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https://www.readbyqxmd.com/read/29453410/molecular-characterization-of-colorectal-adenomas-with-and-without-malignancy-reveals-distinguishing-genome-transcriptome-and-methylome-alterations
#1
Brooke R Druliner, Panwen Wang, Taejeong Bae, Saurabh Baheti, Seth Slettedahl, Douglas Mahoney, Nikolaos Vasmatzis, Hang Xu, Minsoo Kim, Matthew Bockol, Daniel O'Brien, Diane Grill, Nathaniel Warner, Miguel Munoz-Gomez, Kimberlee Kossick, Ruth Johnson, Mohamad Mouchli, Donna Felmlee-Devine, Jill Washechek-Aletto, Thomas Smyrk, Ann Oberg, Junwen Wang, Nicholas Chia, Alexej Abyzov, David Ahlquist, Lisa A Boardman
The majority of colorectal cancer (CRC) arises from precursor lesions known as polyps. The molecular determinants that distinguish benign from malignant polyps remain unclear. To molecularly characterize polyps, we utilized Cancer Adjacent Polyp (CAP) and Cancer Free Polyp (CFP) patients. CAPs had tissues from the residual polyp of origin and contiguous cancer; CFPs had polyp tissues matched to CAPs based on polyp size, histology and dysplasia. To determine whether molecular features distinguish CAPs and CFPs, we conducted Whole Genome Sequencing, RNA-seq, and RRBS on over 90 tissues from 31 patients...
February 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29452952/phasevarions-of-bacterial-pathogens-methylomics-sheds-new-light-on-old-enemies
#2
REVIEW
John M Atack, Aimee Tan, Lauren O Bakaletz, Michael P Jennings, Kate L Seib
A wide variety of bacterial pathogens express phase-variable DNA methyltransferases that control expression of multiple genes via epigenetic mechanisms. These randomly switching regulons - phasevarions - regulate genes involved in pathogenesis, host adaptation, and antibiotic resistance. Individual phase-variable genes can be identified in silico as they contain easily recognized features such as simple sequence repeats (SSRs) or inverted repeats (IRs) that mediate the random switching of expression. Conversely, phasevarion-controlled genes do not contain any easily identifiable features...
February 13, 2018: Trends in Microbiology
https://www.readbyqxmd.com/read/29451304/distinct-methylation-profile-of-mucinous-ovarian-carcinoma-reveals-susceptibility-to-proteasome-inhibitors
#3
Phui-Ly Liew, Rui-Lan Huang, Yu-Chun Weng, Chia-Lang Fang, Tim Hui-Ming Huang, Hung-Cheng Lai
Mucinous type of epithelial ovarian cancer (MuOC) is a unique subtype with a poor survival outcome in recurrent and advanced stages. The role of type-specific epigenomics and its clinical significance remain uncertain. We analyzed the methylomic profiles of six benign mucinous adenomas, 24 MuOCs, 103 serous type of epithelial ovarian cancers (SeOCs), and 337 nonepithelial ovarian cancers. MuOC and SeOC exhibited distinct DNA methylation profiles comprising 101 genes, 81 of which exhibited low methylation in MuOC and were associated with the response to glucocorticoid, ATP hydrolysis-coupled proton transport, proteolysis involved in the cellular protein catabolic process, and ion transmembrane transport...
February 16, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29447401/ramwas-fast-methylome-wide-association-study-pipeline-for-enrichment-platforms
#4
Andrey A Shabalin, Mohammad W Hattab, Shaunna L Clark, Robin F Chan, Gaurav Kumar, Karolina A Aberg, Edwin J C G van den Oord, Inanc Birol
Motivation: Enrichment-based technologies can provide measurements of DNA methylation at tens of millions of CpGs for thousands of samples. Existing tools for methylome-wide association studies cannot analyze data sets of this size and lack important features like principal component analysis, combined analysis with SNP data, and outcome predictions that are based on all informative methylation sites. Results: We present a Bioconductor R package called RaMWAS with a full set of tools for large-scale methylome-wide association studies...
February 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29444314/diffuse-astrocytoma-idh-wildtype-a-dissolving-diagnosis
#5
Martin Hasselblatt, Mohammed Jaber, David Reuss, Oliver Grauer, Annkatrin Bibo, Stephanie Terwey, Uta Schick, Heinrich Ebel, Thomas Niederstadt, Walter Stummer, Andreas von Deimling, Werner Paulus
The histological and molecular features and even the mere existence of diffuse astrocytoma, IDH-wildtype, remain unclear. We therefore examined 212 diffuse astrocytomas (grade II WHO) in adults using IDH1(R132H) immunohistochemistry followed by IDH1/IDH2 sequencing and neuroimaging review. DNA methylation status and copy number profiles were assessed by Infinium HumanMethylation450k BeadChip. Only 25/212 patients harbored tumors without IDH1/IDH2 hotspot mutations and without contrast enhancement. By DNA methylation profiling, 10/25 tumors were classified as glioblastoma, IDH-wildtype, and an additional 7 cases could not be classified using methylome analysis, but showed genetic characteristics of glioblastoma...
