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methylation sequencing

Haruna Saeki, Ryota Hara, Hironobu Takahashi, Miu Iijima, Ryosuke Munakata, Hiromichi Kenmoku, Kazuma Fuku, Ai Sekihara, Yoko Yasuno, Tetsuro Shinada, Daijiro Ueda, Tomoyuki Nishi, Tsutomu Sato, Yoshinori Asakawa, Fumiya Kurosaki, Kazufumi Yazaki, Futoshi Taura
Rhododendron dauricum produces daurichromenic acid, an anti-HIV meroterpenoid, via oxidative cyclization of the farnesyl group of grifolic acid. The prenyltransferase (PT) that synthesizes grifolic acid is a farnesyltransferase in plant specialized metabolism. In this study, we demonstrated that the isoprenoid moiety of grifolic acid is derived from the 2-C-methyl-D-erythritol-4-phosphate pathway that takes place in plastids. We explored candidate sequences of plastid-localized PT homologs and identified a cDNA for this PT, RdPT1, which shares moderate sequence similarity with known aromatic PTs...
August 10, 2018: Plant Physiology
Jianzhong Su, Yung-Hsin Huang, Xiaodong Cui, Xinyu Wang, Xiaotian Zhang, Yong Lei, Jianfeng Xu, Xueqiu Lin, Kaifu Chen, Jie Lv, Margaret A Goodell, Wei Li
BACKGROUND: Cancers have long been recognized to be not only genetically but also epigenetically distinct from their tissues of origin. Although genetic alterations underlying oncogene upregulation have been well studied, to what extent epigenetic mechanisms, such as DNA methylation, can also induce oncogene expression remains unknown. RESULTS: Here, through pan-cancer analysis of 4174 genome-wide profiles, including whole-genome bisulfite sequencing data from 30 normal tissues and 35 solid tumors, we discover a strong correlation between gene-body hypermethylation of DNA methylation canyons, defined as broad under-methylated regions, and overexpression of approximately 43% of homeobox genes, many of which are also oncogenes...
August 10, 2018: Genome Biology
Mohanalakshmi Narasumani, Paul M Harrison
Intrinsically disordered regions (IDRs) of proteins play significant biological functional roles despite lacking a well-defined 3D structure. For example, IDRs provide efficient housing for large numbers of post-translational modification (PTM) sites in eukaryotic proteins. Here, we study the distribution of more than 15,000 experimentally determined human methylation, acetylation and ubiquitination sites (collectively termed 'MAU' sites) in ordered and disordered regions, and analyse their conservation across 380 eukaryotic species...
August 10, 2018: PLoS Computational Biology
Cristiana Lo Nigro, Daniela Vivenza, Nerina Denaro, Laura Lattanzio, Mirella Fortunato, Tim Crook, Marco Carlo Merlano
Background: Biomarkers predictive of response to chemoradiotherapy (CRT) regimens for locally advanced head and neck squamous cell carcinoma (LA-HNSCC) are urgently required to identify patients in whom this approach is likely to be effective. TP53 mutations and epidermal growth factor (EGFR) overexpression are common markers of disease. Dual-specificity-phosphatase-2 (DUSP2) has an essential role in cell proliferation, cancer and immune responses. Methods: Aberrant DUSP2 methylation was investigated by pyrosequencing in 5 HNSCC cell lines, 112 LA-HNSCC tumours...
July 2018: Annals of Translational Medicine
Masako Suzuki, Will Liao, Frank Wos, Andrew D Johnston, Justin DeGrazia, Jennifer Ishii, Toby Bloom, Michael C Zody, Soren Germer, John M Greally
DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopulations of cells, whereas genome-wide chromatin studies lack the same quantitative capacity. Testing DNA methylation throughout the genome is possible using whole-genome bisulfite sequencing (WGBS), but the high costs associated with the assay have made it impractical for studies involving more than limited numbers of samples...
