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Methylomics

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https://www.readbyqxmd.com/read/28499430/genome-wide-dna-methylation-analysis-in-lung-fibroblasts-co-cultured-with-silica-exposed-alveolar-macrophages
#1
Juan Li, Wu Yao, Lin Zhang, Lei Bao, Huiting Chen, Di Wang, Zhongzheng Yue, Yiping Li, Miao Zhang, Changfu Hao
BACKGROUND: Exposure to crystalline silica is considered to increase the risk of lung fibrosis. The primary effector cell, the myofibroblast, plays an important role in the deposition of extracellular matrix (ECM). DNA methylation change is considered to have a potential effect on myofibroblast differentiation. Therefore, the present study was designed to investigate the genome-wide DNA methylation profiles of lung fibroblasts co-cultured with alveolar macrophages exposed to crystalline silica in vitro...
May 12, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28498935/the-association-of-changes-in-dna-methylation-with-temperature-dependent-sex-determination-in-cucumber
#2
Yun-Song Lai, Xiaohui Zhang, Wei Zhang, Di Shen, Haiping Wang, Yudong Xia, Yang Qiu, Jiangping Song, Chenchen Wang, Xixiang Li
Cucumber (Cucumis sativus L.) is characterized by its diverse and flexible sexual types. Here, we evaluated the effect of low temperature (LT) exposure on cucumber femaleness under short-day conditions. Shoot apices were subjected to whole-genome bisulfate sequencing (WGBS), mRNA-seq, and sRNA-seq. The results showed that temperature had a substantial and global impact on transposable element (TE)-related small RNA-directed DNA methylation (RdDM) mechanisms, resulting in large amounts of CHH-type cytosine demethylation...
May 12, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28498318/dna-methylation-dynamics-and-cocaine-in-the-brain-progress-and-prospects
#3
REVIEW
Kathryn Vaillancourt, Carl Ernst, Deborah Mash, Gustavo Turecki
Cytosine modifications, including DNA methylation, are stable epigenetic marks that may translate environmental change into transcriptional regulation. Research has begun to investigate DNA methylation dynamics in relation to cocaine use disorders. Specifically, DNA methylation machinery, including methyltransferases and binding proteins, are dysregulated in brain reward pathways after chronic cocaine exposure. In addition, numerous methylome-wide and candidate promoter studies have identified differential methylation, at the nucleotide level, in rodent models of cocaine abuse and drug seeking behavior...
May 12, 2017: Genes
https://www.readbyqxmd.com/read/28487883/genetic-and-epigenetic-profiling-of-a-solitary-peutz-jeghers-colon-polyp
#4
Heinz Linhart, Felix Bormann, Barbara Hutter, Benedikt Brors, Frank Lyko
Colon polyps represent precursor lesions of colon cancers and their malignant potential varies according to histological subtype. A rare subtype of colon polyps is the Peutz-Jeghers (PJ) polyp. PJ polyps mostly occur in the context of Peutz-Jeghers syndrome, which is characterized by the development of multiple polyps in the intestinal tract and hyperpigmentation of oral mucosa and lips. Peutz-Jeghers is an autosomal dominant disorder caused by pathogenic variants of the serine threonine kinase STK11. PJ polyps very rarely occur outside of the syndrome and are then referred to as solitary PJ polyps...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28480579/longitudinal-epigenetic-predictors-of-amygdala-hippocampus-volume-ratio
#5
Esther Walton, Charlotte A M Cecil, Matthew Suderman, Jingyu Liu, Jessica A Turner, Vince Calhoun, Stefan Ehrlich, Caroline L Relton, Edward D Barker
BACKGROUND: The ratio between amygdala:hippocampal (AH) volume has been associated with multiple psychiatric problems, including anxiety and aggression. Yet, little is known about its biological underpinnings. Here, we used a methylome-wide approach to test (a) whether DNA methylation in early life (birth, age 7) prospectively associates with total AH volume ratio in early adulthood, and (b) whether significant DNA methylation markers are influenced by prenatal risk factors. METHODS: Analyses were based on a subsample (n = 109 males) from the Avon Longitudinal Study of Parents and Children, which included measures of prenatal risk, DNA methylation (Infinium Illumina 450k), T1-weighted brain scans and psychopathology in early adulthood (age 18-21)...
