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Epigenomics

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https://www.readbyqxmd.com/read/30638414/evidence-for-dna-methylation-mediating-genetic-liability-to-non-syndromic-cleft-lip-palate
#1
Laurence J Howe, Tom G Richardson, Ryan Arathimos, Lucas Alvizi, Maria R Passos-Bueno, Philip Stanier, Ellen Nohr, Kerstin U Ludwig, Elisabeth Mangold, Michael Knapp, Evie Stergiakouli, Beate St Pourcain, George Davey Smith, Jonathan Sandy, Caroline L Relton, Sarah J Lewis, Gibran Hemani, Gemma C Sharp
AIM: To determine if nonsyndromic cleft lip with or without cleft palate (nsCL/P) genetic risk variants influence liability to nsCL/P through gene regulation pathways, such as those involving DNA methylation. MATERIALS & METHODS: nsCL/P genetic summary data and methylation data from four studies were used in conjunction with Mendelian randomization and joint likelihood mapping to investigate potential mediation of nsCL/P genetic variants. RESULTS & CONCLUSION: Evidence was found at VAX1 (10q25...
January 14, 2019: Epigenomics
https://www.readbyqxmd.com/read/30638056/endometriosis-related-cerna-network-to-identify-predictive-biomarkers-of-endometrial-receptivity
#2
Xi Wang, Qi Yu
AIM: As RNA, which plays a role in the regulation of endometrial receptivity, can be modulated via ceRNA mechanisms, we constructed a ceRNA network to explore potential RNA/ceRNA biomarkers indicating endometrial receptivity associated with endometriosis. MATERIALS & METHODS: RNA sequencing was performed on eutopic endometrium from eight patients with and without endometriosis. Bioinformatics algorithms were used to predict ceRNA network and pathway analysis...
January 14, 2019: Epigenomics
https://www.readbyqxmd.com/read/30638052/circulating-mirnas-as-mediators-in-cell-to-cell-communication
#3
Christian Bär, Thomas Thum, David de Gonzalo-Calvo
No abstract text is available yet for this article.
January 14, 2019: Epigenomics
https://www.readbyqxmd.com/read/30618290/measured-maternal-prepregnancy-anthropometry-and-newborn-dna-methylation
#4
Edwina H Yeung, Weihua Guan, Sunni L Mumford, Robert M Silver, Cuilin Zhang, Michael Y Tsai, Enrique F Schisterman
AIM: We examined maternal prepregnancy anthropometry and cord blood DNA methylation. METHODS: Associations between maternal measures (i.e., weight, height, waist circumference, hip circumference, skinfolds, leptin) and methylation β-values at each CpG (measured by the Infinium MethylationEPIC BeadChip) were estimated among 391 singletons. RESULTS:  Total of 18% of mothers were obese (body mass index ≥ 30) and 27% centrally obese (waist-to-hip ratio ≥ 0...
January 8, 2019: Epigenomics
https://www.readbyqxmd.com/read/30569756/expression-profiles-of-exosomal-mirnas-isolated-from-plasma-of-patients-with-desmoplastic-small-round-cell-tumor
#5
Marta Colletti, Alessandro Paolini, Angela Galardi, Virginia Di Paolo, Luisa Pascucci, Ida Russo, Biagio De Angelis, Hector Peinado, Rita De Vito, Giuseppe M Milano, Franco Locatelli, Andrea Masotti, Angela Di Giannatale
AIM: Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive mesenchymal tumor, lacking biomarkers for diagnosis, treatment stratification and prognosis. We investigated the exosomal miRNA profile in plasma samples collected from DSRCT patients, evaluating their potential as circulating biomarkers for this tumor. PATIENTS & METHODS: We isolated exosomes from plasma of three DSRCT adolescents and four age-matched healthy controls; expression of circulating miRNAs was quantified by qPCR...
December 20, 2018: Epigenomics
https://www.readbyqxmd.com/read/30565492/translation-regulation-in-skin-cancer-from-a-trna-point-of-view
#6
Katerina Grafanaki, Dimitrios Anastasakis, George Kyriakopoulos, Ilias Skeparnias, Sophia Georgiou, Constantinos Stathopoulos
Protein synthesis is a central and dynamic process, frequently deregulated in cancer through aberrant activation or expression of translation initiation factors and tRNAs. The discovery of tRNA-derived fragments, a new class of abundant and, in some cases stress-induced, small noncoding RNAs has perplexed the epigenomics landscape and highlights the emerging regulatory role of tRNAs in translation and beyond. Skin is the biggest organ in human body, which maintains homeostasis of its multilayers through regulatory networks that induce translational reprogramming, and modulate tRNA transcription, modification and fragmentation, in response to various stress signals, like UV irradiation...
