, Ake T Lu, Austin Quach, Brian H Chen, Themistocles L Assimes, Stefania Bandinelli, Lifang Hou, Andrea A Baccarelli, James D Stewart, Yun Li, Eric A Whitsel, James G Wilson, Alex P Reiner, Abraham Aviv, Kurt Lohman, Yongmei Liu, Luigi Ferrucci, Steve Horvath
Identifying reliable biomarkers of aging is a major goal in geroscience. While the first generation of epigenetic biomarkers of aging were developed using chronological age as a surrogate for biological age, we hypothesized that incorporation of composite clinical measures of phenotypic age that capture differences in lifespan and healthspan may identify novel CpGs and facilitate the development of a more powerful epigenetic biomarker of aging. Using an innovative two-step process, we develop a new epigenetic biomarker of aging, DNAm PhenoAge, that strongly outperforms previous measures in regards to predictions for a variety of aging outcomes, including all-cause mortality, cancers, healthspan, physical functioning, and Alzheimer's disease...
April 18, 2018: Aging
https://www.readbyqxmd.com/read/29676649/asbestos-induces-epigenetic-repression-of-ras-association-domain-containing-protein-1-p16-kinase-4a-inhibitor-and-p14-alternative-reading-frame-in-normal-human-mesothelial-cells
#13
Sichuan Xi, Eden C Payabyab, David M Straughan, Emily S Reardon, Mary Zhang, Julie A Hong, R Taylor Ripley, Chuong D Hoang, David S Schrump
RATIONALE: Whereas asbestos burden has been linked to cytogenetic alterations in malignant pleural mesotheliomas, epigenetic aberrations induced by these fibers have not been fully delineated. OBJECTIVES: The objective of this study was to establish an in vitro model to characterize early epigenetic events potentially contributing to malignant pleural mesothelioma. METHODS: Normal human mesothelial cells (LP9 and LP3) were cultured with or without crocidolite asbestos fibers (1 or 2 μg/cm2 ) for up to 10 days...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29676638/identification-of-novel-targets-for-lung-cancer-therapy-using-an-induced-pluripotent-stem-cell-model
#14
Vivek Shukla, Mahadev Rao, Hongen Zhang, Jeanette Beers, Darawalee Wangsa, Danny Wangsa, Floryne O Buishand, Yonghong Wang, Zhiya Yu, Holly Stevenson, Emily Reardon, Kaitlin C McLoughlin, Andrew Kaufman, Eden Payabyab, Julie A Hong, Mary Zhang, Sean R Davis, Daniel C Edelman, Guokai Chen, Markku Miettinen, Nicholas Restifo, Thomas Ried, Paul S Meltzer, David S Schrump
RATIONALE: Despite extensive studies, the genetic and epigenetic mechanisms that mediate initiation and progression of lung cancers have not been fully elucidated. Previously, we have demonstrated that via complementary mechanisms, including DNA methylation, polycomb repressive complexes, and noncoding RNAs, cigarette smoke induces stem-like phenotypes that coincide with progression to malignancy in normal respiratory epithelia as well as enhanced growth and metastatic potential of lung cancer cells...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29676631/understanding-root-causes-of-asthma-perinatal-environmental-exposures-and-epigenetic-regulation
#15
Rachel L Miller, Jennifer Lawrence
A common explanation for the origins and rising prevalence of asthma is that they involve complex interactions between hereditary predispositions and environmental exposures that are incompletely understood. Yet, emerging evidence substantiates the paradigm that environmental exposures prenatally and during very early childhood induce epigenetic alterations that affect the expression of asthma genes and, thereby, asthma itself. Here, we review much of the key evidence supporting this paradigm. First, we describe evidence that the prenatal and early postnatal periods are key time windows of susceptibility to environmental exposures that may trigger asthma...
