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Methylomics

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https://www.readbyqxmd.com/read/28914256/mettl3-mettl14-mediated-mrna-n-6-methyladenosine-modulates-murine-spermatogenesis
#1
Zhen Lin, Phillip J Hsu, Xudong Xing, Jianhuo Fang, Zhike Lu, Qin Zou, Ke-Jia Zhang, Xiao Zhang, Yuchuan Zhou, Teng Zhang, Youcheng Zhang, Wanlu Song, Guifang Jia, Xuerui Yang, Chuan He, Ming-Han Tong
Spermatogenesis is a differentiation process during which diploid spermatogonial stem cells (SSCs) produce haploid spermatozoa. This highly specialized process is precisely controlled at the transcriptional, posttranscriptional, and translational levels. Here we report that N(6)-methyladenosine (m(6)A), an epitranscriptomic mark regulating gene expression, plays essential roles during spermatogenesis. We present comprehensive m(6)A mRNA methylomes of mouse spermatogenic cells from five developmental stages: undifferentiated spermatogonia, type A1 spermatogonia, preleptotene spermatocytes, pachytene/diplotene spermatocytes, and round spermatids...
September 15, 2017: Cell Research
https://www.readbyqxmd.com/read/28912427/dna-methylation-profiling-reveals-common-signatures-of-tumorigenesis-and-defines-epigenetic-prognostic-subtypes-of-canine-diffuse-large-b-cell-lymphoma
#2
Serena Ferraresso, Arianna Aricò, Tiziana Sanavia, Silvia Da Ros, Massimo Milan, Luciano Cascione, Stefano Comazzi, Valeria Martini, Mery Giantin, Barbara Di Camillo, Sandro Mazzariol, Diana Giannuzzi, Laura Marconato, Luca Aresu
Epigenetic deregulation is a hallmark of cancer characterized by frequent acquisition of new DNA methylation in CpG islands. To gain insight into the methylation changes of canine DLBCL, we investigated the DNA methylome in primary DLBCLs in comparison with control lymph nodes by genome-wide CpG microarray. We identified 1,194 target loci showing different methylation levels in tumors compared with controls. The hypermethylated CpG loci included promoter, 5'-UTRs, upstream and exonic regions. Interestingly, targets of polycomb repressive complex in stem cells were mostly affected suggesting that DLBCL shares a stem cell-like epigenetic pattern...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28911331/dynamic-dna-methylation-reconfiguration-during-seed-development-and-germination
#3
Taiji Kawakatsu, Joseph R Nery, Rosa Castanon, Joseph R Ecker
BACKGROUND: Unlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene expression and genome integrity. In animals, reprogramming erases and re-establishes DNA methylation during development. However, knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared time-series methylomes of dry and germinating seeds to publicly available seed development methylomes...
September 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28911330/extensive-transcriptomic-and-epigenomic-remodelling-occurs-during-arabidopsis-thaliana-germination
#4
Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G Lewsey, James Whelan
BACKGROUND: Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination...
September 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/28903050/changes-in-the-coding-and-non-coding-transcriptome-and-dna-methylome-that-define-the-schwann-cell-repair-phenotype-after-nerve-injury
#5
Peter J Arthur-Farraj, Claire C Morgan, Martyna Adamowicz, Jose A Gomez-Sanchez, Shaline V Fazal, Anthony Beucher, Bonnie Razzaghi, Rhona Mirsky, Kristjan R Jessen, Timothy J Aitman
Repair Schwann cells play a critical role in orchestrating nerve repair after injury, but the cellular and molecular processes that generate them are poorly understood. Here, we perform a combined whole-genome, coding and non-coding RNA and CpG methylation study following nerve injury. We show that genes involved in the epithelial-mesenchymal transition are enriched in repair cells, and we identify several long non-coding RNAs in Schwann cells. We demonstrate that the AP-1 transcription factor C-JUN regulates the expression of certain micro RNAs in repair Schwann cells, in particular miR-21 and miR-34...
