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Lili Tang, Yuyan Cheng, Caihong Zhu, Chao Yang, Lu Liu, Yuanjing Zhang, Leilei Wen, Xuejun Zhang, Fusheng Zhou, Sen Yang
BACKGROUND: Recent studies have revealed that DNA methylation (DNAm) could modulate gene expression in psoriasis (Ps). However, the relationship between whole-genome DNAm and gene expression in Ps has not been studied yet. OBJECTIVES: To better characterize the relationship between DNAm and gene expression, and to identify biological pathways triggered by changes in methylation involved in the pathogenesis of Ps. METHODS: Differentially methylated sites (DMSs) and differentially expressed genes (DEGs) were analysed by comparing 20 involved psoriatic (PP) skin, 20 uninvolved psoriatic (PN) skin and 20 normal (NN) skin biopsies...
June 9, 2018: Journal of Dermatological Science
Antti Häkkinen, Amjad Alkodsi, Chiara Facciotto, Kaiyang Zhang, Katja Kaipio, Sirpa Leppä, Olli Carpén, Seija Grénman, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Motivation: DNA methylation aberrations are common in many cancer types. A major challenge hindering comparison of patient-derived samples is that they comprise of heterogeneous collection of cancer and microenvironment cells. We present a computational method that allows comparing cancer methylomes in two or more heterogeneous tumor samples featuring differing, unknown fraction of cancer cells. The method is unique in that it allows comparison also in the absence of normal cell control samples and without prior tumor purity estimates, as these are often unavailable or unreliable in clinical samples...
April 18, 2018: Bioinformatics
Z Jiang, J Lin, H Dong, X Zheng, S L Marjani, J Duan, Z Ouyang, J Chen, X C Tian
DNA methylation is an important epigenetic modification that undergoes dynamic changes in mammalian embryogenesis, during which both parental genomes are reprogrammed. Despite the many immunostaining studies that have assessed global methylation, the gene-specific DNA methylation patterns in bovine preimplantation embryos are unknown. Using reduced representation bisulfite sequencing, we determined genome-scale DNA methylation of bovine sperm and individual in vivo developed oocytes and preimplantation embryos...
June 14, 2018: Biology of Reproduction
Takeyuki Tsuchida, Tatsuo Mano, Kagari-Koshi-Mano, Taro Bannai, Tomoyasu Matsubara, Satoshi Yamashita, Toshikazu Ushijima, Kenichi Nagata, Shigeo Murayama, Tatsushi Toda, Shoji Tsuji, Atsushi Iwata
Lewy body disease (LBD) is characterized by accumulation of aggregated α-synuclein in the central nervous system as eosinophilic cytoplasmic inclusions called Lewy bodies. According to their distribution pattern, it is classified into brainstem LBD, limbic LBD and diffuse neocortical LBD. It has been reported that α-synuclein affects various points in the MAPK cascade but its relationship with FGF receptors, which are the most upstream of the pathway, has not been previously investigated. We discovered that among the four FGFRs, FGFR3 showed neuronal upregulation in LBD brains histopathologically...
June 14, 2018: Brain Research
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
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
Guy Journo, Carmel Tushinsky, Asia Shterngas, Nir Avital, Yonatan Eran, Marcela Viviana Karpuj, Milana Frenkel-Morgenstern, Meir Shamay
Kaposi's sarcoma associated herpesvirus (KSHV, HHV-8) is a gamma herpesvirus associated with several human malignancies. DNA methylation at CpG dinucleotides is an epigenetic mark dysregulated in many cancer types, and in KSHV infected cells. Several previous studies have analyzed in detail the CpG methylation of the KSHV episomal genomes, but little is known about the impact of KSHV on the human genome. Our knowledge of cellular CpG methylation in the context of KSHV infection is currently limited to four hyper-methylated human gene promoters...
June 13, 2018: Journal of Virology
A Fu, H R Chang, Z F Zhang
Increasingly affordable high-throughput molecular profiling technologies have made feasible the measurement of omics-wide interindividual variations for the purposes of predicting cancer prognosis. While multiple types of genetic, epigenetic, and expression changes have been implicated in ovarian cancer, existing prognostic biomarker strategies are constrained to analyzing single classes of molecular variations. The extra predictive power afforded by the integration of multiple omics types remains largely unexplored...
