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methylation sequencing

Ye Liu, Jen-Chien Chang, Chung-Chau Hon, Naoshi Fukui, Nobuho Tanaka, Zhenya Zhang, Ming Ta Michael Lee, Aki Minoda
Osteoarthritis (OA) is a common joint disorder with increasing impact in an aging society. While genetic and transcriptomic analyses have revealed some genes and non-coding loci associated to OA, the pathogenesis remains incompletely understood. Chromatin profiling, which provides insight into gene regulation, has not been reported in OA mainly due to technical difficulties. Here, we employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients...
October 19, 2018: Scientific Reports
Olya Yarychkivska, Zoha Shahabuddin, Nicole Comfort, Mathieu Boulard, Timothy H Bestor
DNA methyltransferase 1 (DNMT1) is a multidomain protein believed to be involved only in the passive transmission of genomic methylation patterns via maintenance methylation.  The mechanisms that regulate DNMT1 activity and targeting are complex and poorly understood. We used ES cells to investigate the function of the uncharacterized bromo-adjacent homology (BAH) domains and the glycine-lysine (GK) repeats that join the regulatory and catalytic domains of DNMT1. We removed the BAH domains by means of a CRISPR/Cas9-mediated deletion within the endogenous Dnmt1 locus...
October 19, 2018: Journal of Biological Chemistry
Haruhisa Suga, Mitsuhiro Arai, Emi Fukasawa, Keiichi Motohashi, Hiroyuki Nakagawa, Hideaki Tateishi, Shin-Ichi Fuji, Masafumi Shimizu, Koji Kageyama, Mitsuro Hyakumachi
Fusarium fujikuroi is a pathogenic fungus that infects rice. It produces several important mycotoxins such as fumonisins. Fumonisin production has been detected in strains of maize, strawberry, and wheat, whereas it has not been detected in strains from rice seedlings infested with bakanae disease in Japan. We investigated the genetic relationships, pathogenicity, and resistance to a fungicide-thiophanate-methyl (TM)-in 51 fumonisin-producing strains and 44 non-producing strains. Phylogenetic analyses based on amplified fragment length polymorphism (AFLP) markers and two specific genes-combined sequence of translation elongation factor 1α ( TEF1α ) and RNA polymerase II second largest-subunit ( RPB2 )-indicated differential clustering between the fumonisin-producing and non-producing strains...
October 19, 2018: Applied and Environmental Microbiology
Céline Bruno, Oxana Blagoskonov, Julie Barberet, Magali Guilleman, Sandrine Daniel, Benjamin Tournier, Christine Binquet, Cécile Choux, Patricia Fauque
BACKGROUND: Testicular germ cell tumor such as seminoma is strongly associated with male reproductive problems commonly associated with the alteration of sperm parameters as described in testicular dysgenesis syndrome. Interestingly, numerous studies have reported that the precursor of germ cell cancer, germ cell neoplasia in situ (GCNIS), present similarities to fetal gonocytes, specifically characterized by global DNA hypomethylation particularly on imprinting sequences. These disorders may have a common origin derived from perturbations of embryonal programming during fetal development...
October 19, 2018: Clinical Epigenetics
Gaurav Sharma, Rebecca Parales, Mitchell Singer
BACKGROUND: An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability to reside and thrive in its current environment. Similar to external signaling molecules, cytoplasmic signals are also sensed by methyl-accepting chemotaxis proteins (MCPs) via diverse ligand binding domains...
October 19, 2018: BMC Genomics
Mariko Murata
Infection and inflammation account for approximately 25% of cancer-causing factors. Inflammation-related cancers are characterized by mutagenic DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Our previous studies demonstrated the formation of 8-oxodG and 8-nitroguanine in the tissues of cancer and precancerous lesions due to infection (e.g., Opisthorchis viverrini-related cholangiocarcinoma, Schistosoma haematobium-associated bladder cancer, Helicobacter pylori-infected gastric cancer, human papillomavirus-related cervical cancer, Epstein-Barr virus-infected nasopharyngeal carcinoma) and pro-inflammatory factors (e...
October 20, 2018: Environmental Health and Preventive Medicine
Attila Bartal, Aruna Vigneshwari, Bettina Bóka, Mónika Vörös, István Takács, László Kredics, László Manczinger, Mónika Varga, Csaba Vágvölgyi, András Szekeres
Surfactins are lipopeptide-type biosurfactants produced mainly by Bacillus species, consisting of a peptide loop of seven amino acids and a hydrophobic fatty acid chain (C12 ⁻C16 ). These molecules have been proven to exhibit various biological activities; thus, their therapeutic and environmental applications are considered. Within the surfactin lipopeptide family, there is a wide spectrum of different homologues and isomers; to date, more than 30 variants have been described. Since the newest members of these lipopeptides were described recently, there is no information that is available on their characteristic features, e...