May 8, 2017: Journal of Child Psychology and Psychiatry, and Allied Disciplines
https://www.readbyqxmd.com/read/28473875/genome-wide-dna-methylation-analysis-reveals-loci-that-distinguish-different-types-of-adipose-tissue-in-obese-individuals
#6
Donia Macartney-Coxson, Miles C Benton, Ray Blick, Richard S Stubbs, Ronald D Hagan, Michael A Langston
BACKGROUND: Epigenetic mechanisms provide an interface between environmental factors and the genome and are known to play a role in complex diseases such as obesity. These mechanisms, including DNA methylation, influence the regulation of development, differentiation and the establishment of cellular identity. Here we employ two approaches to identify differential methylation between two white adipose tissue depots in obese individuals before and after gastric bypass and significant weight loss...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28473874/regional-differences-in-mitochondrial-dna-methylation-in-human-post-mortem-brain-tissue
#7
Matthew Devall, Rebecca G Smith, Aaron Jeffries, Eilis Hannon, Matthew N Davies, Leonard Schalkwyk, Jonathan Mill, Michael Weedon, Katie Lunnon
BACKGROUND: DNA methylation is an important epigenetic mechanism involved in gene regulation, with alterations in DNA methylation in the nuclear genome being linked to numerous complex diseases. Mitochondrial DNA methylation is a phenomenon that is receiving ever-increasing interest, particularly in diseases characterized by mitochondrial dysfunction; however, most studies have been limited to the investigation of specific target regions. Analyses spanning the entire mitochondrial genome have been limited, potentially due to the amount of input DNA required...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28473707/dna-methylation-and-transcriptome-changes-associated-with-cisplatin-resistance-in-ovarian-cancer
#8
Riikka J Lund, Kaisa Huhtinen, Jussi Salmi, Juha Rantala, Elizabeth V Nguyen, Robert Moulder, David R Goodlett, Riitta Lahesmaa, Olli Carpén
High-grade serous ovarian cancer is the most common ovarian cancer type. Although the combination of surgery and platinum-taxane chemotherapy provide an effective treatment, drug resistance frequently occurs leading to poor outcome. In order to clarify the molecular mechanisms of drug resistance, the DNA methylation and transcriptomic changes, associated with the development of drug resistance in high-grade serous ovarian cancer, were examined from patient derived malignant ascites cells. In parallel with large-scale transcriptome changes, cisplatin resistance was associated with loss of hypermethylation at several CpG sites primarily localized in the intergenic regions of the genome...
May 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28467809/functional-dissection-of-the-role-of-uhrf1-in-the-regulation-of-retinoblastoma-methylome
#9
Guangyan Kan, Heng He, Qi Zhao, Xiubo Li, Min Li, Huasheng Yang, Jong Kyong Kim
UHRF1 (ubiquitin-like with PHD and RING finger domains 1) is a critical regulator for DNA methylation, and its frequent overexpression in human cancers has been associated with tumor-promoting effects. However, whether the overexpressed UHRF1 contributes to the establishment and maintenance of tumor methylomes and whether this process can affect the tumorigenesis remain unclear. In this study, we show that UHRF1 is highly expressed in retinoblastoma, and genomes of human primary retinoblastoma and cell lines have differential DNA methylation patterns compared with those of normal retina, characterized by lower global methylation and higher promoter methylation of tumor suppressors...
April 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28457232/the-evolution-of-chromomethylases-and-gene-body-dna-methylation-in-plants
#10
Adam J Bewick, Chad E Niederhuth, Lexiang Ji, Nicholas A Rohr, Patrick T Griffin, Jim Leebens-Mack, Robert J Schmitz
BACKGROUND: The evolution of gene body methylation (gbM), its origins, and its functional consequences are poorly understood. By pairing the largest collection of transcriptomes (>1000) and methylomes (77) across Viridiplantae, we provide novel insights into the evolution of gbM and its relationship to CHROMOMETHYLASE (CMT) proteins. RESULTS: CMTs are evolutionary conserved DNA methyltransferases in Viridiplantae. Duplication events gave rise to what are now referred to as CMT1, 2 and 3...