August 9, 2018: Genome Research
Miho Kashino-Fujii, Kengo Yokosho, Naoki Yamaji, Miki Yamane, Daisuke Saisho, Kazuhiro Sato, Jian Feng Ma
Aluminum (Al) toxicity is a major stress factor limiting crop productivity in acid soil. Although there is great genotypic variation in tolerance to Al toxicity, the underlying molecular mechanisms are poorly understood. Here, we report that in barley (Hordeum vulgare L.), the fourth largest cereal crop produced in the world, both retrotransposon insertion and DNA methylation are involved in regulating differential Al tolerance. HvAACT1 is a major gene responsible for citrate secretion from the roots for external detoxification of Al...
August 9, 2018: Plant Physiology
John H Yim, Audrey H Choi, Arthur X Li, Hanjun Qin, Sue Chang, Sun-Wing T Tong, Peiguo Chu, Byung-Wook Kim, Daniel Schmolze, Ryan Lew, Yasmine Ibrahim, Valeriy A Poroyko, Sylvana Salvatierra, Alysha Baker, Jinhui Wang, Xiwei Wu, Gerd P Pfeifer, Yuman Fong, Maria A Hahn
PURPOSE: Thyroid cancer is frequently difficult to diagnose due to an overlap of cytological features between malignant and benign nodules. This overlap leads to unnecessary removal of the thyroid in patients without cancer. While providing some improvement over cytopathologic diagnostics, molecular methods frequently fail to provide a correct diagnosis for thyroid nodules. These approaches are based on the difference between cancer and adjacent thyroid tissue and assume that adjacent tissues are the same as benign nodules...
August 9, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Rebecca A Luchtel, Surendra Dasari, Naoki Oishi, Martin Bjerregård Pedersen, Guangzhen Hu, Karen L Rech, Rhett P Ketterling, Jagmohan Sidhu, Xueju Wang, Ryohei Katoh, Ahmet Dogan, N Sertac Kip, Julie M Cunningham, Zhifu Sun, Saurabh Baheti, Julie C Porcher, Jonathan W Said, Liuyan Jiang, Stephen Jacques Hamilton-Dutoit, Michael Boe Møller, Peter Nørgaard, N Nora Bennani, Wee-Joo Chng, Gaofeng Huang, Brian K Link, Fabio Facchetti, James R Cerhan, Francesco d'Amore, Stephen M Ansell, Andrew L Feldman
Anaplastic large cell lymphomas (ALCLs) are CD30-positive T-cell non-Hodgkin lymphomas broadly segregated into ALK-positive and ALK-negative types. While ALK-positive ALCLs consistently bear rearrangements of the ALK tyrosine kinase gene, ALK-negative ALCLs are clinically and genetically heterogeneous. About 30% of ALK-negative ALCLs have rearrangements of DUSP22 and have excellent long-term outcomes with standard therapy. To better understand this group of tumors, we evaluated their molecular signature using gene expression profiling...
August 9, 2018: Blood
Jana Biermann, Toshima Z Parris, Szilárd Nemes, Anna Danielsson, Hanna Engqvist, Elisabeth Werner Rönnerman, Eva Forssell-Aronsson, Anikó Kovács, Per Karlsson, Khalil Helou
BACKGROUND: Molecular classification of tumour clonality is currently not evaluated in multiple invasive breast carcinomas, despite evidence suggesting common clonal origins. There is no consensus about which type of data (e.g. copy number, mutation, histology) and especially which statistical method is most suitable to distinguish clonal recurrences from independent primary tumours. METHODS: Thirty-seven invasive breast tumour pairs were stratified according to laterality and time interval between the diagnoses of the two tumours...
