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Methylation enrichment

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https://www.readbyqxmd.com/read/28645561/boris-up-regulates-oct4-via-histone-methylation-to-promote-cancer-stem-cell-like-properties-in-human-liver-cancer-cells
#1
Qiuying Liu, Kefei Chen, Zhongjian Liu, Yuan Huang, Rongce Zhao, Ling Wei, Xiaoqin Yu, Jingyang He, Jun Liu, Jianguo Qi, Yang Qin, Bo Li
Accumulating evidence has revealed the importance of cancer stem cells (CSCs) in chemoresistance and recurrence. BORIS, a testes-specific CTCF paralog, has been shown to be associated with stemness traits of embryonic cancer cells and epithelial CSCs. We previously reported that BORIS is correlated with the expression of the CSC marker CD90 in hepatocellular carcinoma (HCC). These results encourage us to wonder whether BORIS exerts functions on CSC-like traits of human liver cancer cells. Here, we report that BORIS was enriched in HCC tissues...
June 20, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28645103/colxv-promotes-adipocyte-differentiation-via-inhibiting-dna-methylation-and-camp-pka-pathway-in-mice
#2
Guannv Liu, Meihang Li, Yatao Xu, Song Wu, Muhammad Saeed, Chao Sun
Extracellular matrix (ECM), as an essential component of adipose tissue, not only provides mechanical support for adipocyte growth, but also participates in ECM-adipocyte communication via various secreted proteins, including highly enriched collagens. Collagen XV (ColXV) is a secreted non-fibrillar collagen within ECM Basement Membrane (BM) zones and well recognized as a tumor suppressor. However, the role of ColXV in adipose tissue is still unknown. In this study, high fat diet (HFD) fed mice were used as obese model, in which we deeply investigated the interaction between ColXV and adipocyte differentiation or adipose metabolism...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28641578/methylome-analysis-of-extreme-chemoresponsive-patients-identifies-novel-markers-of-platinum-sensitivity-in-high-grade-serous-ovarian-cancer
#3
Tushar Tomar, Nicolette G Alkema, Leroy Schreuder, Gert Jan Meersma, Tim de Meyer, Wim van Criekinge, Harry G Klip, Heidi Fiegl, Els van Nieuwenhuysen, Ignace Vergote, Martin Widschwendter, Ed Schuuring, Ate G J van der Zee, Steven de Jong, G Bea A Wisman
BACKGROUND: Despite an early response to platinum-based chemotherapy in advanced stage high-grade serous ovarian cancer (HGSOC), the majority of patients will relapse with drug-resistant disease. Aberrant epigenetic alterations like DNA methylation are common in HGSOC. Differences in DNA methylation are associated with chemoresponse in these patients. The objective of this study was to identify and validate novel epigenetic markers of chemoresponse using genome-wide analysis of DNA methylation in extreme chemoresponsive HGSOC patients...
June 23, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28637691/settling-the-m-6-a-debate-methylation-of-mature-mrna-is-not-dynamic-but-accelerates-turnover
#4
REVIEW
Nicolle A Rosa-Mercado, Johanna B Withers, Joan A Steitz
Post-transcriptional modification of RNA nucleosides has been implicated as a pivotal regulator of mRNA biology. In this issue of Genes & Development, Ke and colleagues (pp. 990-1006) provide insights into the temporal and spatial distribution of N(6)-methyladenosine (m(6)A) in RNA transcripts by analyzing different subcellular fractions. Using a recently developed biochemical approach for detecting m(6)A, the researchers show that m(6)A methylations are enriched in exons and are added to transcripts prior to splicing...
May 15, 2017: Genes & Development
https://www.readbyqxmd.com/read/28637314/dna-methylation-signatures-and-coagulation-factors-in-the-peripheral-blood-leucocytes-of-epithelial-ovarian-cancer
#5
Lian Li, Hong Zheng, Yubei Huang, Caiyun Huang, Shuang Zhang, Jing Tian, Pei Li, Anil K Sood, Wei Zhang, Kexin Chen
Solid tumors are increasingly recognized as a systemic disease that is manifested by changes in DNA, RNA, proteins, and metabolites in the blood. Whereas many studies have reported gene mutation events in the circulation, few studies have focused on epigenetic DNA methylation markers. To identify DNA methylation biomarkers in peripheral blood for ovarian cancer, we performed a two-stage epigenome-wide association study. In the discovery stage, we measured genome wide DNA methylation for 485,000 CpG sites in peripheral blood in 24 epithelial ovarian cancer cases and 24 age-matched healthy controls...