December 19, 2018: Epigenomics
https://www.readbyqxmd.com/read/30526041/effects-of-nsun2-deficiency-on-the-mrna-5-methylcytosine-modification-and-gene-expression-profile-in-hek293-cells
#7
Zhen Sun, Songlei Xue, Hui Xu, Xuming Hu, Shihao Chen, Zhe Yang, Yu Yang, Juan Ouyang, Hengmi Cui
AIM: To study the biological function of NSUN2 in regulating gene expression and cell proliferation. MATERIALS & METHODS: The NSUN2 gene was knocked down in HEK293 cells via CRISPR/Cas9 system. mRNA m5C modification and gene expression were assessed using RNA-BisSeq and RNA-Seq. RESULTS: NSUN2 deficiency could inhibit proliferation and migration of HEK293 cells. A total of 1185 differentially methylated genes and 790 differentially expressed genes were identified...
December 11, 2018: Epigenomics
https://www.readbyqxmd.com/read/30526034/identification-and-regulation-pattern-analysis-of-long-noncoding-rnas-in-meibomian-gland-carcinoma
#8
Xin Song, Jiayan Fan, Renbing Jia, Yixiong Zhou, Shengfang Ge, Ge Zhang, Haibo Wang, Xianqun Fan
AIM: To identify long noncoding RNAs (lncRNAs) and to elucidate regulation patterns of lncRNAs in meibomian gland carcinoma (MGC). MATERIALS & METHODS: We used RNA-Seq, gene ontology, ClueGO, Ingenuity Pathway Analysis and co-expression network analyses to profile the expression and regulation patterns of lncRNAs and mRNAs in MGC. RESULTS: We identified 500 lncRNAs and 326 mRNAs as differentially expressed. Co-expression regulatory networks with lncRNAs and mRNAs were constructed...
December 7, 2018: Epigenomics
https://www.readbyqxmd.com/read/30523707/integrated-comparison-of-the-mirnaome-and-mrnaome-in-muscles-of-dermatomyositis-and-polymyositis-reveals-common-and-specific-mirna-mrnas
#9
Siming Gao, Huali Zhang, Xiaoxia Zuo, Yizhi Xiao, Di Liu, Honglin Zhu, Hui Luo
AIM: Dermatomyositis (DM) and polymyositis (PM) are refractory systemic autoimmune diseases with unknown pathogenesis. miRNAs is an important epigenetic mechanism to regulate gene expression. METHODS: We performed whole miRNAs analysis, transcription analysis and the association between miRNAome and mRNAome. RESULTS: For transcription and miRNAs analysis, there were common and specific mRNAs and miRNAs in the muscles of DM and PM. Among them, the expression levels of miR-196a-5p and CPM were negatively correlated in PM, miR-193b-3p and NECAP2 were negatively correlated in DM and PM...
December 7, 2018: Epigenomics
https://www.readbyqxmd.com/read/30456986/epigenetic-meta-analysis-across-three-civilian-cohorts-identifies-nrg1-and-hgs-as-blood-based-biomarkers-for-post-traumatic-stress-disorder
#10
Monica Uddin, Andrew Ratanatharathorn, Don Armstrong, Pei-Fen Kuan, Allison E Aiello, Evelyn J Bromet, Sandro Galea, Karestan C Koenen, Benjamin Luft, Kerry J Ressler, Derek E Wildman, Caroline M Nievergelt, Alicia Smith
AIM: Trauma exposure is a necessary, but not deterministic, contributor to post-traumatic stress disorder (PTSD). Epigenetic factors may distinguish between trauma-exposed individuals with versus without PTSD. MATERIALS & METHODS: We conducted a meta-analysis of PTSD epigenome-wide association studies in trauma-exposed cohorts drawn from civilian contexts. Whole blood-derived DNA methylation levels were analyzed in 545 study participants, drawn from the three civilian cohorts participating in the PTSD working group of the Psychiatric Genomics Consortium...