February 9, 2018: Journal of Neuropathology and Experimental Neurology
https://www.readbyqxmd.com/read/29444255/identification-of-the-dna-methyltransferases-establishing-the-methylome-of-the-cyanobacterium-synechocystis-sp-pcc-6803
#6
Martin Hagemann, Katrin Gärtner, Matthias Scharnagl, Paul Bolay, Steffen C Lott, Janina Fuss, Bruno Huettel, Richard Reinhardt, Stephan Klähn, Wolfgang R Hess
DNA methylation in bacteria is important for defense against foreign DNA, but is also involved in DNA repair, replication, chromosome partitioning, and regulatory processes. Thus, characterization of the underlying DNA methyltransferases in genetically tractable bacteria is of paramount importance. Here, we characterized the methylome and orphan methyltransferases in the model cyanobacterium Synechocystis sp. PCC 6803. Single molecule real-time (SMRT) sequencing revealed four DNA methylation recognition sequences in addition to the previously known motif m5CGATCG, which is recognized by M...
February 12, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29439055/complete-genome-sequence-and-methylome-analysis-of-bacillus-caldolyticus-neb414
#7
Alexey Fomenkov, Tamas Vincze, Fana Mersha, Richard J Roberts
Bacillus caldolyticus NEB414 is the original source strain for the restriction enzyme BclI. Its complete sequence and full methylome were determined using single-molecule real-time sequencing.
February 8, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29435496/zika-virus-alters-dna-methylation-of-neural-genes-in-an-organoid-model-of-the-developing-human-brain
#8
Sylvie Janssens, Michael Schotsaert, Rahul Karnik, Vinod Balasubramaniam, Marion Dejosez, Alexander Meissner, Adolfo García-Sastre, Thomas P Zwaka
Zika virus (ZIKV) infection during early pregnancy can cause microcephaly and associated defects at birth, but whether it can induce neurologic sequelae that appear later in life remains unclear. Using a model of the developing brain based on embryonic stem cell-derived brain organoids, we studied the impact of ZIKV infection on the DNA methylation pattern across the entire genome in selected neural cell types. The virus unexpectedly alters the DNA methylome of neural progenitors, astrocytes, and differentiated neurons at genes that have been implicated in the pathogenesis of a number of brain disorders, most prominently mental retardation and schizophrenia...
January 2018: MSystems
https://www.readbyqxmd.com/read/29430824/dna-methylation-analyses-of-the-candidate-genes-identified-by-a-methylome-wide-association-study-revealed-common-epigenetic-alterations-in-schizophrenia-and-bipolar-disorder
#9
Hiroko Sugawara, Yui Murata, Tempei Ikegame, Rie Sawamura, Shota Shimanaga, Yusuke Takeoka, Takeo Saito, Masashi Ikeda, Akane Yoshikawa, Fumichika Nishimura, Yoshiya Kawamura, Chihiro Kakiuchi, Tsukasa Sasaki, Nakao Iwata, Mamoru Hashimoto, Kiyoto Kasai, Tadafumi Kato, Miki Bundo, Kazuya Iwamoto
AIM: Schizophrenia (SZ) and bipolar disorder (BD) have been known to share genetic and environmental risk factors, and complex gene-environmental interactions may contribute to their pathophysiology. In contrast to high genetic overlap between SZ and BD, as revealed by genome-wide association studies, the extent of epigenetic overlap remains largely unknown. In the present study, we explore if SZ and BD share epigenetic risk factors in the same manner as they share genetic components...
February 11, 2018: Psychiatry and Clinical Neurosciences
https://www.readbyqxmd.com/read/29429977/zfx-acts-as-a-transcriptional-activator-in-multiple-types-of-human-tumors-by-binding-downstream-of-transcription-start-sites-at-the-majority-of-cpg-island-promoters
#10
Suhn Kyong Rhie, Lijun Yao, Zhifei Luo, Heather Witt, Shannon Schreiner, Yu Guo, Andrew A Perez, Peggy J Farnham
High expression of the transcription factor ZFX is correlated with proliferation, tumorigenesis, and patient survival in multiple types of human cancers. However, the mechanism by which ZFX influences transcriptional regulation has not been determined. We performed ChIP-seq in four cancer cell lines (representing kidney, colon, prostate, and breast cancers) to identify ZFX binding sites throughout the human genome. We identified ~9,000 ZFX binding sites and found that the majority of the sites are in CpG island promoters...