June 16, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28636652/integrative-analysis-of-genomic-alterations-in-triple-negative-breast-cancer-in-association-with-homologous-recombination-deficiency
#6
Masahito Kawazu, Shinya Kojima, Toshihide Ueno, Yasushi Totoki, Hiromi Nakamura, Akiko Kunita, Wei Qu, Jun Yoshimura, Manabu Soda, Takahiko Yasuda, Natsuko Hama, Mihoko Saito-Adachi, Kazuhito Sato, Shinji Kohsaka, Eirin Sai, Masako Ikemura, Shigeru Yamamoto, Tomoko Ogawa, Masashi Fukayama, Keiichiro Tada, Yasuyuki Seto, Shinichi Morishita, Shoichi Hazama, Tatsuhiro Shibata, Yoshihiro Yamashita, Hiroyuki Mano
Triple-negative breast cancer (TNBC) cells do not express estrogen receptors, progesterone receptors, or human epidermal growth factor receptor 2. Currently, apart from poly ADP-ribose polymerase inhibitors, there are few effective therapeutic options for this type of cancer. Here, we present comprehensive characterization of the genetic alterations in TNBC performed by high coverage whole genome sequencing together with transcriptome and whole exome sequencing. Silencing of the BRCA1 gene impaired the homologous recombination pathway in a subset of TNBCs, which exhibited similar phenotypes to tumors with BRCA1 mutations; they harbored many structural variations (SVs) with relative enrichment for tandem duplication...
June 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28636597/phase-separation-drives-heterochromatin-domain-formation
#7
Amy R Strom, Alexander V Emelyanov, Mustafa Mir, Dmitry V Fyodorov, Xavier Darzacq, Gary H Karpen
Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA...
June 21, 2017: Nature
https://www.readbyqxmd.com/read/28630453/longitudinal-analyses-of-the-dna-methylome-in-deployed-military-servicemen-identify-susceptibility-loci-for-post-traumatic-stress-disorder
#8
B P F Rutten, E Vermetten, C H Vinkers, G Ursini, N P Daskalakis, E Pishva, L de Nijs, L C Houtepen, L Eijssen, A E Jaffe, G Kenis, W Viechtbauer, D van den Hove, K G Schraut, K-P Lesch, J E Kleinman, T M Hyde, D R Weinberger, L Schalkwyk, K Lunnon, J Mill, H Cohen, R Yehuda, D G Baker, A X Maihofer, C M Nievergelt, E Geuze, M P M Boks
In order to determine the impact of the epigenetic response to traumatic stress on post-traumatic stress disorder (PTSD), this study examined longitudinal changes of genome-wide blood DNA methylation profiles in relation to the development of PTSD symptoms in two prospective military cohorts (one discovery and one replication data set). In the first cohort consisting of male Dutch military servicemen (n=93), the emergence of PTSD symptoms over a deployment period to a combat zone was significantly associated with alterations in DNA methylation levels at 17 genomic positions and 12 genomic regions...
June 20, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28627734/role-of-cytoskeletal-mechanics-and-cell-membrane-fluidity-in-the-intracellular-delivery-of-molecules-mediated-by-laser-activated-carbon-nanoparticles
#9
Stefany Y Holguin, Caleb F Anderson, Naresh N Thadhani, Mark R Prausnitz
Exposure of cells and nanoparticles to near-infrared nanosecond pulsed laser light can lead to efficient intracellular delivery of molecules while maintaining high cell viability by a photoacoustic phenomenon known as transient nanoparticle energy transduction (TNET). Here, we examined the influence of cytoskeletal mechanics and plasma membrane fluidity on intracellular uptake of molecules and loss of cell viability due to TNET. We found that destabilization of actin filaments using latrunculin A led to greater uptake of molecules and less viability loss caused by TNET...
June 19, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28621701/epigenetics-insights-into-chronic-pain-dna-hypomethylation-in-fibromyalgia-a-controlled-pilot-study
#10
Daniel Ciampi de Andrade, Mariana Maschietto, Ricardo Galhardoni, Gisele Gouveia, Thais Chile, Ana C Victorino Krepischi, Camila S Dale, André R Brunoni, Daniella C Parravano, Ana S Cueva Moscoso, Irina Raicher, Helena H S Kaziyama, Manoel J Teixeira, Helena P Brentani
To evaluate changes in DNA methylation profiles in patients with fibromyalgia (FM) compared to matched healthy controls (HCs). All individuals underwent full clinical and neurophysiological assessment by cortical excitability (CE) parameters measured by transcranial magnetic stimulation. DNA from the peripheral blood of patients with FM (n = 24) and HC (n = 24) were assessed using the Illumina-HumanMethylation450 BeadChips. We identified 1610 differentially methylated positions (DMPs) in patients with FM displaying a nonrandom distribution in regions of the genome...