November 20, 2018: Epigenomics
https://www.readbyqxmd.com/read/30444423/circular-rna-circrhot1-is-upregulated-and-promotes-cell-proliferation-and-invasion-in-pancreatic-cancer
#11
Shibin Qu, Xiaokun Hao, Wenjie Song, Kunwei Niu, Xisheng Yang, Xuan Zhang, Runze Shang, Quancheng Wang, Haimin Li, Zhengcai Liu
AIM: We aimed to identify the roles of circRHOT1 in pancreatic cancer. MATERIALS & METHODS: The circRHOT1 was acquired from our previous study followed by quantitative real-time PCR and fluorescence in situ hybridization validation in pancreatic cancer. We used siRNA and shRNA to explore the function of circRHOT1 in pancreatic cancer cells. Bioinformatic analyses were applied to study the potential mechanism of circRHOT1. RESULTS: The circRHOT1 was upregulated in pancreatic cancer and predominantly located in the cytoplasm...
November 16, 2018: Epigenomics
https://www.readbyqxmd.com/read/30427216/dna-methylation-hydroxymethylation-regulate-gene-expression-and-alternative-splicing-during-terminal-granulopoiesis
#12
Dadi Gao, Natalia Pinello, Trung V Nguyen, Annora Thoeng, Rajini Nagarajah, Jeff Holst, John Ej Rasko, Justin J-L Wong
AIM: To determine whether epigenetic modifications of DNA regulate gene expression and alternative splicing during terminal granulopoiesis. MATERIALS & METHODS: Using whole genome bisulfite sequencing, reduced representation hydroxymethylation profiling and mRNA sequencing, we compare changes in DNA methylation, DNA hydroxymethylation, gene expression and alternative splicing in mouse promyelocytes and granulocytes. RESULTS & CONCLUSION: We show reduced DNA methylation at the promoters and enhancers of key granulopoiesis genes, indicating a regulatory role in the activation of lineage-specific genes during differentiation...
November 14, 2018: Epigenomics
https://www.readbyqxmd.com/read/30426784/the-quantitative-profiling-of-blood-msept9-determines-the-detection-performance-on-colorectal-tumors
#13
Lele Song, Jiayu Wang, Huaiqing Wang, Yan Chen, Jia Jia, Shaohua Guo, Hongyi Liu, Xiumei Peng, Wenhua Xiao, Yuan Gong, Bo Yang, Yinying Lu, Yuemin Li
AIM: To investigate the quantitative relationship between the positive detection rate (PDR) in colorectal tumor detection and the mSEPT9 level. MATERIALS & METHODS: The level of blood mSEPT9 in various colorectal diseases was quantified by the Epi proColon 2.0 assay. ΔΔCt values were calculated representing the mSEPT9 level. A total of 1347 subjects were recruited in this quantitative study. RESULTS: PDR or sensitivity was positively correlated with the progression of colorectal tumors and the mSEPT9 level in an exponential relationship...
November 14, 2018: Epigenomics
https://www.readbyqxmd.com/read/30426778/comprehensive-analysis-of-mirna-mrna-lncrna-networks-in-severe-asthma
#14
Yi Chen, Zheng-Dao Mao, Yu-Jia Shi, Yan Qian, Zhi-Guang Liu, Xiao-Wei Yin, Qian Zhang
AIM: This study aimed to explore the molecular mechanism of severe asthma. MATERIALS & METHODS: The shared and divergent differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and lncRNAs (DElncRNAs) in asthma and severe asthma were identified by RNA-sequencing. Severe asthma-specific and shared DEmiRNA-DEmRNA-DElncRNA interaction networks were performed. RESULTS: Compared with normal control, 1328 DEmRNAs, 608 DElncRNAs and 63 DEmiRNAs were identified in severe asthma...
November 14, 2018: Epigenomics
https://www.readbyqxmd.com/read/30426768/dna-hydroxymethylation-changes-in-response-to-spinal-cord-damage-in-a-multiple-sclerosis-mouse-model
#15
Yan Tang, Man Luo, Kailing Pan, Tina Ahmad, Ting Zhou, Zhigang Miao, Hang Zhou, Hao Sun, Xingshun Xu, Michael Namaka, Yongxiang Wang
AIM: Roles of DNA 5-hydroxymethylcytosine (5hmC) in myelin repair were investigated in an experimental autoimmune encephalomyelitis (EAE) mouse model via its regulation on brain-derived neurotrophic factor (BDNF). METHODS: DNA 5hmC level and its limiting enzymes were detected in EAE mice. RESULTS: Global 5hmC modification, Tet1 and Tet2 significantly decreased in the spinal cord tissues of EAE mice. BDNF protein and mRNA decreased and were highly associated with BDNF 5hmC...