February 2, 2018: Genome Research
https://www.readbyqxmd.com/read/29427646/epigenetic-deregulation-in-chronic-lymphocytic-leukemia-clinical-and-biological-impact
#11
REVIEW
Larry Mansouri, Justyna Anna Wierzbinska, Christoph Plass, Richard Rosenquist
Deregulated transcriptional control caused by aberrant DNA methylation and/or histone modifications is a hallmark of cancer cells. In chronic lymphocytic leukemia (CLL), the most common adult leukemia, the epigenetic 'landscape' has added a new layer of complexity to our understanding of this clinically and biologically heterogeneous disease. Early studies identified aberrant DNA methylation, often based on single gene promoter analysis with both biological and clinical impact. Subsequent genome-wide profiling studies revealed differential DNA methylation between CLLs and controls and in prognostics subgroups of the disease...
February 7, 2018: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/29422656/methylation-profiling-identifies-two-subclasses-of-squamous-cell-carcinoma-related-to-distinct-cells-of-origin
#12
Manuel Rodríguez-Paredes, Felix Bormann, Günter Raddatz, Julian Gutekunst, Carlota Lucena-Porcel, Florian Köhler, Elisabeth Wurzer, Katrin Schmidt, Stefan Gallinat, Horst Wenck, Joachim Röwert-Huber, Evgeniya Denisova, Lars Feuerbach, Jeongbin Park, Benedikt Brors, Esther Herpel, Ingo Nindl, Thomas G Hofmann, Marc Winnefeld, Frank Lyko
Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer and usually progresses from a UV-induced precancerous lesion termed actinic keratosis (AK). Despite various efforts to characterize these lesions molecularly, the etiology of AK and its progression to cSCC remain partially understood. Here, we use Infinium MethylationEPIC BeadChips to interrogate the DNA methylation status in healthy, AK and cSCC epidermis samples. Importantly, we show that AK methylation patterns already display classical features of cancer methylomes and are highly similar to cSCC profiles...
February 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29422066/genome-wide-analyses-reveal-a-role-of-polycomb-in-promoting-hypomethylation-of-dna-methylation-valleys
#13
Yuanyuan Li, Hui Zheng, Qiujun Wang, Chen Zhou, Lei Wei, Xuehui Liu, Wenhao Zhang, Yu Zhang, Zhenhai Du, Xiaowo Wang, Wei Xie
BACKGROUND: Previous studies showed that the majority of developmental genes are devoid of DNA methylation at promoters even when they are repressed. Such hypomethylated regions at developmental genes are unusually large and extend well beyond proximal promoters, forming DNA methylation valleys (DMVs) or DNA methylation canyons. However, it remains elusive how most developmental genes can evade DNA methylation regardless of their transcriptional states. RESULTS: We show that DMVs are hypomethylated in development and are highly conserved across vertebrates...
February 8, 2018: Genome Biology
https://www.readbyqxmd.com/read/29420690/omicsprint-detection-of-data-linkage-errors-in-multiple-omics-studies
#14
Maarten van Iterson, Davy Cats, Paul Hop, Bastiaan T Heijmans, Oliver Stegle
Summary: OmicsPrint is a versatile method for the detection of data linkage errors inmultiple omics studies encompassing genetic, transcriptome and/or methylome data. OmicsPrint evaluates data linkage within and between omics data types using genotype calls from SNP arrays, DNA sequencing or RNA sequencing data and includes an algorithm to infer genotypes from Illumina DNA methylation array data. The method uses classification to verify assumed relationships and detect any data linkage errors, for example arising from sample mix-ups and mislabeling...
February 6, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29416619/the-inhibitory-activity-of-gallic-acid-against-dna-methylation-application-of-gallic-acid-on-epigenetic-therapy-of-human-cancers
#15
Yui-Ping Weng, Pin-Feng Hung, Wen-Yen Ku, Chang-Yuan Chang, Bo-Han Wu, Ming-Han Wu, Jau-Ying Yao, Ji-Rui Yang, Chia-Huei Lee
Epigenome aberrations have been observed in tobacco-associated human malignancies. (-)-epigallocatechin-3-gallate (EGCG) has been proven to modulate gene expression by targeting DNA methyltransferases (DNMTs) through a proposed mechanism involving the gallate moiety of EGCG. We show that gallic acid (GA) changes the methylome of lung cancer and pre-malignant oral cell lines and markedly reduces both nuclear and cytoplasmic DNMT1 and DNMT3B within 1 week. GA exhibits stronger cytotoxicity against the lung cancer cell line H1299 than EGCG...
