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https://www.readbyqxmd.com/read/29909200/epigenetic-control-of-variation-and-stochasticity-in-metabolic-disease
#1
REVIEW
Ilaria Panzeri, John Andrew Pospisilik
BACKGROUND: The alarming rise of obesity and its associated comorbidities represents a medical burden and a major global health and economic issue. Understanding etiological mechanisms underpinning susceptibility and therapeutic response is of primary importance. Obesity, diabetes, and metabolic diseases are complex trait disorders with only partial genetic heritability, indicating important roles for environmental programing and epigenetic effects. SCOPE OF THE REVIEW: We will highlight some of the reasons for the scarce predictability of metabolic diseases...
May 18, 2018: Molecular Metabolism
https://www.readbyqxmd.com/read/29908908/myocardin-related-transcription-factor-a-mrtf-a-contributes-to-acute-kidney-injury-by-regulating-macrophage-ros-production
#2
Li Liu, Xiaoyan Wu, Huihui Xu, Liming Yu, Xinjian Zhang, Luyang Li, Jianliang Jin, Tao Zhang, Yong Xu
A host of pathogenic factors induce acute kidney injury (AKI) leading to insufficiencies of renal function. In the present study we evaluated the role of myocardin-related transcription factor A (MRTF-A) in the pathogenesis of AKI. We report that systemic deletion of MRTF-A or inhibition of MRTF-A activity with CCG-1423 significantly attenuated AKI in mice induced by either ischemia-reperfusion or LPS injection. Of note, MRTF-A deficiency or suppression resulted in diminished renal ROS production in AKI models with down-regulation of NAPDH oxdiase 1 (NOX1) and NOX4 expression...
June 14, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29908485/myeloid-kdm6b-deficiency-results-in-advanced-atherosclerosis
#3
Annette E Neele, Marion J J Gijbels, Saskia van der Velden, Marten A Hoeksema, Marieke C S Boshuizen, Koen H M Prange, Hung-Jen Chen, Jan Van den Bossche, Cindy P P A van Roomen, Annelie Shami, Johannes H M Levels, Jeffrey Kroon, Tina Lucas, Stefanie Dimmeler, Esther Lutgens, Menno P J de Winther
BACKGROUND AND AIMS: Atherosclerosis is a lipid-driven chronic inflammatory disorder of the arteries, and monocytes and macrophages play a central role in this process. Within the atherosclerotic lesion, macrophages can scavenge modified lipids and become the so-called foam cells. We previously reported that the epigenetic enzyme Kdm6b (also known as Jmjd3) controls the pro-fibrotic transcriptional profile of peritoneal foam cells. Given the importance of these cells in atherosclerosis, we now studied the effect of myeloid Kdm6b on disease progression...
June 1, 2018: Atherosclerosis
https://www.readbyqxmd.com/read/29908427/epigenome-regulation-during-germ-cell-specification-and-development-from-pluripotent-stem-cells
#4
REVIEW
Kazuki Kurimoto, Mitinori Saitou
Germ cells undergo epigenome reprogramming for proper development of the next generation. The realization of germ cell derivation from human and mouse pluripotent stem cells offers unprecedented opportunity for investigation of germline development. Primordial germ cells reconstituted in vitro (PGC-like cells [PGCLCs]) show progressive dilution of genomic DNA methylation, tightly linked with chromatin remodeling, during their specification. PGCLCs can be further expanded by plane culture, allowing maintenance of the gene-expression profiles of early PGCs and continuance of the DNA methylation erasure, thereby establishing an epigenetic `blank slate'...
June 13, 2018: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/29908298/hydrogen-sulfide-epigenetically-mitigates-bone-loss-through-opg-rankl-regulation-during-hyperhomocysteinemia-in-mice
#5
Jyotirmaya Behera, Akash K George, Michael J Voor, Suresh C Tyagi, Neetu Tyagi
Hydrogen sulfide (H2 S) is a novel gasotransmitter produced endogenously in mammalian cells, which works by mediating diverse physiological functions. An imbalance in H2 S metabolism is associated with defective bone homeostasis. However, it is unknown whether H2 S plays any epigenetic role in bone loss induced by hyperhomocysteinemia (HHcy). We demonstrate that diet-induced HHcy, a mouse model of metabolite induced osteoporosis, alters homocysteine metabolism by decreasing plasma levels of H2 S. Treatment with NaHS (H2 S donor), normalizes the plasma level of H2 S and further alleviates HHcy induced trabecular bone loss and mechanical strength...