May 1, 2017: Genome Biology
https://www.readbyqxmd.com/read/28454518/transcriptome-wide-n-6-methyladenosine-methylome-profiling-of-porcine-muscle-and-adipose-tissues-reveals-a-potential-mechanism-for-transcriptional-regulation-and-differential-methylation-pattern
#11
Xuelian Tao, Jianning Chen, Yanzhi Jiang, Yingying Wei, Yan Chen, Huaming Xu, Li Zhu, Guoqing Tang, Mingzhou Li, Anan Jiang, Surong Shuai, Lin Bai, Haifeng Liu, Jideng Ma, Long Jin, Anxiang Wen, Qin Wang, Guangxiang Zhu, Meng Xie, Jiayun Wu, Tao He, Chunyu Huang, Xiang Gao, Xuewei Li
BACKGROUND: N (6) -methyladenosine (m(6)A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m(6)A methylation on mRNA have been revealed by mapping of m(6)A methylomes in several species. m(6)A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m(6)A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth...
April 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28450872/comparative-analysis-of-ralstonia-solanacearum-methylomes
#12
Ivan Erill, Marina Puigvert, Ludovic Legrand, Rodrigo Guarischi-Sousa, Céline Vandecasteele, João C Setubal, Stephane Genin, Alice Guidot, Marc Valls
Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28449092/genome-wide-dna-methylomes-from-discrete-developmental-stages-reveal-the-predominance-of-non-cpg-methylation-in-tribolium-castaneum
#13
Xiaowen Song, Fei Huang, Juanjuan Liu, Chengjun Li, Shanshan Gao, Wei Wu, Mengfan Zhai, Xiaojuan Yu, Wenfeng Xiong, Jia Xie, Bin Li
Cytosine DNA methylation is a vital epigenetic regulator of eukaryotic development. Whether this epigenetic modification occurs in Tribolium castaneum has been controversial, its distribution pattern and functions have not been established. Here, using bisulphite sequencing (BS-Seq), we confirmed the existence of DNA methylation and described the methylation profiles of the four life stages of T. castaneum. In the T. castaneum genome, both symmetrical CpG and non-CpG methylcytosines were observed. Symmetrical CpG methylation, which was catalysed by DNMT1 and occupied a small part in T...
April 25, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28444195/dna-methylome-analysis-reveals-distinct-epigenetic-patterns-of-ascending-aortic-dissection-and-bicuspid-aortic-valve
#14
Sun Pan, Hao Lai, Yiru Shen, Charles Breeze, Stephan Beck, Tao Hong, Chunsheng Wang, Andrew E Teschendorff
Epigenetics may mediate the effects of environmental risk factors on disease, including heart disease. Thus, measuring the DNA methylome offers the opportunity to identify novel disease biomarkers and novel insights into disease mechanisms. The DNA methylation landscape of ascending aortic dissection (AD) and bicuspid aortic valve (BAV) with aortic aneurysmal dilatation remain uncharacterized. The present study aimed to explore the genome-wide DNA methylation landscape underpinning these two diseases. Methods and results: We used Illumina 450k DNA methylation beadarrays to analyze 21 ascending aorta samples, including 10 cases with AD, 5 with BAV and 6 healthy controls...
April 19, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/28443631/a-peripheral-epigenetic-signature-of-immune-system-genes-is-linked-to-neocortical-thickness-and-memory
#15
Virginie Freytag, Tania Carrillo-Roa, Annette Milnik, Philipp G Sämann, Vanja Vukojevic, David Coynel, Philippe Demougin, Tobias Egli, Leo Gschwind, Frank Jessen, Eva Loos, Wolfgang Maier, Steffi G Riedel-Heller, Martin Scherer, Christian Vogler, Michael Wagner, Elisabeth B Binder, Dominique J-F de Quervain, Andreas Papassotiropoulos
Increasing age is tightly linked to decreased thickness of the human neocortex. The biological mechanisms that mediate this effect are hitherto unknown. The DNA methylome, as part of the epigenome, contributes significantly to age-related phenotypic changes. Here, we identify an epigenetic signature that is associated with cortical thickness (P=3.86 × 10(-8)) and memory performance in 533 healthy young adults. The epigenetic effect on cortical thickness was replicated in a sample comprising 596 participants with major depressive disorder and healthy controls...