October 18, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Qin Jiang, Baofa Sun, Qing Liu, Min Cai, Ruifan Wu, Fengqin Wang, Yongxi Yao, Yizhen Wang, Xinxia Wang
Intramuscular fat is considered a potential factor that is associated with meat quality in animal production and insulin resistance in humans. N6 -methyladenosine (m6 A) modification of mRNA plays an important role in regulating adipogenesis. However, the effects of m6 A on the adipogenesis of intramuscular preadipocytes and associated mechanisms remain unknown. Here, we performed m6 A sequencing to compare m6 A methylome of the longissimus dorsi muscles (LDMs) between Landrace pigs (lean-type breed) and Jinhua pigs (obese-type breed with higher levels of intramuscular fat)...
October 19, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Kenneth Arrington, Gregg A Barcan, Nicholas A Calandra, Greg A Erickson, Ling Li, Li Liu, Mark G Nilson, Iulia I Strambeanu, Kelsey Faith VanGelder, John L Woodard, Shiping Xie, C Liana Allen, John A Kowalski, David C Leitch
A convergent eight-stage synthesis of the boron-containing NS5B inhibitor GSK8175 is described. The previous route involves 13 steps in a completely linear sequence, with an overall 10% yield. Key issues include a multi-day SNAr arylation of a secondary sulfonamide using HMPA as solvent, multiple functional group interconversions after all of the carbon atoms are installed (including a Sandmeyer halogenation), use of carcinogenic chloromethyl methyl ether to install a protecting group late in the synthesis, and an unreliable Pd-catalyzed Miyaura borylation as the penultimate step...
October 19, 2018: Journal of Organic Chemistry
Buce Hetharua, Derong Min, Hu Liao, Li'an Lin, Hong Xu, Yun Tian
A Gram-stain-negative Rhodobacterales strain, designated as FSX-11T , was isolated from surface seawater of Xiamen port in China. Strain FSX-11T showed less than 96.5 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel isolate formed a distinct monophyletic clade within the family Rhodobacteriaceae and clustered distantly with the genera Thalassobius and Marivita. Cells of strain FSX-11T were non-motile, oval-shaped and facultative anaerobic...
October 19, 2018: International Journal of Systematic and Evolutionary Microbiology
Jorke H Kamstra, Selma Hurem, Leonardo Martin Martin, Leif C Lindeman, Juliette Legler, Deborah Oughton, Brit Salbu, Dag Anders Brede, Jan Ludvig Lyche, Peter Aleström
Ionizing radiation is known to cause DNA damage, yet the mechanisms underlying potential transgenerational effects of exposure have been scarcely studied. Previously, we observed effects in offspring of zebrafish exposed to gamma radiation during gametogenesis. Here, we hypothesize that these effects are accompanied by changes of DNA methylation possibly inherited by subsequent generations. We assessed DNA methylation in F1 embryos (5.5 hours post fertilization) with whole genome bisulfite sequencing following parental exposure to 8...
October 18, 2018: Scientific Reports
Marina Koutsioumpa, Maria Hatziapostolou, Christos Polytarchou, Ezequiel J Tolosa, Luciana L Almada, Swapna Mahurkar-Joshi, Jennifer Williams, Ana Belen Tirado-Rodriguez, Sara Huerta-Yepez, Dimitrios Karavias, Helen Kourea, George A Poultsides, Kevin Struhl, David W Dawson, Timothy R Donahue, Martín E Fernández-Zapico, Dimitrios Iliopoulos
OBJECTIVE: Despite advances in the identification of epigenetic alterations in pancreatic cancer, their biological roles in the pathobiology of this dismal neoplasm remain elusive. Here, we aimed to characterise the functional significance of histone lysine methyltransferases (KMTs) and demethylases (KDMs) in pancreatic tumourigenesis. DESIGN: DNA methylation sequencing and gene expression microarrays were employed to investigate CpG methylation and expression patterns of KMTs and KDMs in pancreatic cancer tissues versus normal tissues...
October 18, 2018: Gut
Sae Rom Hong, Kyoung-Jin Shin, Sang-Eun Jung, Eun Hee Lee, Hwan Young Lee
Age prediction has been in the spotlight recently because it can provide an important information about the contributors of biological evidence left at crime scenes. Specifically, many researchers have actively suggested age-prediction models using DNA methylation at several CpG sites and tested the candidates using platforms such as the HumanMethylation 450 array and pyrosequencing. With DNA methylation data obtained from each platform, age prediction models were constructed using diverse statistical methods typically with multivariate linear regression...
October 9, 2018: Forensic Science International. Genetics
Balusamy Sri Renuka Devi, Shadi Rahimi, Deok-Chun Yang
Cytochrome P450 genes as the one of the largest superfamily genes mediate a wide range of plant biochemical pathways. In this study, a full-length cytochrome P450 monooxygenase (CYP736B) cDNA was isolated and characterized from Panax ginseng. It was revealed that the deduced amino acid of PgCYP736B shares a high degree of sequence homology with CYP736A12 encoded by P. ginseng. Expression of PgCYP736B was differentially induced not only during a Pseudomonas syringae infection (7.7-fold) and wounding (47.3-fold) but also after exposure to salt (7...
