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DNA methylation miRNA

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https://www.readbyqxmd.com/read/28638398/discovery-of-putative-herbicide-resistance-genes-and-its-regulatory-network-in-chickpea-using-transcriptome-sequencing
#1
Mir A Iquebal, Khela R Soren, Priyanka Gangwar, P S Shanmugavadivel, K Aravind, Deepak Singla, Sarika Jaiswal, Rahul S Jasrotia, Sushil K Chaturvedi, Narendra P Singh, Rajeev K Varshney, Anil Rai, Dinesh Kumar
Background: Chickpea (Cicer arietinum L.) contributes 75% of total pulse production. Being cheaper than animal protein, makes it important in dietary requirement of developing countries. Weed not only competes with chickpea resulting into drastic yield reduction but also creates problem of harboring fungi, bacterial diseases and insect pests. Chemical approach having new herbicide discovery has constraint of limited lead molecule options, statutory regulations and environmental clearance. Through genetic approach, transgenic herbicide tolerant crop has given successful result but led to serious concern over ecological safety thus non-transgenic approach like marker assisted selection is desirable...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28637300/commercial-rodent-diets-differentially-regulate-autoimmune-glomerulonephritis-epigenetics-and-microbiota-in-mrl-lpr-mice
#2
Michael R Edwards, Rujuan Dai, Bettina Heid, Thomas E Cecere, Deena Khan, Qinghui Mu, Catharine Cowan, Xin M Luo, S Ansar Ahmed
The course and severity of lupus in spontaneous murine lupus models varies among laboratories, which may be due to variations in diet, housing and/or local environmental conditions. In this study, we investigated the influence of common rodent diets while keeping other factors constant. Female lupus-prone MRL/lpr mice were subjected to the same housing conditions and given one of the three diets: Teklad 7013 containing isoflavone rich soy and alfalfa, Harlan 2018 isoflavone rich soy-based diet, or ResearchDiets Inc...
June 15, 2017: International Immunology
https://www.readbyqxmd.com/read/28631291/folate-deficiency-disturbs-hsa-let-7-g-level-through-methylation-regulation-in-neural-tube-defects
#3
Li Wang, Shaofang Shangguan, Yu Xin, Shaoyan Chang, Zhen Wang, Xiaolin Lu, Lihua Wu, Bo Niu, Ting Zhang
Folic acid deficiency during pregnancy is believed to be a high-risk factor for neural tube defects (NTDs). Disturbed epigenetic modifications, including miRNA regulation, have been linked to the pathogenesis of NTDs in those with folate deficiency. However, the mechanism by which folic acid-regulated miRNA influences this pathogenesis remains unclear. It is believed that DNA methylation is associated with dysregulated miRNA expression. To clarify this issue, here we measured the methylation changes of 22 miRNAs in 57 human NTD cases to explore whether such changes are involved in miRNA regulation in NTD cases through folate metabolism...
June 19, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28623912/role-of-epigenetics-microrna-axis-in-drug-resistance-of-multiple-myeloma
#4
REVIEW
Nasrin Rastgoo, Jahangir Abdi, Jian Hou, Hong Chang
Despite administration of novel therapies, multiple myeloma (MM) remains incurable with resistance to drugs leading to relapse in most patients. Thus, it is critical to understand the detailed mechanisms underlying the drug resistance of MM and develop more effective therapeutic strategies. Genetic abnormalities are well known to play a central role in MM pathogenesis and therapy resistance; however, epigenetic aberrations mainly affecting the patterns of DNA methylation/histone modifications of genes (especially tumor suppressors) and miRNAs have also been shown to be involved...
June 17, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28622513/comprehensive-and-integrative-genomic-characterization-of-hepatocellular-carcinoma
#5
(no author information available yet)
Liver cancer has the second highest worldwide cancer mortality rate and has limited therapeutic options. We analyzed 363 hepatocellular carcinoma (HCC) cases by whole-exome sequencing and DNA copy number analyses, and we analyzed 196 HCC cases by DNA methylation, RNA, miRNA, and proteomic expression also. DNA sequencing and mutation analysis identified significantly mutated genes, including LZTR1, EEF1A1, SF3B1, and SMARCA4. Significant alterations by mutation or downregulation by hypermethylation in genes likely to result in HCC metabolic reprogramming (ALB, APOB, and CPS1) were observed...