September 12, 2017: Cell Reports
https://www.readbyqxmd.com/read/28899808/complete-genome-sequence-of-the-nematicidal-bacillus-thuringiensis-mybt18247
#6
Jacqueline Hollensteiner, Anja Poehlein, Cathrin Spröer, Boyke Bunk, Anna E Sheppard, Philip Rosenstiel, Hinrich Schulenburg, Heiko Liesegang
The Gram-positive spore forming bacterium Bacillus thuringiensis MYBT18247 encodes three cry toxin genes, (cry6Ba2, cry6Ba3 and cry21-like) which are active against nematodes. For a better understanding of the evolution of virulence and cry toxins, we present here the complete genome sequence of Bacillus thuringiensis MYBT18247. Various additional virulence factors such as bacteriocins, proteases and hemolysins were identified. In addition, the methylome and the metabolic potential of the strain were analyzed and the strain phylogenetically classified...
September 9, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28894120/blood-triglyceride-levels-are-associated-with-dna-methylation-at-the-serine-metabolism-gene-phgdh
#7
Vinh Truong, Siying Huang, Jessica Dennis, Mathieu Lemire, Nora Zwingerman, Dylan Aïssi, Irfahan Kassam, Claire Perret, Philip Wells, Pierre-Emmanuel Morange, Michael Wilson, David-Alexandre Trégouët, France Gagnon
Efficient interventions to reduce blood triglycerides are few; newer and more tolerable intervention targets are needed. Understanding the molecular mechanisms underlying blood triglyceride levels variation is key to identifying new therapies. To explore the role of epigenetic mechanisms on triglyceride levels, a blood methylome scan was conducted in 199 individuals from 5 French-Canadian families ascertained on venous thromboembolism, and findings were replicated in 324 French unrelated patients with venous thromboembolism...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28889375/a-versatile-assay-for-detection-of-aberrant-dna-methylation-in-bladder-cancer
#8
Stella Tommasi, Ahmad Besaratinia
Urothelial carcinoma of the bladder is one of the most common malignancies in the industrialized world, mainly caused by smoking and occupational exposure to chemicals. The favorable prognosis of early stage bladder cancer underscores the importance of early detection for the treatment of this disease. The high recurrence rate of this malignancy also highlights the need for close post-diagnosis monitoring of bladder cancer patients. As for other malignancies, aberrant DNA methylation has been shown to play a crucial role in the initiation and progression of bladder cancer, and thus holds great promise as a diagnostic and prognostic biological marker...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889075/epigenetic-clock-analysis-in-long-term-meditators
#9
Raphaëlle Chaix, Maria Jesús Alvarez-López, Maud Fagny, Laure Lemee, Béatrice Regnault, Richard J Davidson, Antoine Lutz, Perla Kaliman
In this paper, we examined whether meditation practice influences the epigenetic clock, a strong and reproducible biomarker of biological aging, which is accelerated by cumulative lifetime stress and with age-related chronic diseases. Using the Illumina 450K array platform, we analyzed the DNA methylome from blood cells of long-term meditators and meditation-naïve controls to estimate their Intrinsic Epigenetic Age Acceleration (IEAA), using Horvath's calculator. IEAA was similar in both groups. However, controls showed a different IEAA trajectory with aging than meditators: older controls (age≥52) had significantly higher IEAAs compared with younger controls (age <52), while meditators were protected from this epigenetic aging effect...
August 31, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28886082/haloperidol-induces-pharmacoepigenetic-response-by-modulating-mirna-expression-global-dna-methylation-and-expression-profiles-of-methylation-maintenance-genes-and-genes-involved-in-neurotransmission-in-neuronal-cells
#10
Babu Swathy, Moinak Banerjee
INTRODUCTION: Haloperidol has been extensively used in various psychiatric conditions. It has also been reported to induce severe side effects. We aimed to evaluate whether haloperidol can influence host methylome, and if so what are the possible mechanisms for it in neuronal cells. Impact on host methylome and miRNAs can have wide spread alterations in gene expression, which might possibly help in understanding how haloperidol may impact treatment response or induce side effects. METHODS: SK-N-SH, a neuroblasoma cell line was treated with haloperidol at 10μm concentration for 24 hours and global DNA methylation was evaluated...
