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methylation sequencing

Masashi Nomura, Kuniaki Saito, Koki Aihara, Genta Nagae, Shogo Yamamoto, Kenji Tatsuno, Hiroki Ueda, Shiro Fukuda, Takayoshi Umeda, Shota Tanaka, Shunsaku Takayanagi, Ryohei Otani, Takahide Nejo, Taijun Hana, Satoshi Takahashi, Yosuke Kitagawa, Mayu Omata, Fumi Higuchi, Taishi Nakamura, Yoshihiro Muragaki, Yoshitaka Narita, Motoo Nagane, Ryo Nishikawa, Keisuke Ueki, Nobuhito Saito, Hiroyuki Aburatani, Akitake Mukasa
To elucidate the mechanisms of malignant progression of lower-grade glioma, molecular profiling using methylation array, whole-exome sequencing, and RNA sequencing was performed for 122, 36 and 31 gliomas, respectively. This cohort included 24 matched pairs of initial lower-grade gliomas and recurrent tumors, most of which showed malignant progression. Nearly half of IDH-mutant glioblastomas that had progressed from lower-grade gliomas exhibited characteristic partial DNA demethylation in previously methylated genomic regions of their corresponding initial tumors, which had the glioma CpG island methylator phenotype (G-CIMP)...
February 13, 2019: Scientific Reports
Nahyeon Kang, Su Yeon Choi, Bit Na Kim, Chang Dong Yeo, Chan Kwon Park, Young Kyoon Kim, Tae-Jung Kim, Seong-Beom Lee, Sug Hyung Lee, Jong Y Park, Mi Sun Park, Hyeon Woo Yim, Seung Joon Kim
BACKGROUND: A hypoxic microenvironment leads to an increase in the invasiveness and the metastatic potential of cancer cells within tumors via the epithelial-mesenchymal transition (EMT) and cancer stemness acquisition. However, hypoxia-induced changes in the expression and function of candidate stem cell markers and their possible molecular mechanism is still not understood. METHODS: Lung cell lines were analyzed in normoxic or hypoxic conditions. For screening among the stem cell markers, a transcriptome analysis using next-generation sequencing was performed...
February 13, 2019: BMC Cancer
Shenglin Liu, Anne Aageaard, Jesper Bechsgaard, Trine Bilde
Variation in DNA methylation patterns among genes, individuals, and populations appears to be highly variable among taxa, but our understanding of the functional significance of this variation is still incomplete. We here present the first whole genome bisulfite sequencing of a chelicerate species, the social spider Stegodyphus dumicola . We show that DNA methylation occurs mainly in CpG context and is concentrated in genes. This is a pattern also documented in other invertebrates. We present RNA sequence data to investigate the role of DNA methylation in gene regulation and show that, within individuals, methylated genes are more expressed than genes that are not methylated and that methylated genes are more stably expressed across individuals than unmethylated genes...
February 12, 2019: Genes
Garima Garg, Andreas Muschaweckh, Helena Moreno, Ajithkumar Vasanthakumar, Stefan Floess, Gildas Lepennetier, Rupert Oellinger, Yifan Zhan, Tommy Regen, Michael Hiltensperger, Christian Peter, Lilian Aly, Benjamin Knier, Lakshmi Reddy Palam, Reuben Kapur, Mark H Kaplan, Ari Waisman, Roland Rad, Gunnar Schotta, Jochen Huehn, Axel Kallies, Thomas Korn
Foxp3+ regulatory T (Treg) cells restrict immune pathology in inflamed tissues; however, an inflammatory environment presents a threat to Treg cell identity and function. Here, we establish a transcriptional signature of central nervous system (CNS) Treg cells that accumulate during experimental autoimmune encephalitis (EAE) and identify a pathway that maintains Treg cell function and identity during severe inflammation. This pathway is dependent on the transcriptional regulator Blimp1, which prevents downregulation of Foxp3 expression and "toxic" gain-of-function of Treg cells in the inflamed CNS...