November 14, 2018: Epigenomics
https://www.readbyqxmd.com/read/30418048/dna-methylation-profiling-as-a-tool-for-testicular-germ-cell-tumors-subtyping
#16
Ana L Costa, Catarina Moreira-Barbosa, João Lobo, Bárbara Vilela-Salgueiro, Mariana Cantante, Rita Guimarães, Paula Lopes, Isaac Braga, Jorge Oliveira, Luís Antunes, Rui Henrique, Carmen Jerónimo
AIM: Assess differential patterns of selected five genes' promoter methylation among testicular germ cell tumors (TGCT) subtypes. MATERIALS & METHODS:  CRIPTO, HOXA9, MGMT, RASSF1A and SCGB3A1 promoter methylation levels were evaluated by quantitative methylation-specific PCR in 161 TGCT and 16 controls. Associations between clinicopathological parameters and promoter methylation levels were assessed, and receiver operating characteristics curve analysis was performed...
November 12, 2018: Epigenomics
https://www.readbyqxmd.com/read/30417652/identification-and-integrated-analysis-of-key-differentially-expressed-circular-rnas-in-er-positive-subtype-breast-cancer
#17
Chenwei Yuan, Liheng Zhou, Lei Zhang, Kai Yin, Jing Peng, Rui Sha, Shan Zhang, Yaqian Xu, Xiaonan Sheng, Yaohui Wang, Yanping Lin, Shuguang Xu, Wenjin Yin, Jinsong Lu
AIM: To systematically profile and characterize the circular RNA (circRNA) expression pattern in estrogen receptor (ER)-positive breast cancer (BC). MATERIALS & METHODS: CircRNA expression profile was performed in ER-positive BC and adjacent nontumor tissues. The differentially expressed circRNAs (DECs) was analyzed by bioinformatics. The analysis findings were validated by quantitative real-time PCR. RESULTS: In total, 3653 DECs were detected in our ER-positive BC compared with the control...
November 12, 2018: Epigenomics
https://www.readbyqxmd.com/read/30371096/genome-wide-epigenetic-landscape-of-pig-lincrnas-and-their-evolution-during-porcine-domestication
#18
Cencen Li, Cheng Zou, Yong Cui, Yuhua Fu, Chengchi Fang, Yao Li, Jingxuan Li, Wen Wang, Hui Xiang, Changchun Li
AIM: We aimed to identify previously unreported long intergenic noncoding RNAs (lincRNAs) in the porcine liver, an important metabolic tissue, and further illustrate the epigenomic landscapes and the evolution of lincRNAs. MATERIALS & METHODS: We used porcine omics data and comprehensively analyzed and identified lincRNAs and their methylation, expression and evolutionary patterns during pig domestication. RESULTS: LincRNAs exhibit highly methylated promoter and downstream regions, as well as lower expression levels and higher tissue specificity than protein-coding genes...
October 29, 2018: Epigenomics
https://www.readbyqxmd.com/read/30362374/integrated-analysis-of-pseudogene-rp11-564d11-3-expression-and-its-potential-roles-in-hepatocellular-carcinoma
#19
Hui Song, Jue Yang, Yongqiang Zhang, Jianjiang Zhou, Yanmei Li, Xiaojiang Hao
AIM: We aim to identify differentially expressed pseudogenes and investigate their functional roles in carcinogenesis. MATERIALS & METHODS: Here, we identify dysregulated pseudogenes, analyze their prognostic values and investigate their potential functions through pseudogene-miRNA-mRNA network from public -omics repositories. RESULTS: We identified 16 frequently upregulated pseudogenes among which high expression levels of RP11-564D11...
October 26, 2018: Epigenomics
https://www.readbyqxmd.com/read/30351206/the-biological-embedding-of-early-life-socioeconomic-status-and-family-adversity-in-children-s-genome-wide-dna-methylation
#20
Nicole R Bush, Rachel D Edgar, Mina Park, Julia L MacIsaac, Lisa M McEwen, Nancy E Adler, Marilyn J Essex, Michael S Kobor, W Thomas Boyce
AIM: To examine variation in child DNA methylation to assess its potential as a pathway for effects of childhood social adversity on health across the life course. MATERIALS & METHODS: In a diverse, prospective community sample of 178 kindergarten children, associations between three types of social experience and DNA methylation within buccal epithelial cells later in childhood were examined. RESULTS: Family income, parental education and family psychosocial adversity each associated with increased or decreased DNA methylation (488, 354 and 102 sites, respectively) within a unique set of genomic CpG sites...
October 23, 2018: Epigenomics
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