August 9, 2018: Breast Cancer Research: BCR
Pichai Raman, Ravikanth Maddipati, Kian Huat Lim, Aydin Tozeren
Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in the US. Despite multiple large-scale genetic sequencing studies, identification of predictors of patient survival remains challenging. We performed a comprehensive assessment and integrative analysis of large-scale gene expression datasets, across multiple platforms, to enable discovery of a prognostic gene signature for patient survival in pancreatic cancer. PDAC RNA-Sequencing data from The Cancer Genome Atlas was stratified into Survival+ (>2-year survival) and Survival-(<1-year survival) cohorts (n = 47)...
2018: PloS One
Chengliang Cao, Tangyu Xu, Jinjuan Liu, Xiaorui Cai, Yong Sun, Sheng Qin, Jihong Jiang, Ying Huang
A Gram-positive, strictly aerobic actinobacterium, designated BMP B8004T , was isolated from desert soil collected in Xinjiang Province, Northwest China. It produced an extensively branched non-fragmenting substrate mycelium, and very scanty aerial mycelium that formed a short hooked chain of arthrospores with a smooth surface. Optimum growth occurred at 28 °C, pH 7.0 and 0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BMP B8004T formed a distinct phyletic lineage within the genus Actinomadura...
August 9, 2018: International Journal of Systematic and Evolutionary Microbiology
Mark E Pepin, Chae-Myeong Ha, David K Crossman, Silvio H Litovsky, Sooryanarayana Varambally, Joseph P Barchue, Salpy V Pamboukian, Nikolaos A Diakos, Stavros G Drakos, Steven M Pogwizd, Adam R Wende
Ischemic cardiomyopathy (ICM) is the clinical endpoint of coronary heart disease and a leading cause of heart failure. Despite growing demands to develop personalized approaches to treat ICM, progress is limited by inadequate knowledge of its pathogenesis. Since epigenetics has been implicated in the development of other chronic diseases, the current study was designed to determine whether transcriptional and/or epigenetic changes are sufficient to distinguish ICM from other etiologies of heart failure. Specifically, we hypothesize that genome-wide DNA methylation encodes transcriptional reprogramming in ICM...
August 8, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
Elmira Ismaylova, Melissa L Lévesque, Florence B Pomares, Moshe Szyf, Zsofia Nemoda, Cherine Fahim, Frank Vitaro, Mara Brendgen, Ginette Dionne, Michel Boivin, Richard E Tremblay, Linda Booij
Several studies have examined associations between peripheral DNA methylation patterns of the serotonin transporter gene (SLC6A4) promoter and symptoms of depression and anxiety. The SLC6A4 promoter methylation has also been associated with frontal-limbic brain responses to negative stimuli. However, it is unclear how much of this association is confounded by DNA sequence variations. We utilized a monozygotic-twin within-pair discordance design, to test whether DNA methylation at specific CpG sites in the SLC6A4 promoter of peripheral cells is associated with greater frontal-limbic brain responses to negative stimuli (sadness and fear), independently of DNA sequence effects...
August 8, 2018: Translational Psychiatry
Mathewos Tessema, Michael R Rossi, Maria A Picchi, Christin M Yingling, Yong Lin, Suresh S Ramalingam, Steven A Belinsky
OBJECTIVES: Lung adenocarcinoma in never-smokers accounts for 15-20% of all lung cancer. Although targetable mutations are more prevalent in these tumors, the biological and clinical importance of coexisting and/or mutually exclusive abnormalities is just emerging. This study evaluates the relationships between common genetic and epigenetic aberrations in these tumors. MATERIALS AND METHODS: Next-generation sequencing was employed to screen 20 commonly mutated cancer-driver genes in 112 lung adenocarcinomas from never-smokers...
September 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
Agnieszka Sobecka, Wiktoria Blaszczak, Wojciech Barczak, Pawel Golusinski, Blazej Rubis, Michal M Masternak, Wiktoria M Suchorska, Wojciech Golusinski
Cancer cells, including head and neck cancer cell carcinoma (HNSCC), are characterized by an increased telomerase activity. This enzymatic complex is active in approximately 80-90% of all malignancies, and is regulated by various factors, including methylation status of hTERT gene promoter. hTERT methylation pattern has been thoroughly studied so far. It was proved that hTERT is aberrantly methylated in tumor tissue versus healthy counterparts. However, such effect has not yet been investigated in PBLs (peripheral blood leukocytes) of cancer patients...