February 12, 2019: Cell Reports
Yanghao Hou, Jorge Pinheiro, Felix Sahm, David E Reuss, Daniel Schrimpf, Damian Stichel, Belén Casalini, Christian Koelsche, Philipp Sievers, Annika K Wefers, Annekathrin Reinhardt, Azadeh Ebrahimi, Francisco Fernández-Klett, Stefan Pusch, Jochen Meier, Leonille Schweizer, Werner Paulus, Marco Prinz, Christian Hartmann, Karl H Plate, Guido Reifenberger, Torsten Pietsch, Pascale Varlet, Mélanie Pagès, Ulrich Schüller, David Scheie, Karin de Stricker, Stephan Frank, Jürgen Hench, Bianca Pollo, Sebastian Brandner, Andreas Unterberg, Stefan M Pfister, David T W Jones, Andrey Korshunov, Wolfgang Wick, David Capper, Ingmar Blümcke, Andreas von Deimling, Luca Bertero
Papillary glioneuronal tumor (PGNT) is a WHO-defined brain tumor entity that poses a major diagnostic challenge. Recently, SLC44A1-PRKCA fusions have been described in PGNT. We subjected 28 brain tumors from different institutions histologically diagnosed as PGNT to molecular and morphological analysis. Array-based methylation analysis revealed that 17/28 tumors exhibited methylation profiles typical for other tumor entities, mostly dysembryoplastic neuroepithelial tumor and hemispheric pilocytic astrocytoma...
February 13, 2019: Acta Neuropathologica
Caleb Lareau, Divy Kangeyan, Martin J Aryee
Recent technological developments have enabled the characterization of the epigenetic landscape of single cells across a range of tissues in normal and diseased states and under various biological and chemical perturbations. While analysis of these profiles resembles methods from single-cell transcriptomic studies, unique challenges are associated with bioinformatics processing of single-cell epigenetic data, including a much larger (10-1,000×) feature set and significantly greater sparsity, requiring customized solutions...
2019: Methods in Molecular Biology
Suman Lee
Low-density lipoprotein Receptor Related Protein 1B (LRP1B) is homologous to the gigantic lipoprotein receptor-related protein 1 that belongs to the family of Low-density lipoprotein receptors. Previous genetic association studies of the LRP1B gene have shown its genetic association with obesity. Through exome sequencing of the LRP1B gene from a childhood severe obesity cohort (n = 692), we found novel single nucleotide polymorphism (rs431809) in intron 4, which has been significantly correlated with both body mass index (BMI) and waist-hip-ratio (WHR)...
February 12, 2019: Scientific Reports
Naif Abdullah Al-Dhabi, Abdul-Kareem Mohammed Ghilan, Galal Ali Esmail, Mariadhas Valan Arasu, Veeramuthu Duraipandiyan, Karuppiah Ponmurugan
BACKGROUND: Metabolites obtained from the marine microorganisms were known for their important role in microbial inhibition. Interestingly, bioprospecting of secondary metabolites from marine derived actinomycetes has huge demand especially in the treatment of multi drug resistant clinical pathogens. The present study subjected towards the identification of promising antimicrobial actinomycetes from the Arabian Gulf regions and metabolic profiling of the crude organic solvent extract by chromatographic techniques...
February 9, 2019: Journal of Infection and Public Health
Ksenia Skvortsova, Etienne Masle-Farquhar, Phuc-Loi Luu, Jenny Z Song, Wenjia Qu, Elena Zotenko, Cathryn M Gould, Qian Du, Timothy J Peters, Yolanda Colino-Sanguino, Ruth Pidsley, Shalima S Nair, Amanda Khoury, Grady C Smith, Lisa A Miosge, Joanne H Reed, James G Kench, Mark A Rubin, Lisa Horvath, Ozren Bogdanovic, Sue Mei Lim, Jose M Polo, Christopher C Goodnow, Clare Stirzaker, Susan J Clark
Promoter CpG islands are typically unmethylated in normal cells, but in cancer a proportion are subject to hypermethylation. Using methylome sequencing we identified CpG islands that display partial methylation encroachment across the 5' or 3' CpG island borders. CpG island methylation encroachment is widespread in prostate and breast cancer and commonly associates with gene suppression. We show that the pattern of H3K4me1 at CpG island borders in normal cells predicts the different modes of cancer CpG island hypermethylation...