January 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29416007/genome-wide-dna-methylation-analysis-reveals-that-mouse-chemical-ipscs-have-closer-epigenetic-features-to-mescs-than-oskm-integrated-ipscs
#16
Wangfang Ping, Jian Hu, Gongcheng Hu, Yawei Song, Qing Xia, Mingze Yao, Shixin Gong, Cizhong Jiang, Hongjie Yao
Induced pluripotent stem cells can be derived from somatic cells through ectopic expression of transcription factors or chemical cocktails. Chemical iPSCs (C-iPSCs) and OSKM-iPSCs (4F-iPSCs) have been suggested to have similar characteristics to mouse embryonic stem cells (mESCs). However, their epigenetic equivalence remains incompletely understood throughout the genome. In this study, we have generated mouse C-iPSCs and 4F-iPSCs, and further compared the genome-wide DNA methylomes of C-iPSCs, 4F-iPSCs, and mESCs that were maintained in 2i and LIF...
February 7, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29410710/identification-of-reliable-biomarkers-of-human-papillomavirus-16-methylation-in-cervical-lesions-based-on-integration-status-using-high-resolution-melting-analysis
#17
Lu Liu, Chunmei Ying, Zhen Zhao, Long Sui, Xinyan Zhang, Chunyan Qian, Qing Wang, Limei Chen, Qisang Guo, Jiangnan Wu
Background: The dynamic methylation of human papillomavirus (HPV) 16 DNA is thought to be associated with the progression of cervical lesions. Previous studies that did not consider the physical status of HPV 16 may have incorrectly mapped HPV 16 methylomes. In order to identify reliable biomarkers for squamous cervical cancer (SCC), we comprehensively evaluated the methylation of HPV 16 depending on the integration incidence of each sample. Methods: Based on the integration status of 115 HPV 16-infected patients (50 SCC, 30 high-grade squamous intraepithelial lesion [HSIL], and 35 low-grade squamous intraepithelial lesion [LSIL]) and HPV 16-infected Caski cell lines by PCR detection of integrated papillomavirus sequences, we designed a series of primers that would not be influenced by breakpoints for a high-resolution melting (HRM) PCR method to detect the genome methylation...
2018: Clinical Epigenetics
https://www.readbyqxmd.com/read/29409498/dna-methylome-profiling-at-single-base-resolution-through-bisulfite-sequencing-of-5mc-immunoprecipitated-dna
#18
Zhen Jia, Yueyi Shi, Lei Zhang, Yipeng Ren, Tong Wang, Lejun Xing, Baorong Zhang, Guolan Gao, Rongfa Bu
BACKGROUND: Detection of DNA methylome at single-base resolution is a significant challenge but promises to shed considerable light on human disease etiology. Current technologies could not detect DNA methylation genome-wide at single-base resolution with small amount of sequencing data and could not avoid detecting the methylation of repetitive elements which are considered as "junk DNA". METHODS: In this study, we have developed a novel DNA methylome profiling technology named MB-seq with its ability to identify genome-wide 5mC and quantify DNA methylation levels by introduced an assistant adapter AluI-linker This linker can be ligated to sonicated DNA and then be digested after the bisulfite treatment and amplification, which has no effect of MeDIP enrichment...
February 6, 2018: BMC Biotechnology
https://www.readbyqxmd.com/read/29409445/integrative-analysis-of-methylomic-and-transcriptomic-data-in-fetal-sheep-muscle-tissues-in-response-to-maternal-diet-during-pregnancy
#19
Hadjer Namous, Francisco Peñagaricano, Marcello Del Corvo, Emanuele Capra, David L Thomas, Alessandra Stella, John L Williams, Paolo Ajmone Marsan, Hasan Khatib
BACKGROUND: Numerous studies have established a link between maternal diet and the physiological and metabolic phenotypes of their offspring. In previous studies in sheep, we demonstrated that different maternal diets altered the transcriptome of fetal tissues. However, the mechanisms underlying transcriptomic changes are poorly understood. DNA methylation is an epigenetic mark regulating transcription and is largely influenced by dietary components of the one-carbon cycle that generate the methyl group donor, SAM...
February 6, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29396421/conserved-noncoding-sequences-conserve-biological-networks-and-influence-genome-evolution
#20
Jianbo Xie, Kecheng Qian, Jingna Si, Liang Xiao, Dong Ci, Deqiang Zhang
Comparative genomics approaches have identified numerous conserved cis-regulatory sequences near genes in plant genomes. Despite the identification of these conserved noncoding sequences (CNSs), our knowledge of their functional importance and selection remains limited. Here, we used a combination of DNA methylome analysis, microarray expression analyses, and functional annotation to study these sequences in the model tree Populus trichocarpa. Methylation in CG contexts and non-CG contexts was lower in CNSs, particularly CNSs in the 5'-upstream regions of genes, compared with other sites in the genome...
February 3, 2018: Heredity
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