April 2018: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29676232/pharmacoepigenetics-and-pharmacoepigenomics-an-overview
#16
Jacob Peedicayil
The rapid and major advances being made in epigenetics is impacting pharmacology, giving rise to new sub-disciplines in pharmacology, pharmacoepigenetics, the study of the epigenetic basis of variation in response to drugs; and pharmacoepigenomics, the application of pharmacoepigenetics on a genome-wide scale. This article gives an overview of the current state of knowledge of pharmacoepigenetics and pharmacoepigenomics. The article highlights the following areas: epigenetic therapy, the role of epigenetics in pharmacokinetics, the relevance of epigenetics to adverse drug reactions, personalized medicine, drug addiction, and drug resistance, and the use of epigenetic biomarkers in drug therapy...
April 19, 2018: Current Drug Discovery Technologies
https://www.readbyqxmd.com/read/29676175/epigenetic-agents-in-combined-anticancer-therapy
#17
Zdeněk Kejík, Milan Jakubek, Robert Kaplánek, Jarmila Králová, Ivan Mikula, Pavel Martásek, Vladimír Král
In the last decade, epigenetic drugs (such as inhibitors of DNA methyltransferases and histone deacetylases) have been intensively used for cancer treatment. Their applications have shown high anticancer effectivity and tolerable side effects. However, they are unfortunately not effective in the treatment of some types and phenotypes of cancers. Nevertheless, several studies have demonstrated that problems of drug efficacy can be overcome through the combined application of therapeutic modulates. Therefore, combined applications of epigenetic agents with chemotherapy, radiation therapy, immunotherapy, oncolytic virotherapy and hyperthermia have been presented...
April 20, 2018: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/29675945/epigenetically-enhanced-pdt-epdt-induces-significantly-higher-levels-of-multiple-extrinsic-pathway-apoptotic-factors-than-standard-pdt-resulting-in-greater-extrinsic-and-overall-apoptosis-of-ctcl
#18
Katrin A Salva, Youn H Kim, Ziba Rahbar, Gary S Wood
Aminolevulinate-based photodynamic therapy (ALA-PDT) selectively eliminates diseased tissues primarily through the induction of intrinsic apoptotic pathway. ALA-PDT is a first-line therapy for actinic keratosis, however, it is less effective for cutaneous T-cell lymphoma (CTCL). We have previously demonstrated that the resistance of CTCL to apoptosis correlates with decreased expression of death receptors such as FAS, and that methotrexate functions as an epigenetic regulator that re-establishes the susceptibility of CTCL to extrinsic pathway apoptosis...
April 20, 2018: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/29675884/specific-breast-cancer-prognosis-subtype-distinctions-based-on-dna-methylation-patterns
#19
Shumei Zhang, Yihan Wang, Yue Gu, Jiang Zhu, Ce Ci, Zhongfu Guo, Chuangeng Chen, Yanjun Wei, Wenhua Lv, Hongbo Liu, Dongwei Zhang, Yan Zhang
Tumor heterogeneity is an obstacle to effective breast cancer diagnosis and therapy. DNA methylation is an important regulator of gene expression, thus characterizing tumor heterogeneity by epigenetic features can be clinically informative. In this study, we explored specific prognosis-subtypes based on DNA methylation status using 669 breast cancers from TCGA database. Nine subgroups were distinguished by consensus clustering using 3869 CpGs that significantly influenced survival. The specific DNA methylation patterns were reflected by different races, ages, tumor stages, receptor status, histological types, metastasis status and prognosis...
April 19, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29675472/low-input-and-multiplexed-microfluidic-assay-reveals-epigenomic-variation-across-cerebellum-and-prefrontal-cortex
#20
Sai Ma, Yuan-Pang Hsieh, Jian Ma, Chang Lu
Extensive effort is under way to survey the epigenomic landscape of primary ex vivo tissues to establish normal reference data and to discern variation associated with disease. The low abundance of some tissue types and the isolation procedure required to generate a homogenous cell population often yield a small quantity of cells for examination. This difficulty is further compounded by the need to profile a myriad of epigenetic marks. Thus, technologies that permit both ultralow input and high throughput are desired...
April 2018: Science Advances
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