August 7, 2018: Journal of Applied Genetics
Yun Feng, Jintian Song, Zixuan Zhao, Feiyi Zhao, Lingjuan Yang, Chengjin Jiao
The potato lectin has been identified to consist of two chitin-binding modules, each containing twin hevein domains. Based on the thermotolerance of the hevein polypeptide, a simple, rapid, and effective protocol for the small-scale purification of the potato lectin has been developed in this study. The method involves only one anion exchange chromatographic step beyond the ammonium sulfate precipitation and the heating treatment. With this method, the potato lectin, a glycoprotein with molecular mass of approximately 60 kDa was found and purified to homogeneity with 9513...
August 7, 2018: Glycoconjugate Journal
Shinya Kodani, Hisayuki Komaki, Hikaru Hemmi, Yuto Miyake, Issara Kaweewan, Hideo Dohra
Cyanopeptolin-type peptides are cyclic depsipeptides that commonly have 3-amino-6-hydroxy-2-piperidone (Ahp) unit in the molecules. So far, cyanopeptolin-type peptides have been isolated as protease inhibitors from a wide variety of cyanobacteria. In the course of screening for new peptides, a new peptide streptopeptolin, which had the similar structure to cyanopeptolin, was isolated from the extract of Streptomyces olivochromogenes NBRC 3561. Streptopeptolin is the first cyanopeptolin-type peptide isolated from actinobacteria...
July 31, 2018: ACS Omega
Emil H Ernst, Julie Nielsen, Malene B Ipsen, Palle Villesen, Karin Lykke-Hartmann
Emerging evidence indicated that many long non-coding (lnc)RNAs function in multiple biological processes and dysregulation of their expression can cause diseases. Most regulatory lncRNAs interact with biological macromolecules such as DNA, RNA, and protein. LncRNAs regulate gene expression through epigenetic modification, transcription, and posttranscription, through DNA methylation, histone modification, and chromatin remodeling. Interestingly, differential lncRNA expression profiles in human oocytes and cumulus cells was recently assessed, however, lncRNAs in human follicle development has not previously been described...
2018: Frontiers in Cell and Developmental Biology
Kai-Feng Ma, Qi-Xiang Zhang, Tang-Ren Cheng, Xiao-Lan Yan, Hui-Tang Pan, Jia Wang
Epigenetic changes caused by methylcytosine modification participate in gene regulation and transposable element (TE) repression, resulting in phenotypic variation. Although the effects of DNA methylation and TE repression on flower, fruit, seed coat, and leaf pigmentation have been investigated, little is known about the relationship between methylation and flower color chimerism. In this study, we used a comparative methylomic⁻transcriptomic approach to explore the molecular mechanism responsible for chimeric flowers in Prunus mume "Danban Tiaozhi"...
August 7, 2018: International Journal of Molecular Sciences
Longqing Niu, Xinxin Wang, Guobin Mao, Zheng Li, Xinghu Ji, Zhike He
DNA methyltransferase (MTase) has a crucial role in many biological processes, its abnormal expression level has been regarded as a predictive cancer biomarker. Herein, a sensitive fluorescence method based on thermosensitive poly (N-isopr-opylacrylamide) was developed to assay of M.SssI activity. When the M.SssI was introduced, dsDNA was methylated at palindromic sequence 5'-Cm CGG-3' and became resistant to cleavage by the endonuclease HpaII. Therefore, a biotin modified ssDNA and a FAM modified ssDNA were designed including the recognized sites for both methyltransferase M...
November 1, 2018: Talanta
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