June 15, 2017: Cell
https://www.readbyqxmd.com/read/28617821/supplementation-with-small-extracellular-vesicles-from-ovarian-follicular-fluid-during-in-vitro-production-modulates-bovine-embryo-development
#6
Juliano C da Silveira, Gabriella M Andrade, Maite Del Collado, Rafael V Sampaio, Juliano R Sangalli, Luciano A Silva, Fábio V L Pinaffi, Izabelle B Jardim, Marcelo C Cesar, Marcelo F G Nogueira, Aline S M Cesar, Luiz L Coutinho, Rinaldo W Pereira, Felipe Perecin, Flávio V Meirelles
Pregnancy success results from the interaction of multiple factors, among them are folliculogenesis and early embryonic development. Failure during these different processes can lead to difficulties in conception. Alternatives to overcome these problems are based on assisted reproductive techniques. Extracellular vesicles are cell-secreted vesicles present in different body fluids and contain bioactive materials, such as messenger RNA, microRNAs (miRNAs), and proteins. Thus, our hypothesis is that extracellular vesicles from follicular fluid from 3-6 mm ovarian follicles can modulate bovine embryo development in vitro...
2017: PloS One
https://www.readbyqxmd.com/read/28612612/-molecular-aspects-of-thyroid-tumors-with-emphasis-on-microrna-and-their-clinical-implications
#7
M Ludvíková, I Kholová, D Kalfeřt
BACKGROUND: Central to neoplastic transformation and tumor progression is alteration of the signaling pathways that control cell proliferation and apoptosis. The key mechanisms for this neoplastic process are genetic changes (mutations of cancer-related genes) and recently identified epigenetic changes that involve DNA methylation, chromatin remodeling (which has a profound effect on the control of gene expression), and noncoding, regulatory RNA (notably, microRNA - miRNA). MiRNAs control expression of their target gene post-transcriptionally...
2017: Klinická Onkologie: Casopis Ceské a Slovenské Onkologické Spolecnosti
https://www.readbyqxmd.com/read/28611800/small-rna-sequencing-links-physiological-changes-and-rddm-process-to-vegetative-to-floral-transition-in-apple
#8
Xinwei Guo, Zeyang Ma, Zhonghui Zhang, Lailiang Cheng, Xiuren Zhang, Tianhong Li
Transition from vegetative to floral buds is a critical physiological change during flower induction that determines fruit productivity. Small non-coding RNAs (sRNAs) including microRNAs (miRNAs) and small interfering RNAs (siRNAs) are pivotal regulators of plant growth and development. Although the key role of sRNAs in flowering regulation has been well-described in Arabidopsis and some other annual plants, their relevance to vegetative-to-floral transition (hereafter, referred to floral transition) in perennial woody trees remains under defined...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28605519/cancersubtypes-an-r-bioconductor-package-for-molecular-cancer-subtype-identification-validation-and-visualization
#9
Taosheng Xu, Thuc Duy Le, Lin Liu, Ning Su, Rujing Wang, Bingyu Sun, Antonio Colaprico, Gianluca Bontempi, Jiuyong Li
Summary: Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes , an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization...
June 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28600480/mir-193a-3p-is-a-key-tumor-suppressor-in-ulcerative-colitis-associated-colon-cancer-and-promotes-carcinogenesis-through-up-regulation-of-il17rd
#10
Joel Pekow, Katherine Meckel, Urszula Dougherty, Yong Huang, Xindi Chen, Anas Almoghrabi, Reba Mustafi, Fatma Ayaloglu-Butun, Zifeng Deng, Haider I Haider, John Hart, David T Rubin, John H Kwon, Marc Bissonnette
Purpose: Patients with ulcerative colitis (UC) are at increased risk for colorectal cancer, although mechanisms underlying neoplastic transformation are poorly understood. We sought to evaluate the role of microRNAs in neoplasia development in this high-risk population.   <p>Experimental Design: Tissue from 12 controls, 9 UC patients without neoplasia, and 11 UC patients with neoplasia was analyzed. miRNA array analysis was performed and select miRNAs assayed by real-time PCR on the discovery cohort and a validation cohort...