April 20, 2018: Carcinogenesis
Ting Qi, Yang Wu, Jian Zeng, Futao Zhang, Angli Xue, Longda Jiang, Zhihong Zhu, Kathryn Kemper, Loic Yengo, Zhili Zheng, Riccardo E Marioni, Grant W Montgomery, Ian J Deary, Naomi R Wray, Peter M Visscher, Allan F McRae, Jian Yang
Understanding the difference in genetic regulation of gene expression between brain and blood is important for discovering genes for brain-related traits and disorders. Here, we estimate the correlation of genetic effects at the top-associated cis-expression or -DNA methylation (DNAm) quantitative trait loci (cis-eQTLs or cis-mQTLs) between brain and blood (r b ). Using publicly available data, we find that genetic effects at the top cis-eQTLs or mQTLs are highly correlated between independent brain and blood samples ([Formula: see text] for cis-eQTLs and [Formula: see text] for cis-mQTLs)...
June 11, 2018: Nature Communications
Prasad G Iyer, William R Taylor, Michele L Johnson, Ramona L Lansing, Kristyn A Maixner, Tracy C Yab, Julie A Simonson, Mary E Devens, Seth W Slettedahl, Douglas W Mahoney, Calise K Berger, Patrick H Foote, Thomas C Smyrk, Kenneth K Wang, Herbert C Wolfsen, David A Ahlquist
BACKGROUND: Minimally invasive methods have been described to detect Barrett's esophagus (BE), but are limited by subjectivity and suboptimal accuracy. We identified methylated DNA markers (MDMs) for BE in tissue and assessed their accuracy on whole esophagus brushings and capsule sponge samples. METHODS: Step 1: Unbiased whole methylome sequencing was performed on DNA from BE and normal squamous esophagus (SE) tissue. Discriminant MDM candidates were validated on an independent patient cohort (62 BE cases, 30 controls) by quantitative methylation specific PCR (qMSP)...
June 12, 2018: American Journal of Gastroenterology
Toshiki Aiba, Toshiyuki Saito, Akiko Hayashi, Shinji Sato, Harunobu Yunokawa, Toru Maruyama, Wataru Fujibuchi, Seiichiroh Ohsako
Background: There is still considerable debate about the effects of exposure to bisphenol A (BPA) an endocrine disrupter at low doses. Recently, many studies using animal models have shown that prenatal BPA exposure induces behavioral and neuronal disorders due to epigenetic changes in the brain. However, striking evidence of epigenomic changes has to be shown. Methods: To investigate whether low-dose BPA exposure in the fetal stage can alter CpG methylation levels in the central nervous system, the hippocampus of the inbred C57BL/6 J mouse as the target tissue was collected to detect alterations in CpG methylation levels using a highly sensitive method of genome-wide DNA methylation analysis, methylated site display-amplified fragment length polymorphism (MSD-AFLP)...
2018: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
Aaron Taudt, David Roquis, Amaryllis Vidalis, René Wardenaar, Frank Johannes, Maria Colome-Tatché-Tatché
BACKGROUND: Whole-genome bisulfite sequencing (WGBS) has become the standard method for interrogating plant methylomes at base resolution. However, deep WGBS measurements remain cost prohibitive for large, complex genomes and for population-level studies. As a result, most published plant methylomes are sequenced far below saturation, with a large proportion of cytosines having either missing data or insufficient coverage. RESULTS: Here we present METHimpute, a Hidden Markov Model (HMM) based imputation algorithm for the analysis of WGBS data...
June 7, 2018: BMC Genomics
Ru Li, Sisi Zhou, Yongbing Li, Xiaorui Shen, Zhiqiang Wang, Baoshan Chen
In eukaryotic genomes, DNA methylation is an important type of epigenetic modification that plays crucial roles in many biological processes. To investigate the impact of a hypovirus infection on the methylome of Cryphonectria parasitica , the chestnut blight fungus, whole-genome bisulfite sequencing (WGBS) was employed to generate single-base resolution methylomes of the fungus with/without hypovirus infection. The results showed that hypovirus infection alters methylation in all three contexts (CG, CHG, and CHH), especially in gene promoters...