June 15, 2017: Pain
https://www.readbyqxmd.com/read/28621677/genome-wide-methylome-and-chromatin-interactome-identify-abnormal-enhancer-to-be-risk-factor-of-breast-cancer
#11
Yuan Wang, Da-Peng Hao, Jing-Jing Li, Li Wang, Li-Jun Di
Enhancer is critical cis regulatory elements in gene expression. To understand whether and how the aberrant enhancer activation may contribute to cancer risk, the differentially methylated enhancers (eDMRs) in normal and malignant breast tissues were identified and analyzed. By incorporating genome-wide chromatin interaction, integrated analysis of eDMRs and target gene expression identified 1,272 enhancer-promoter pairs. Surprisingly, two functionally distinct groups of genes were identified in these pairs, one showing better correlation to enhancer methylation (eRGs) and the other showing better correlation to promoter methylation (pRGs), and the former group is functionally enriched with cancer related genes...
June 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28621329/single-cell-multi-omics-sequencing-of-mouse-early-embryos-and-embryonic-stem-cells
#12
Fan Guo, Lin Li, Jingyun Li, Xinglong Wu, Boqiang Hu, Ping Zhu, Lu Wen, Fuchou Tang
Single-cell epigenome sequencing techniques have recently been developed. However, the combination of different layers of epigenome sequencing in an individual cell has not yet been achieved. Here, we developed a single-cell multi-omics sequencing technology (single-cell COOL-seq) that can analyze the chromatin state/nucleosome positioning, DNA methylation, copy number variation and ploidy simultaneously from the same individual mammalian cell. We used this method to analyze the reprogramming of the chromatin state and DNA methylation in mouse preimplantation embryos...
June 16, 2017: Cell Research
https://www.readbyqxmd.com/read/28620075/experience-dependent-epigenomic-reorganization-in-the-hippocampus
#13
Corey G Duke, Andrew J Kennedy, Cristin F Gavin, Jeremy J Day, J David Sweatt
Using a hippocampus-dependent contextual threat learning and memory task, we report widespread, coordinated DNA methylation changes in CA1 hippocampus of Sprague-Dawley rats specific to threat learning at genes involved in synaptic transmission. Experience-dependent alternations in gene expression and DNA methylation were observed as early as 1 h following memory acquisition and became more pronounced after 24 h. Gene ontology analysis revealed significant enrichment of functional categories related to synaptic transmission in genes that were hypomethylated at 24 h following threat learning...
July 2017: Learning & Memory
https://www.readbyqxmd.com/read/28617821/supplementation-with-small-extracellular-vesicles-from-ovarian-follicular-fluid-during-in-vitro-production-modulates-bovine-embryo-development
#14
Juliano C da Silveira, Gabriella M Andrade, Maite Del Collado, Rafael V Sampaio, Juliano R Sangalli, Luciano A Silva, Fábio V L Pinaffi, Izabelle B Jardim, Marcelo C Cesar, Marcelo F G Nogueira, Aline S M Cesar, Luiz L Coutinho, Rinaldo W Pereira, Felipe Perecin, Flávio V Meirelles
Pregnancy success results from the interaction of multiple factors, among them are folliculogenesis and early embryonic development. Failure during these different processes can lead to difficulties in conception. Alternatives to overcome these problems are based on assisted reproductive techniques. Extracellular vesicles are cell-secreted vesicles present in different body fluids and contain bioactive materials, such as messenger RNA, microRNAs (miRNAs), and proteins. Thus, our hypothesis is that extracellular vesicles from follicular fluid from 3-6 mm ovarian follicles can modulate bovine embryo development in vitro...
2017: PloS One
https://www.readbyqxmd.com/read/28613929/dna-methylation-and-hydroxymethylation-profile-of-cd34-enriched-cell-products-intended-for-autologous-cd34-cell-transplantation
#15
Jasmina-Ziva Rozman, Maja Pohar Perme, Mojca Jez, Elvira Malicev, Metka Krasna, Bojan Vrtovec, Primoz Rozman
Epigenetic dysregulation has been shown to limit functional capacity of aging hematopoietic stem cells, which may contribute to impaired outcome of hematopoietic stem cell-based therapies. The aim of our study was to gain better insight into the epigenetic profile of CD34(+)-enriched cell products intended for autologous CD34(+) cell transplantation in patients with cardiomyopathy. We found global DNA methylation content significantly higher in immunoselected CD34(+) cells compared to leukocytes in leukapheresis products (2...