June 9, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28589857/identification-of-epigenetic-interactions-between-mirna-and-dna-methylation-associated-with-gene-expression-as-potential-prognostic-markers-in-bladder-cancer
#11
Manu Shivakumar, Younghee Lee, Lisa Bang, Tullika Garg, Kyung-Ah Sohn, Dokyoon Kim
BACKGROUND: One of the fundamental challenges in cancer is to detect the regulators of gene expression changes during cancer progression. Through transcriptional silencing of critical cancer-related genes, epigenetic change such as DNA methylation plays a crucial role in cancer. In addition, miRNA, another major component of epigenome, is also a regulator at the post-transcriptional levels that modulate transcriptome changes. However, a mechanistic role of synergistic interactions between DNA methylation and miRNA as epigenetic regulators on transcriptomic changes and its association with clinical outcomes such as survival have remained largely unexplored in cancer...
May 24, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28586056/microrna-497-acts-as-a-tumor-suppressor-in-gastric-cancer-and-is-downregulated-by-dna-methylation
#12
Jichao Liu, Yongshuang Li, Ying Zou, Jiakui Zhang, Jiaxiang An, Jiao Guo, Minghui Ma, Dongqiu Dai
Gastric cancer (GC) is one of the most common malignant tumors in the world and microRNAs (miRNAs) play an important role in GC. In this study, we found miR‑497 played an important role and served as a novel biomarker in GC. Quantitative real-time PCR (qRT-PCR) was used to measure the miR‑497 expression in GC cell lines and 86 paired GC samples and we also analyzed its correlation with GC clinicopathological parameters. A series of cellular function experiments were applied to validate the effects of miR‑497 on GC...
June 6, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28586038/mir-1247-5p-functions-as-a-tumor-suppressor-in-human-hepatocellular-carcinoma-by-targeting-wnt3
#13
Yuankui Chu, Weining Fan, Wenwei Guo, Yixin Zhang, Lixin Wang, Le Guo, Xiangguo Duan, Jun Wei, Guangxian Xu
Increasing evidence suggests that aberrant expression of certain microRNAs (miRNAs) may participate in the genesis and progression of tumors. Several studies have indicated that miR-1247-5p plays different roles in various types of cancer cells. The effects of miR-1247-5p on human hepatocellular carcinoma (HCC) cells are elusive. In the present study, we investigated the effects of miR-1247-5p on the progression of HCC. The transcript of miR-1247-5p was markedly downregulated in clinical samples of patients with HCC and HCC cell lines, and ectopic overexpression of miR‑1247-5p markedly inhibited the proliferation and invasion of HepG2 cells, induced cell apoptosis in vitro, and suppressed the growth of transplanted tumors in vivo...
June 6, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28582843/acute-lymphoblastic-leukemia-and-genetic-variations-in-bhmt-gene-case-control-study-and-computational-characterization
#14
Ravishankara Bellampalli, Manik Vohra, Kashish Sharma, Nalini Bhaskaranand, Kamalakshi G Bhat, Krishna Prasad, Anu R Sharma, Kapaettu Satyamoorthy, Padmalatha S Rai
BACKGROUND: Remethylation of homocysteine is catalyzed by B12 dependent methionine synthase (MTR) in all types of cells and by B12 non-dependent betaine homocysteine methyltransferase (BHMT) in liver and kidney cells. Of many etiologies of cancer, an unexplored area is the variations of genes implicated in methylation reaction. OBJECTIVE: The study evaluated the association of BHMT (rs3733890) with acute lymphoblastic leukemia (ALL), followed by in-silico characterization of variations in BHMT gene...
May 19, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28572541/pulmonary-endothelial-cell-dna-methylation-signature-in-pulmonary-arterial-hypertension
#15
Aurélie Hautefort, Julie Chesné, Jens Preussner, Soni S Pullamsetti, Jorg Tost, Mario Looso, Fabrice Antigny, Barbara Girerd, Marianne Riou, Saadia Eddahibi, Jean-François Deleuze, Werner Seeger, Elie Fadel, Gerald Simonneau, David Montani, Marc Humbert, Frédéric Perros
Pulmonary arterial hypertension (PAH) is a severe and incurable pulmonary vascular disease. One of the primary origins of PAH is pulmonary endothelial dysfunction leading to vasoconstriction, aberrant angiogenesis and smooth muscle cell proliferation, endothelial-to-mesenchymal transition, thrombosis and inflammation. Our objective was to study the epigenetic variations in pulmonary endothelial cells (PEC) through a specific pattern of DNA methylation.DNA was extracted from cultured PEC from idiopathic PAH (n = 11), heritable PAH (n = 10) and controls (n = 18)...