April 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28442560/obesity-and-menopause-modify-the-epigenomic-profile-of-breast-cancer
#16
Ana B Crujeiras, Angel Díaz-Lagares, Olafur A Stefansson, Manuel Macias, Juan Sandoval, Juan Cueva, Rafael López-López, Sebastian Moran, Jon G Jonasson, Laufey Tryggvadottir, Elinborg Olafsdottir, Francisco J Tinahones, Marcos C Carreira, Felipe F Casanueva, Manel Esteller
Obesity is a high risk factor for breast cancer. This relationship could be marked by a specific methylome. The current work was aimed to explore the impact of obesity and menopausal status on variation in breast cancer methylomes. Data from Infinium 450K array-based methylomes of 64 breast tumor were coupled with information on BMI and menopausal status. Additionally, DNA methylation results were validated in 18 non-tumor and 81 tumor breast samples. Breast tumors arising in either pre- or postmenopausal women stratified by BMI or menopausal status alone were not associated with a specific DNA methylation pattern...
April 25, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28439531/genome-and-cd4-t-cell-methylome-wide-association-study-of-circulating-trimethylamine-n-oxide-in-the-genetics-of-lipid-lowering-drugs-and-diet-network-goldn
#17
Stella Aslibekyan, Marguerite R Irvin, Bertha A Hidalgo, Rodney T Perry, Elias J Jeyarajah, Erwin Garcia, Irina Shalaurova, Paul N Hopkins, Michael A Province, Hemant K Tiwari, Jose M Ordovas, Devin M Absher, Donna K Arnett
BACKGROUND: Trimethylamine-N-oxide (TMAO), an atherogenic metabolite species, has emerged as a possible new risk factor for cardiovascular disease. Animal studies have shown that circulating TMAO levels are regulated by genetic and environmental factors. However, large-scale human studies have failed to replicate the observed genetic associations, and epigenetic factors such as DNA methylation have never been examined in relation to TMAO levels. METHODS AND RESULTS: We used data from the family-based Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) to investigate the heritable determinants of plasma TMAO in humans...
June 2017: Journal of Nutrition & Intermediary Metabolism
https://www.readbyqxmd.com/read/28423671/genome-wide-dna-methylation-analysis-reveals-molecular-subtypes-of-pancreatic-cancer
#18
Nitish Kumar Mishra, Chittibabu Guda
Pancreatic cancer (PC) is the fourth leading cause of cancer deaths in the United States with a five-year patient survival rate of only 6%. Early detection and treatment of this disease is hampered due to lack of reliable diagnostic and prognostic markers. Recent studies have shown that dynamic changes in the global DNA methylation and gene expression patterns play key roles in the PC development; hence, provide valuable insights for better understanding the initiation and progression of PC. In the current study, we used DNA methylation, gene expression, copy number, mutational and clinical data from pancreatic patients...
April 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28418886/histone-hypoacetylation-contributes-to-cxcl12-downregulation-in-colon-cancer-impact-on-tumor-growth-and-cell-migration
#19
Benoît Romain, Radhia Benbrika-Nehmar, Laetitia Marisa, Michèle Legrain, Viviane Lobstein, Attila Oravecz, Laetitia Poidevin, Cyril Bour, Jean-Noël Freund, Isabelle Duluc, Dominique Guenot, Erwan Pencreach
CXCL12 has been shown to be involved in colon cancer metastasis, but its expression level and molecular mechanisms regulating its expression remain controversial. We thus evaluated CXCL12 expression in a large cohort of colon adenomas and carcinomas, investigated for an epigenetic mechanism controlling its expression and evaluated the impact of CXCL12 levels on cell migration and tumor growth. CXCL12 expression was measured in human colon adenomas and carcinomas with transcriptome array and RT-qPCR. The promoter methylation was analyzed with whole-genome DNA methylation chips and protein expression by immunohistochemistry...
March 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28409894/genomic-responses-of-mouse-synovial-fibroblasts-during-tnf-driven-arthritogenesis-greatly-mimic-those-of-human-rheumatoid-arthritis
#20
Evangelos Ntougkos, Panagiotis Chouvardas, Fani Roumelioti, Caroline Ospelt, Mojca Frank-Bertoncelj, Andrew Filer, Christopher D Buckley, Steffen Gay, Christoforos Nikolaou, George Kollias
OBJECTIVE: Aberrant activation of synovial fibroblasts (SFs) is a key determinant in the pathogenesis of rheumatoid arthritis (RA). We aimed to produce a map of gene expression and epigenetic changes occurring in this cell type during disease progression in the human TNF-transgenic model of arthritis, and identify commonalities with human SFs. METHODS: We used deep sequencing to probe the transcriptome, the methylome and the chromatin landscape of cultured mouse arthritogenic SFs at three stages of disease, as well as SFs stimulated with human TNF...
April 13, 2017: Arthritis & Rheumatology
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