October 15, 2018: International Journal of Biological Macromolecules
Yurong Liu, Alexander Johs, Li Bi, Xia Lu, Hangwei Hu, Dan Sun, Ji-Zheng He, Baohua Gu
Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically diverse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and diversity of Hg methylators in microbial communities of rice paddy soils remain unclear. We characterized the abundance and distribution of hgcAB genes using 3rd-generation PacBio long-read sequencing and Illumina short-read metagenomic sequencing, in combination with quantitative PCR analyses in several mine-impacted paddy soils from southwest China...
October 17, 2018: Environmental Science & Technology
Bahareldin A Abdalla, Zhenhui Li, Hongjia Ouyang, Endashaw Jebessa, Tianhao Sun, Jia-Ao Yu, Bolin Cai, Biao Chen, Qinghua Nie, Xiquan Zhang
DNA (cytosine-5)-methyltransferase 3a ( Dnmt3a ) is an enzyme that catalyzes the transfer of methyl groups to specific CpG forms in DNA. In mammals, two variant transcripts of Dnmt3a have been successfully identified. To the best of our knowledge, no Dnmt3a transcripts in an avian have been successfully identified. This study was performed to detect different transcripts of Dnmt3a in chickens and to examine whether a novel Dnmt3a transcript named Dnmt3a1 may regulate adipogenesis. In addition to cloning, sequencing, transcript detection, and expression studies, a novel Dnmt3a1 transcript overexpression and knockdown were conducted to explore the potential role of Dnmt3a1 in preadipocyte proliferation and the early stage of adipocyte differentiation...
2018: Frontiers in Physiology
Yajing Xu, Jing Yang, Yuanyuan Zhang, Enyi Liu, Jie Peng, Xu Chen, Fangping Chen, Minyuan Peng
To study the molecular mechanism for DNA hypomethylation of STAT3 promoter in CD4+ T cells from acute graft-versus-host disease (aGVHD) patients.
 Methods: We collected CD4+ T cells from peripheral blood of 42 patients who underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT) from HLA-identical sibling donors. GADD45A expression level in CD4+ T cells was measured by real-time PCR and Western blot. The binding level between HMGB1 and GADD45A in CD4+ T cells was analyzed by co-immunoprecipitation, while the binding levels of HMGB1/GADD45A with STAT3 promoter were detected by chromatin immunoprecipitation-quantitative real-time PCR (ChIP-qPCR)...
September 28, 2018: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
Vijayapalani Paramasivan, Tarek Hewezi, Frederic Pontvianne, Thomas J Baum
Cyst nematodes are plant-pathogenic animals that secrete effector proteins into plant root cells to alter host gene expression and reprogram these cells to form specialized feeding sites, known as syncytia. The molecular mechanisms of these effectors are mostly unknown. We determined that the sugar beet cyst nematode (Heterodera schachtii) 32E03 effector protein strongly inhibits the activities of Arabidopsis thaliana histone deacetylases including the HDT1 enzyme, which has a known function in the regulation of rRNA gene expression through chromatin modifications...
October 17, 2018: Plant Cell
Amin Mahpour, Benjamin S Scruggs, Dominic Smiraglia, Toru Ouchi, Irwin H Gelman
How TATA-less promoters such as those within CpG islands (CGI) control gene expression is still a subject of active research. Here, we have identified the "CGCG element", a ten-base pair motif with a consensus sequence of TCTCGCGAGA present in a group of promoter-associated CGI-enriched in ribosomal protein and housekeeping genes. This element is evolutionarily conserved in vertebrates, found in DNase-accessible regions and employs RNA Pol II to activate gene expression. Through analysis of capped-nascent transcripts and supporting evidence from reporter assays, we demonstrate that this element activates bidirectional transcription through divergent start sites...
2018: PloS One
Andrey Korshunov, Belen Casalini, Lukas Chavez, Thomas Hielscher, Martin Sill, Marina Ryzhova, Tanvi Sharma, Daniel Schrimpf, Damian Stichel, David Capper, David E Reuss, Dominik Sturm, Oxana Absalyamova, Andrey Golanov, Sander Lambo, Melanie Bewerunge-Hudler, Peter Lichter, Christel Herold-Mende, Wolfgang Wick, Stefan M Pfister, Marcel Kool, David T W Jones, Andreas von Deimling, Felix Sahm
AIMS: Mutations of isocitrate dehydrogenase (IDH)1/2 affect almost all astrocytomas of WHO grade II and III. A subset of IDH-mutant astrocytic tumours progresses to IDH-mutant glioblastoma or presents with the histology of a glioblastoma at first presentation. We set out here to assess the molecular spectrum of IDH-mutant glioblastomas. METHODS: We performed an integrated molecular analysis of a mono-centric cohort (n = 97); assessed through genome-wide DNA methylation analysis, copy-number profiling, and targeted next generation sequencing using a neurooncology-tailored gene panel...
October 16, 2018: Neuropathology and Applied Neurobiology
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