May 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28548108/drugging-the-pain-epigenome
#16
REVIEW
Ellen Niederberger, Eduard Resch, Michael J Parnham, Gerd Geisslinger
More than 20% of adults worldwide experience different types of chronic pain, which are frequently associated with several comorbidities and a decrease in quality of life. Several approved painkillers are available, but current analgesics are often hampered by insufficient efficacy and/or severe adverse effects. Consequently, novel strategies for safe, highly efficacious treatments are highly desirable, particularly for chronic pain. Epigenetic mechanisms such as DNA methylation, histone modifications and microRNAs (miRNAs) strongly affect the regulation of gene expression, potentially for long periods over years or even generations, and have been associated with pathophysiological pain...
May 26, 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/28546713/current-concepts-of-epigenetics-in-testicular-cancer
#17
REVIEW
Alfredo Harb-De la Rosa, Meenakkshy Manoharan, Ahmed Saeed Goolam
Testicular germ cell tumors (GCTs) are characterized into seminomas (SGCTs) and non-seminomatous testicular germ cell tumors (NSGCTs). Serum tumor markers (STMs) play an important role in testicular cancer as they provide useful information for diagnosis, staging, and detection of recurrence. Nonetheless, additional tumor markers for early diagnosis and therapeutic options are required to enhance specificity of serological diagnosis of testes cancers. Epigenetics is defined as inherited changes in gene expression that are not encoded in the DNA structure...
June 2017: Indian Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28545228/aberrant-dna-methylation-as-a-biomarker-and-a-therapeutic-target-of-cholangiocarcinoma
#18
REVIEW
Toshiaki Nakaoka, Yoshimasa Saito, Hidetsugu Saito
Cholangiocarcinoma is an epithelial malignancy arising in the region between the intrahepatic bile ducts and the ampulla of Vater at the distal end of the common bile duct. The effect of current chemotherapy regimens against cholangiocarcinoma is limited, and the prognosis of patients with cholangiocarcinoma is poor. Aberrant DNA methylation and histone modification induce silencing of tumor suppressor genes and chromosomal instability during carcinogenesis. Studies have shown that the tumor suppressor genes and microRNAs (miRNAs) including MLH1, p14, p16, death-associated protein kinase (DAPK), miR-370 and miR-376c are frequently methylated in cholangiocarcinoma...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28543390/the-effect-of-ebv-on-wif1-nlk-and-apc-gene-methylation-and-expression-in-gastric-carcinoma-and-nasopharyngeal-cancer
#19
Zhenzhen Zhao, Wen Liu, Jincheng Liu, Jiayi Wang, Bing Luo
Epstein-Barr virus (EBV) is an important DNA tumor virus that is associated with approximately 10% of gastric carcinomas and 99% of nasopharyngeal cancers. DNA methylation and microRNAs (miRNAs) are the most studied epigenetic mechanisms that can prompt disease susceptibility. This study aimed to detect the effect of EBV on Wnt inhibitory factor 1 (WIF1), Nemo-like kinase (NLK), and adenomatous polyposis coli (APC) gene methylation and expression in gastric carcinoma and nasopharyngeal cancer. METHODS: The WIF1, NLK, and APC gene mRNA expression levels were measured by real-time quantitative RT-PCR in four EBV-positive cell lines and four EBV-negative cell lines...
May 23, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/28538662/maternal-factors-that-induce-epigenetic-changes-contribute-to-neurological-disorders-in-offspring
#20
REVIEW
Avijit Banik, Deepika Kandilya, Seshadri Ramya, Walter Stünkel, Yap Seng Chong, S Thameem Dheen
It is well established that the regulation of epigenetic factors, including chromatic reorganization, histone modifications, DNA methylation, and miRNA regulation, is critical for the normal development and functioning of the human brain. There are a number of maternal factors influencing epigenetic pathways such as lifestyle, including diet, alcohol consumption, and smoking, as well as age and infections (viral or bacterial). Genetic and metabolic alterations such as obesity, gestational diabetes mellitus (GDM), and thyroidism alter epigenetic mechanisms, thereby contributing to neurodevelopmental disorders (NDs) such as embryonic neural tube defects (NTDs), autism, Down's syndrome, Rett syndrome, and later onset of neuropsychological deficits...
May 24, 2017: Genes
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