February 11, 2019: Cancer Cell
Joel Pekow, Kyle Hernandez, Katherine Meckel, Zifeng Deng, Haider I Haider, Abdurahman Khalil, Chunling Zhang, Nitya Talisila, Shivi Siva, Farzana Jasmine, Yan Chun Li, David T Rubin, Neil Hyman, Marc Bissonnette, Christopher Weber, Muhammad G Kibriya
Background and Aims: As ulcerative colitis (UC)-associated colorectal cancer (CRC) and sporadic CRC differ in presentation and molecular features, we sought to evaluate differences in the impact of DNA methylation on gene expression. Methods : NA methylation was assessed in 11 UC-CRCs and adjacent tissue and 11 sporadic CRCs and adjacent tissue using Illumina arrays. RNA sequencing was performed on 10 UC-CRCs and adjacent tissue and 8 sporadic CRCs and adjacent tissues...
February 11, 2019: Journal of Crohn's & Colitis
Jennifer Pasquier, Mark Spurgeon, Martina Bradic, Binitha Thomas, Amal Robay, Omar Chidiac, Marie-Joe Dib, Rebal Turjoman, Alexandra Liberska, Michelle Staudt, Khalid A Fakhro, Robert Menzies, Amin Jayyousi, Mahmoud Zirie, Jassim Al Suwaidi, Rayaz A Malik, Talal Talal, Arash Rafii, Jason Mezey, Juan Rodriguez-Flores, Ronald G Crystal, Charbel Abi Khalil
AIM: To assess whether DNA methylation of monocytes play a role in the development of acute diabetic Charcot foot (CF). PATIENTS & METHODS: We studied the whole methylome (WM) of circulating monocytes in 18 patients with Type 2 diabetes (T2D) and acute CF, 18 T2D patients with equivalent neuropathy and 18 T2D patients without neuropathy, using the enhanced reduced representation bisulfite sequencing technique. RESULTS & CONCLUSION: WM analysis demonstrated that CF monocytes are differentially methylated compared with non-CF monocytes, in both CpG-site and gene-mapped analysis approaches...
February 2019: Epigenomics
Stephanie M Linker, Lara Urban, Stephen J Clark, Mariya Chhatriwala, Shradha Amatya, Davis J McCarthy, Ingo Ebersberger, Ludovic Vallier, Wolf Reik, Oliver Stegle, Marc Jan Bonder
BACKGROUND: Alternative splicing is a key regulatory mechanism in eukaryotic cells and increases the effective number of functionally distinct gene products. Using bulk RNA sequencing, splicing variation has been studied across human tissues and in genetically diverse populations. This has identified disease-relevant splicing events, as well as associations between splicing and genomic features, including sequence composition and conservation. However, variability in splicing between single cells from the same tissue or cell type and its determinants remains poorly understood...
February 11, 2019: Genome Biology
Yinghong Zhang, Yangyang Chen, Hongmei Qu, Yuanli Wang
BACKGROUND: Gestational diabetes mellitus (GDM) is defined as any degree of glucose intolerance during pregnancy, and will lead to high risk of diabetes even after pregnancy. Hypoxia-inducible factor (HIF) family proteins are transcriptional factors that are highly correlated with methylation, which might be involved in the regulation of GDM. METHODS: Baseline clinical characteristics of the GDM patients and healthy women were analyzed. Omental tissue from GDM patients and control groups were collected and detected for the expression levels of HIF1A, HIF2A, and HIF3A...
February 11, 2019: Molecular Genetics & Genomic Medicine
Shangang Jia, Kyla Morton, Chi Zhang, David Holding
Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 × Mo17 F2 ears. To better understand the functional genomics of kernel development, we developed a mapping and gene identification pipeline, bulked segregant exome sequencing (BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size...
February 8, 2019: Genomics, Proteomics & Bioinformatics
Xiang Yu, Vincent De Waele, Axel Löfberg, Vitaly Ordomsky, Andrei Y Khodakov
Chemical utilization of vast fossil and renewable feedstocks of methane remains one of the most important challenges of modern chemistry. Herein, we report direct and selective methane photocatalytic oxidation at ambient conditions into carbon monoxide, which is an important chemical intermediate and a platform molecule. The composite catalysts on the basis of zinc, tungstophosphoric acid and titania exhibit exceptional performance in this reaction, high carbon monoxide selectivity and quantum efficiency of 7...