June 13, 2018: Bone
https://www.readbyqxmd.com/read/29908293/reversible-rna-modification-n-1-methyladenosine-m-1-a-in-mrna-and-trna
#6
REVIEW
Chi Zhang, Guifang Jia
More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from N6 -methyladenosine (m6 A), N1 -methyladenosine (m1 A) has been found as a reversible modification in tRNA and mRNA. m1 A occurs at positions 9, 14, and 58 of tRNA, with m1 A58 being critical for tRNA stability. Other than the hundreds of m1 A sites in mRNA and long non-coding RNA transcripts, transcriptome-wide mapping of m1 A also identifies > 20 m1 A sites in mitochondrial genes...
June 13, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29908284/downregulation-of-scara5-may-contribute-to-breast-cancer-via-promoter-hypermethylation
#7
Damla Ulker, Yeliz Emine Ersoy, Zuhal Gucin, Mahmut Muslumanoglu, Nur Buyru
Breast cancer is the most common malignant tumor in women worldwide. Breast tumors mostly exhibit aberrant gene expression and DNA hypermethylation patterns that predispose the disease. Understanding the genetic and epigenetic factors that contribute to breast cancer development is important to identify novel diagnostic and prognostic markers. SCARA5: Scavenger receptor class A, member 5; is a member of the scavenger receptor family located on chromosome 8p21 which is a frequently deleted region in human cancers...
June 13, 2018: Gene
https://www.readbyqxmd.com/read/29907862/publisher-correction-ncor-smrt-co-repressors-cooperate-with-c-myc-to-create-an-epigenetic-barrier-to-somatic-cell-reprogramming
#8
Qiang Zhuang, Wenjuan Li, Christina Benda, Zhijian Huang, Tanveer Ahmed, Ping Liu, Xiangpeng Guo, David P Ibañez, Zhiwei Luo, Meng Zhang, Mazid Md Abdul, Zhongzhou Yang, Jiayin Yang, Yinghua Huang, Hui Zhang, Dehao Huang, Jianguo Zhou, Xiaofen Zhong, Xihua Zhu, Xiuling Fu, Wenxia Fan, Yulin Liu, Yan Xu, Carl Ward, Muhammad Jadoon Khan, Shahzina Kanwal, Bushra Mirza, Micky D Tortorella, Hung-Fat Tse, Jiayu Chen, Baoming Qin, Xichen Bao, Shaorong Gao, Andrew P Hutchins, Miguel A Esteban
In the version of this Article originally published, in Fig. 2c, the '+' sign and 'OSKM' were superimposed in the label '+OSKM'. In Fig. 4e, in the labels, all instances of 'Ant' should have been 'Anti-'. And, in Fig. 7a, the label '0.0' was misplaced; it should have been on the colour scale bar. These figures have now been corrected in the online versions.
June 15, 2018: Nature Cell Biology
https://www.readbyqxmd.com/read/29907786/a-gene-co-expression-network-model-identifies-yield-related-vicinity-networks-in-jatropha-curcas-shoot-system
#9
Nisha Govender, Siju Senan, Zeti-Azura Mohamed-Hussein, Ratnam Wickneswari
The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes...
June 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29907738/epigenetic-regulation-of-the-oxytocin-receptor-is-associated-with-neural-response-during-selective-social-attention
#10
Meghan H Puglia, Jessica J Connelly, James P Morris
Aberrant attentional biases to social stimuli have been implicated in a number of disorders including autism and social anxiety disorder. Oxytocin, a naturally-occurring mammalian hormone and neuromodulator involved in regulating social behavior, has been proposed to impact basic biological systems that facilitate the detection of and orientation to social information. Here, we investigate a role for naturally-occurring variability in the endogenous oxytocinergic system in regulating neural response during attention to social information...
June 15, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29907588/bai1-stabilizes-p53-to-suppress-medulloblastoma-tumorigenesis
#11
(no author information available yet)
Epigenetic silencing of BAI1 results in p53 degradation and accelerated medulloblastoma tumorigenesis.