2018: Frontiers in Microbiology
Susanne N Gröbner, Barbara C Worst, Joachim Weischenfeldt, Ivo Buchhalter, Kortine Kleinheinz, Vasilisa A Rudneva, Pascal D Johann, Gnana Prakash Balasubramanian, Maia Segura-Wang, Sebastian Brabetz, Sebastian Bender, Barbara Hutter, Dominik Sturm, Elke Pfaff, Daniel Hübschmann, Gideon Zipprich, Michael Heinold, Jürgen Eils, Christian Lawerenz, Serap Erkek, Sander Lambo, Sebastian Waszak, Claudia Blattmann, Arndt Borkhardt, Michaela Kuhlen, Angelika Eggert, Simone Fulda, Manfred Gessler, Jenny Wegert, Roland Kappler, Daniel Baumhoer, Stefan Burdach, Renate Kirschner-Schwabe, Udo Kontny, Andreas E Kulozik, Dietmar Lohmann, Simone Hettmer, Cornelia Eckert, Stefan Bielack, Michaela Nathrath, Charlotte Niemeyer, Günther H Richter, Johannes Schulte, Reiner Siebert, Frank Westermann, Jan J Molenaar, Gilles Vassal, Hendrik Witt, Birgit Burkhardt, Christian P Kratz, Olaf Witt, Cornelis M van Tilburg, Christof M Kramm, Gudrun Fleischhack, Uta Dirksen, Stefan Rutkowski, Michael Frühwald, Katja von Hoff, Stephan Wolf, Thomas Klingebiel, Ewa Koscielniak, Pablo Landgraf, Jan Koster, Adam C Resnick, Jinghui Zhang, Yanling Liu, Xin Zhou, Angela J Waanders, Danny A Zwijnenburg, Pichai Raman, Benedikt Brors, Ursula D Weber, Paul A Northcott, Kristian W Pajtler, Marcel Kool, Rosario M Piro, Jan O Korbel, Matthias Schlesner, Roland Eils, David T W Jones, Peter Lichter, Lukas Chavez, Marc Zapatka, Stefan M Pfister, Peter Lichter, Ursula Weber, Roland Eils, Andrey Korshunov, Olaf Witt, Stefan Pfister, Guido Reifenberger, Jörg Felsberg, Christof von Kalle, Manfred Schmidt, Cynthia Bartholomä, Michael Taylor, Stefan Pfister, David Jones, Peter Lichter, Natalie Jäger, Ivo Buchhalter, Jan Korbel, Adrian Stütz, Tobias Rausch, Bernhard Radlwimmer, Marie-Laure Yaspo, Hans Lehrach, Hans-Jörg Warnatz, Pablo Landgraf, Arndt Borkhardt, Benedikt Brors, Marc Zapatka, Roland Eils, Roland Eils, Jürgen Eils, Christian Lawerenz, Reiner Siebert, Susanne Wagner, Andrea Haake, Julia Richter, Gesine Richter, Roland Eils, Chris Lawerenz, Jürgen Eils, Jules Kerssemakers, Christina Jaeger-Schmidt, Ingrid Scholz, Anke K Bergmann, Christoph Borst, Birgit Burkhardt, Alexander Claviez, Martin Dreyling, Sonja Eberth, Hermann Einsele, Norbert Frickhofen, Siegfried Haas, Martin-Leo Hansmann, Dennis Karsch, Michael Kneba, Jasmin Lisfeld, Luisa Mantovani-Löffler, Marius Rohde, German Ott, Christina Stadler, Peter Staib, Stephan Stilgenbauer, Lorenz Trümper, Thorsten Zenz, Martin-Leo Hansmann, Dieter Kube, Ralf Küppers, Marc Weniger, Michael Hummel, Wolfram Klapper, Ulrike Kostezka, Dido Lenze, Peter Möller, Andreas Rosenwald, German Ott, Monika Szczepanowski, Ole Ammerpohl, Sietse M Aukema, Vera Binder, Arndt Borkhardt, Andrea Haake, Jessica I Hoell, Ellen Leich, Peter Lichter, Cristina López, Inga Nagel, Jordan Pischimariov, Bernhard Radlwimmer, Julia Richter, Philip Rosenstiel, Andreas Rosenwald, Markus Schilhabel, Stefan Schreiber, Inga Vater, Rabea Wagener, Reiner Siebert, Stephan H Bernhart, Hans Binder, Benedikt Brors, Gero Doose, Roland Eils, Steve Hoffmann, Lydia Hopp, Daniel Hübschmann, Kortine Kleinheinz, Helene Kretzmer, Markus Kreuz, Jan Korbel, David Langenberger, Markus Loeffler, Maciej Rosolowski, Matthias Schlesner, Peter F Stadler, Stephanie Sungalee
In this Article, author Benedikt Brors was erroneously associated with affiliation number '8' (Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, Tennessee, USA); the author's two other affiliations (affiliations '3' and '7', both at the German Cancer Research Center (DKFZ)) were correct. This has been corrected online.