February 11, 2019: Nature Communications
Jessica Piché, Natacha Gosset, Lisa-Marie Legault, Alain Pacis, Andrea Oneglia, Maxime Caron, Philippe Chetaille, Luis Barreiro, Donghai Liu, Xioyan Qi, Stanley Nattel, Séverine Leclerc, Mélanie Breton-Larrivée, Serge McGraw, Gregor Andelfinger
BACKGROUND & AIMS: A generalized human pacemaking syndrome, chronic atrial and intestinal dysrhythmia (CAID) (OMIM 616201), is caused by a homozygous SGO1 mutation (K23E), leading to chronic intestinal pseudo-obstruction and arrhythmias. Because CAID patients do not show phenotypes consistent with perturbation of known roles of SGO1, we hypothesized that noncanonical roles of SGO1 drive the clinical manifestations observed. METHODS: To identify a molecular signature for CAID syndrome, we achieved unbiased screens in cell lines and gut tissues from CAID patients vs wild-type controls...
October 24, 2018: Cellular and Molecular Gastroenterology and Hepatology
Sirisha Marreddy Cheedipudi, Scot J Matkovich, Cristian Coarfa, Xin Hu, Matthew J Robertson, Mary E Sweet, Matthew Taylor, Luisa Mestroni, Joseph C Cleveland, James T Willerson, Priyatansh Gurha, Ali J Marian
RATIONALE: Lamin A/C (LMNA), a nuclear membrane protein, interacts with genome through lamin-associated domains (LADs) and regulates gene expression. Mutations in the LMNA gene cause a diverse array of diseases, including dilated cardiomyopathy (DCM). DCM is the leading cause of death in laminopathies. OBJECTIVE: To identify LADs and characterize their associations with CpG methylation and gene expression in human cardiac myocytes in DCM. METHODS AND RESULTS: LMNA chromatin immunoprecipitation-sequencing, reduced representative bisulfite sequencing, and RNA-sequencing were performed in 5 control and 5 LMNA-associated DCM hearts...
February 11, 2019: Circulation Research
Chuanyu Han, Junwei Zhao, Bing Yu, Haoran Shi, Chen Zhang, Xiaowei Guo, Wensheng Xiang, Xiangjing Wang
A novel actinomycete, designated strain NEAU-HRGS1-13T , was isolated from a root of wheat (Triticum aestivum L.) and characterised using a polyphasic approach. Morphological and chemotaxonomic characteristics were consistent with those of members of the genus Microbispora. The major menaquinones were identified as MK-9(H2 ) and MK-9(H4 ) and the whole cell hydrolysates found to contain meso-diaminopimelic acid and madurose. The phospholipid profile was found to consist of diphosphatidylglycerol, a ninhydrin-positive glycophospholipid, phosphatidylinositol mannosides, phosphatidylmonomethylethanolamine, an unidentified glycolipid and an unidentified lipid...
February 9, 2019: Antonie Van Leeuwenhoek
Rufin Marie Kouipou Toghueo, Eugénie Aimée Madiesse Kemgne, Pierre Eke, Michelle Ines Mbekou Kanko, Darline Dize, Dinkar Sahal, Fabrice Fekam Boyom
ETHNOPHARMACOLOGICAL RELEVANCE: Annona muricata (Annonaceae) is a commonly used medicinal plants in Cameroonian traditional medecines to treat various diseases including malaria. Previous studies have shown that extracts from this plant have antiplasmodial activity. AIM OF THE STUDY: This study aimed to explore the endophyic fungi associated with some parts of this plant for their ability to produce antiplasmodial metabolites. MATERIALS AND METHODS: One hundred and fifty-two endophytic fungi isolated from twelve different organs of A...
February 6, 2019: Journal of Ethnopharmacology
Jing Li, Jing-Ren Zhang
Streptococcus pneumoniae undergoes phase variation or spontaneous, reversible phenotypic variation in colony opacity, encapsulation, and pilus expression. The variation in colony opacity appears to occur in all strains, whereas the switches in the production of the capsule and pilus have been observed in several strains. This chapter elaborates on the variation in colony opacity since this phenomenon has been extensively characterized. S. pneumoniae produces opaque and transparent colonies on the translucent agar medium...
January 2019: Microbiology Spectrum
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