2017: PloS One
https://www.readbyqxmd.com/read/28885036/postnatal-diet-remodels-hepatic-dna-methylation-in-metabolic-pathways-established-by-a-maternal-high-fat-diet
#11
Laura Moody, Hong Chen, Yuan-Xiang Pan
AIM: We investigate how postweaning diet may modify the epigenetic landscape to meet metabolic demands later in life. METHODS: Sprague-Dawley rats were exposed to a high-fat (HF) diet during gestation and lactation. At weaning, male offspring were placed either on an HF diet (HF/HF) or a control diet (HF/C). Methylation-dependent immunoprecipitation sequencing and methylation-sensitive restriction enzyme sequencing were used to quantify hepatic DNA methylation. RESULTS: Out of the 3966 identified differentially methylated regions, 37% were mapped to gene bodies while 6% fell within promoter or downstream regions...
September 8, 2017: Epigenomics
https://www.readbyqxmd.com/read/28882057/interethnic-dna-methylation-difference-and-its-implications-in-pharmacoepigenetics
#12
Shih-Kai Chu, Hsin-Chou Yang
AIM: This is the first systematic study to examine the population differentiation effect of DNA methylation on the treatment response and drug absorption, distribution, metabolism and excretion in multiple tissue types and cancer types. MATERIALS & METHODS: We analyzed the whole methylome and transcriptome data of primary tumor tissues of four cancer types (breast, colon, head & neck and uterine corpus) and lymphoblastoid cell lines for African and European ancestry populations...
September 8, 2017: Epigenomics
https://www.readbyqxmd.com/read/28881822/an-epigenetic-signature-of-adhesion-molecules-predicts-poor-prognosis-of-ovarian-cancer-patients
#13
Ping-Ying Chang, Yu-Ping Liao, Hui-Chen Wang, Yu-Chih Chen, Rui-Lan Huang, Yu-Chi Wang, Chiou-Chung Yuan, Hung-Cheng Lai
DNA methylation is a promising biomarker for cancer. The epigenetic effects of cell adhesion molecules may affect the therapeutic outcome and the present study examined their effects on survival in ovarian cancer. We integrated methylomics and genomics datasets in The Cancer Genome Atlas (n = 391) and identified 106 highly methylated adhesion-related genes in ovarian cancer tissues. Univariate analysis revealed the methylation status of eight genes related to progression-free survival. In multivariate Cox regression analysis, four highly methylated genes (CD97, CTNNA1, DLC1, HAPLN2) and three genes (LAMA4, LPP, MFAP4) with low methylation were significantly associated with poor progression-free survival...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28877596/what-the-human-sperm-methylome-tells-us
#14
Cristina Camprubí, Riccardo Aiese Cigliano, Albert Salas-Huetos, Nicolas Garrido, Joan Blanco
AIM: To characterize the sperm methylome in semen samples from 19 donors with proven fertility. MATERIALS & METHODS: Bisulfite-converted sperm DNA was hybridized on the HumanMethylation450 Infinium BeadChip platform. CpG fluorescence intensities were extracted and converted to β-values. RESULTS: The sperm methylome is highly homogeneous and hypomethylated. Genes with hypomethylated promoters are ontologically associated to biological functions related to spermatogenesis and embryogenesis...
September 7, 2017: Epigenomics
https://www.readbyqxmd.com/read/28869969/m-6-a-modulates-haematopoietic-stem-and-progenitor-cell-specification
#15
Chunxia Zhang, Yusheng Chen, Baofa Sun, Lu Wang, Ying Yang, Dongyuan Ma, Junhua Lv, Jian Heng, Yanyan Ding, Yuanyuan Xue, Xinyan Lu, Wen Xiao, Yun-Gui Yang, Feng Liu
N(6)-methyladenosine (m(6)A) has been identified as the most abundant modification on eukaryote messenger RNA (mRNA). Although the rapid development of high-throughput sequencing technologies has enabled insight into the biological functions of m(6)A modification, the function of m(6)A during vertebrate embryogenesis remains poorly understood. Here we show that m(6)A determines cell fate during the endothelial-to-haematopoietic transition (EHT) to specify the earliest haematopoietic stem/progenitor cells (HSPCs) during zebrafish embryogenesis...