June 15, 2018: Cancer Discovery
https://www.readbyqxmd.com/read/29907340/roles-of-aldolase-family-genes-in-human-cancers-and-diseases
#12
REVIEW
Yu-Chan Chang, Yi-Chieh Yang, Chia-Ping Tien, Chih-Jen Yang, Michael Hsiao
The aldolase family members involved in metabolism and glycolysis are present in three isoforms: ALDOA, ALDOB, and ALDOC. Aldolases are differentially expressed in human tissues, and aberrant expression has been observed in several human diseases and cancer types. However, non-enzymatic functions through protein-protein interactions or epigenetic modifications have been reported in recent years. Using high-throughput screening and -omics database integration, aldolase has been validated as an independent clinical prognostic marker of human cancers...
June 12, 2018: Trends in Endocrinology and Metabolism: TEM
https://www.readbyqxmd.com/read/29907088/development-and-application-of-an-integrated-allele-specific-pipeline-for-methylomic-and-epigenomic-analysis-mea
#13
Julien Richard Albert, Tasuku Koike, Hamid Younesy, Richard Thompson, Aaron B Bogutz, Mohammad M Karimi, Matthew C Lorincz
BACKGROUND: Allele-specific transcriptional regulation, including of imprinted genes, is essential for normal mammalian development. While the regulatory regions controlling imprinted genes are associated with DNA methylation (DNAme) and specific histone modifications, the interplay between transcription and these epigenetic marks at allelic resolution is typically not investigated genome-wide due to a lack of bioinformatic packages that can process and integrate multiple epigenomic datasets with allelic resolution...
June 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29906745/long-noncoding-rna-linc00460-targets-mir-539-mmp-9-to-promote-meningioma-progression-and-metastasis
#14
Hongshun Xing, Shilei Wang, Quancai Li, Yongqian Ma, Peng Sun
Emerging evidence reveal that long noncoding RNAs (lncRNAs) participates in the epigenetic regulation of pathophysiological process. However, the deepgoing role of lncRNAs on meningioma is still unclear. In present study, we investigate the roles of lncRNA LINC00460 in meningeoma tissue and uncover its molecular mechanism. Results revealed that LINC00460 expression level was significantly up-regulated in meningeoma tissues and malignant meningeoma cell lines (IOMM-Lee, CH157-MN). Mechanically, loss-of-function assays showed that LINC00460 knockdown significantly suppressed the proliferation ability, increased the apoptosis and decreased the proteins (MMP-2, MMP-9, ZEB1) expression...
June 12, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29906417/selection-and-application-of-tissue-micrornas-for-non-endoscopic-diagnosis-of-barrett-s-esophagus
#15
Xiaodun Li, Sam Kleeman, Sally B Coburn, Carlo Fumagalli, Juliane Perner, Sriganesh Jammula, Ruth M Pfeiffer, Linda Orzolek, Haiping Hao, Philip R Taylor, Ahmad Miremadi, Núria Galeano-Dalmau, Pierre Lao-Sirieix, Maria Tennyson, Shona MacRae, Michael B Cook, Rebecca C Fitzgerald
BACKGROUND & AIMS: MicroRNA (miRNA) is highly stable in biospecimens and provides tissue-specific profiles, making it a useful biomarker of carcinogenesis. We aimed to discover a set of miRNAs that could accurately discriminate Barrett's esophagus (BE) from normal esophageal tissue and to test its diagnostic accuracy when applied to samples collected by a non-invasive esophageal cell sampling device. METHODS: We analyzed miRNA expression profiles of 2 independent sets of esophageal biopsy tissues collected during endoscopy from 38 patients with BE and 26 patients with normal esophagus (controls) using Agilent microarray and Nanostring counter assays...