June 6, 2018: Nature
Alan M O'Doherty, Paul McGettigan, Rachelle E Irwin, David A Magee, Dominic Gagne, Eric Fournier, Abdullah Al-Naib, Marc-André Sirard, Colum P Walsh, Claude Robert, Trudee Fair
BACKGROUND: Assisted reproductive technologies (ART) are widely used to treat fertility issues in humans and for the production of embryos in mammalian livestock. The use of these techniques, however, is not without consequence as they are often associated with inauspicious pre- and postnatal outcomes including premature birth, intrauterine growth restriction and increased incidence of epigenetic disorders in human and large offspring syndrome in cattle. Here, global DNA methylation profiles in the trophectoderm and embryonic discs of in vitro produced (IVP), superovulation-derived (SOV) and unstimulated, synchronised control day 17 bovine conceptuses (herein referred to as AI) were interrogated using the EmbryoGENE DNA Methylation Array (EDMA)...
June 5, 2018: BMC Genomics
Kyle J Burghardt, Jacyln M Goodrich, Brittany N Lines, Vicki L Ellingrod
Introduction: The mechanism by which metabolic syndrome occurs in schizophrenia is not completely known; however, previous work suggests that changes in DNA methylation may be involved which is further influenced by sex. Within this study, the DNA methylome was profiled to identify altered methylation associated with metabolic syndrome in a schizophrenia population on atypical antipsychotics. Methods: Peripheral blood from schizophrenia subjects was utilized for DNA methylation analyses...
2018: International Journal of Genomics
Zhaoxue Han, Peter A Crisp, Scott Stelpflug, Shawn M Kaeppler, Qing Li, Nathan M Springer
DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. To investigate heritable epigenetic changes as a consequence of tissue culture, a sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ∼15Mb of the maize genome for a population of plants that had been regenerated from tissue culture...
May 30, 2018: Genetics
Sonia García-Calzón, Alexander Perfilyev, Vanessa D Mello, Jussi Pihlajamäki, Charlotte Ling
Context: Epigenetics may contribute to sex-specific differences in human liver metabolism. Objective: To study the impact of sex on DNA methylation and gene expression in human liver. Design/setting: cross-sectional, Kuopio Obesity Surgery Study. Participants/Intervention: We analyzed DNA methylation with the Infinium HumanMethylation450 BeadChip in liver of an obese population (34 males, 61 females). Females had higher HDL-cholesterol levels compared with males...
May 28, 2018: Journal of Clinical Endocrinology and Metabolism
Zhibin Zhang, Jiawei Wen, Juzuo Li, Xintong Ma, Yanan Yu, Xiao Tan, Qi Wang, Bao Liu, Xiaomeng Li, Yu Li, Lei Gong
Pleurotus tuoliensis (Bailinggu, designated Pt) and P. eryngii var. eryngii (Xingbaogu, designated Pe) are highly valued edible mushrooms. We report de novo assemblies of high-quality genomes for both mushrooms based on PacBio RS II sequencing and annotation of all identified genes. A comparative genomics analysis between Pt and Pe with P. ostreatus as an outgroup taxon revealed extensive genomic divergence between the two mushroom genomes primarily due to the rapid gain of taxon-specific genes and disruption of synteny in either taxon...
May 29, 2018: Scientific Reports
Bradley W Anderson, Yun-Suhk Suh, Boram Choi, Hyuk-Joon Lee, Tracy C Yab, William Taylor, Brian A Dukek, Calise K Berger, Xiaoming Cao, Patrick H Foote, Mary E Devens, Lisa A Boardman, John B Kisiel, Douglas W Mahoney, Seth W Slettedahl, Hatim T Allawi, Graham P Lidgard, Thomas C Smyrk, Han-Kwang Yang, David A Ahlquist
PURPOSE: Gastric adenocarcinoma (GAC) is the third most common cause of cancer mortality worldwide. Accurate and affordable non-invasive detection methods have potential value for screening and surveillance. Herein, we identify novel methylated DNA markers (MDMs) for GAC, validate their discrimination for GAC in tissues from geographically separate cohorts, explore marker acquisition through the oncogenic cascade, and describe distributions of candidate MDMs in plasma from GAC cases and normal controls...
May 29, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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