September 6, 2017: Nature
https://www.readbyqxmd.com/read/28860255/whole-genome-sequence-and-methylome-analysis-of-the-freshwater-colorless-sulfur-bacterium-thioflexothrix-psekupsii-d3
#16
Alexey Fomenkov, Tamas Vincze, Margarita Y Grabovich, Galina Dubinina, Maria Orlova, Elena Belousova, Richard J Roberts
In this report, we announce the availability of a whole-genome sequence and methylome analysis of Thioflexothrix psekupsii strain D3.
August 31, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28859663/sparse-conserved-under-methylated-cpgs-are-associated-with-high-order-chromatin-structure
#17
Xueqiu Lin, Jianzhong Su, Kaifu Chen, Benjamin Rodriguez, Wei Li
BACKGROUND: Whole-genome bisulfite sequencing (WGBS) is the gold standard for studying landscape DNA methylation. Current computational methods for WGBS are mainly designed for gene regulatory regions with multiple under-methylated CpGs (UMCs), such as promoters and enhancers. RESULTS: To reliably predict the functional importance of single isolated UMCs across the genome, which is usually not achievable using traditional methods, we develop a multi-sample-based method...
August 31, 2017: Genome Biology
https://www.readbyqxmd.com/read/28854636/variation-in-dna-methylation-is-not-consistently-reflected-by-sociality-in-hymenoptera
#18
Karl M Glastad, Samuel V Arsenault, Kim L Vertacnik, Scott M Geib, Sasha Kay, Bryan N Danforth, Sandra M Rehan, Catherine R Linnen, Sarah D Kocher, Brendan G Hunt
Changes in gene regulation that underlie phenotypic evolution can be encoded directly in the DNA sequence or mediated by chromatin modifications such as DNA methylation. It has been hypothesized that the evolution of eusocial division of labor is associated with enhanced gene regulatory potential, which may include expansions in DNA methylation in the genomes of Hymenoptera (bees, ants, wasps, and sawflies). Recently, this hypothesis garnered support from analyses of a commonly used metric to estimate DNA methylation in silico, CpG content...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28852164/genome-wide-dna-methylation-and-transcriptome-analyses-reveal-genes-involved-in-immune-responses-of-pig-peripheral-blood-mononuclear-cells-to-poly-i-c
#19
Haifei Wang, Jiying Wang, Chao Ning, Xianrui Zheng, Jinlian Fu, Aiguo Wang, Qin Zhang, Jian-Feng Liu
DNA methylation changes play essential roles in regulating the activities of genes involved in immune responses. Understanding of variable DNA methylation linked to immune responses may contribute to identifying biologically promising epigenetic markers for pathogenesis of diseases. Here, we generated genome-wide DNA methylation and transcriptomic profiles of six pairs of polyinosinic-polycytidylic acid-treated pig peripheral blood mononuclear cell (PBMC) samples and corresponding controls using methylated DNA immunoprecipitation sequencing and RNA sequencing...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28851627/charting-the-dynamic-epigenome-during-b-cell-development
#20
REVIEW
Jose I Martin-Subero, Christopher C Oakes
The epigenetic landscape undergoes a widespread modulation during embryonic development and cell differentiation. Within the hematopoietic system, B cells are perhaps the cell lineage with a more dynamic DNA methylome during their maturation process, which involves approximately one third of all the CpG sites of the genome. Although each B-cell maturation step displays its own DNA methylation fingerprint, the DNA methylome is more extensively modified in particular maturation transitions. These changes are gradually accumulated in specific chromatin environments as cell differentiation progresses and reflect different features and functional states of B cells...
August 26, 2017: Seminars in Cancer Biology
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