June 12, 2018: Gastroenterology
https://www.readbyqxmd.com/read/29906262/exposure-to-polycyclic-aromatic-hydrocarbons-and-accelerated-dna-methylation-aging
#16
Jun Li, Xiaoyan Zhu, Kuai Yu, Haijing Jiang, Yizhi Zhang, Biqi Wang, Xuezhen Liu, Siyun Deng, Jie Hu, Qifei Deng, Huizhen Sun, Huan Guo, Xiaomin Zhang, Weihong Chen, Jing Yuan, Meian He, Yansen Bai, Xu Han, Bing Liu, Chuanyao Liu, Yanjun Guo, Bing Zhang, Zhihong Zhang, Frank B Hu, Wenjing Gao, Liming Li, Mark Lathrop, Catherine Laprise, Liming Liang, Tangchun Wu
BACKGROUND: Aging is related to an increased risk of morbidity and mortality and is affected by environmental factors. Exposure to polycyclic aromatic hydrocarbons (PAHs) is associated with adverse health outcomes; but the association of such exposure with DNA methylation aging, a novel aging marker, is unclear. OBJECTIVES: Our aim was to investigate the association of PAH exposure with methylation aging. METHODS: We trained and validated a methylation age predictor suitable for Chinese populations using whole blood methylation data in 989 Chinese and 160 Caucasians...
June 2018: Environmental Health Perspectives
https://www.readbyqxmd.com/read/29905852/omics-studies-for-comprehensive-understanding-of-immunoglobulin-a-nephropathy-state-of-the-art-and-future-directions
#17
Francesco Paolo Schena, Grazia Serino, Fabio Sallustio, Mario Falchi, Sharon N Cox
Immunoglobulin A nephropathy (IgAN) is the most common worldwide primary glomerulonephritis with a strong autoimmune component. The disease shows variability in both clinical phenotypes and endpoints and can be potentially subdivided into more homogeneous subtypes through the identification of specific molecular biomarkers. This review focuses on the role of omics in driving the identification of potential molecular subtypes of the disease through the integration of multilevel data from genomics, transcriptomics, epigenomics, proteomics and metabolomics...
June 13, 2018: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29905846/5-formylcytosine-mediated-dna-protein-cross-links-block-dna-replication-and-induce-mutations-in-human-cells
#18
Shaofei Ji, Iwen Fu, Spandana Naldiga, Hongzhao Shao, Ashis K Basu, Suse Broyde, Natalia Y Tretyakova
5-Formylcytosine (5fC) is an epigenetic DNA modification introduced via TET protein-mediated oxidation of 5-methyl-dC. We recently reported that 5fC form reversible DNA-protein conjugates (DPCs) with histone proteins in living cells (Ji et al. (2017) Angew. Chem. Int. Ed., 56:14130-14134). We now examined the effects of 5fC mediated DPCs on DNA replication. Synthetic DNA duplexes containing site-specific DPCs between 5fC and lysine-containing proteins and peptides were subjected to primer extension experiments in the presence of human translesion synthesis DNA polymerases η and κ...
June 14, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29905794/a-brief-overview-of-the-swi1-prion-swi
#19
Dustin K Goncharoff, Zhiqiang Du, Liming Li
Prion and prion-like phenomena are involved in the pathology of numerous human neurodegenerative diseases. The budding yeast, Saccharomyces cerevisiae, has a number of endogenous yeast prions-epigenetic elements that are transmitted as altered protein conformations and often manifested as heritable phenotypic traits. One such yeast prion, [SWI+], was discovered and characterized by our laboratory. The protein determinant of [SWI+], Swi1 was found to contain an amino-terminal, asparagine-rich prion domain. Normally, Swi1 functions as part of the SWI/SNF chromatin remodeling complex, thus, acting as a global transcriptional regulator...
September 1, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29905748/protected-2-deoxyribonucleoside-triphosphate-building-blocks-for-the-photocaging-of-epigenetic-5-hydroxymethyl-cytosine-in-dna
#20
Soňa Boháčová, Zuzana Vaníková, Lenka Poštová Slavětínská, Michal Hocek
2'-Deoxyribonucleoside triphosphates (dNTPs) containing 5-(hydroxymethyl)cytosine (5hmC) protected with photocleavable groups (2-nitrobenzyl or 6-nitropiperonyl) were prepared and studied as substrates for the enzymatic synthesis of oligonucleotides and DNA containing a photocaged epigenetic 5hmC base. DNA probes containing photocaged or free 5hmC in the recognition sequence of restriction endonucleases were prepared and used for the study of the photorelease of caged DNA by UV or visible light at different wavelengths...
June 15, 2018: Organic & Biomolecular Chemistry
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