June 14, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28612328/antidepressant-actions-of-ketamine-mediated-by-the-mechanistic-target-of-rapamycin-nitric-oxide-and-rheb
#16
REVIEW
Maged M Harraz, Solomon H Snyder
The weeks/months it takes for traditional antidepressants to act pose an obstacle in the management of depression. Ketamine's prompt and sustained antidepressant effects constitute a major advance. Multiple studies implicate glutamatergic signaling to protein synthesis machinery and synapse formation in ketamine's antidepressant effects. Here we review evidence linking ketamine to glutamate receptor subtypes and protein homeostasis. We describe a signaling cascade wherein nitric oxide drives the formation of a ternary protein complex comprised of glyceraldehyde 3-phosphate dehydrogenase, seven in absentia homolog 1, and Ras homolog enriched in brain downstream of the glutamate N-methyl-D-aspartate receptor...
June 13, 2017: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
https://www.readbyqxmd.com/read/28611663/epigenetic-modifications-to-h3k9-in-renal-tubulointerstitial-cells-after-unilateral-ureteric-obstruction-and-tgf-%C3%AE-1-stimulation
#17
Timothy D Hewitson, Stephen G Holt, Sven-Jean Tan, Belinda Wigg, Chrishan S Samuel, Edward R Smith
Introduction: Epigenetic regulation of fibrogenesis through post-translational histone modifications (marks) may be a key determinant of progression in renal disease. In this study, we examined the distribution and acquisition of histone 3 Lysine 9 (H3K9) marks after injury and stimulation with the pro-fibrotic cytokine TGF-β1. Our focus was on their presence in activated fibroblasts (myofibroblasts) and epithelial cells (epithelial-mesenchymal transition). Methods and Results: Immunofluorescent microscopy was used to examine global H3K9 acetylation (H3K9Ac) and tri-methylation (H3K9Me3) after unilateral ureteric obstruction (UUO) in mice...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28611465/fibroblasts-derived-from-oesophageal-adenocarcinoma-differ-in-dna-methylation-profile-from-normal-oesophageal-fibroblasts
#18
Eric Smith, Helen M Palethorpe, Annette L Hayden, Joanne P Young, Timothy J Underwood, Paul A Drew
Oesophageal adenocarcinoma (OAC) is increasing in incidence and has a poor prognosis. Tumour derived fibroblasts (TDFs) differ functionally from normal fibroblasts (NDFs), and play a pivotal role in cancer. Many of the differences persist through subculture. We measured the DNA methylation profiles of 10 TDFs from OAC with 12 NDF from normal oesophageal mucosa using Infinium HumanMethylation450 Beadchips and found they differed in multidimensional scaling analysis. We identified 4,856 differentially methylated CpGs (DMCs, adjusted p < 0...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28609610/an-rna-aptamer-capable-of-forming-hydrogel-by-self-assembly
#19
Zhen Huang, Gagan N Kangovi, Wei Wen, Sangwoo Lee, Li Niu
Hydrogels are supramolecular assemblies with both solute transport properties like liquids and mechanical properties like elastomers. To date, every type of biomolecules, except ribonucleic acid (RNA), are capable of forming hydrogel. Here we report an RNA that forms hydrogel by self-assembly. This RNA is originally identified by systematic evolution of ligands by exponential enrichment (SELEX) to enhance the activity of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors as a potential RNA drug for treatment of cognitive disorders...
June 13, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28605464/strand-specific-cpg-hemimethylation-a-novel-epigenetic-modification-functional-for-genomic-imprinting
#20
Iris Patiño-Parrado, Álvaro Gómez-Jiménez, Noelia López-Sánchez, José M Frade
Imprinted genes are regulated by allele-specific differentially DNA-methylated regions (DMRs). Epigenetic methylation of the CpGs constituting these DMRs is established in the germline, resulting in a 5-methylcytosine-specific pattern that is tightly maintained in somatic tissues. Here, we show a novel epigenetic mark, characterized by strand-specific hemimethylation of contiguous CpG sites affecting the germline DMR of the murine Peg3, but not Snrpn, imprinted domain. This modification is enriched in tetraploid cortical neurons, a cell type where evidence for a small proportion of formylmethylated CpG sites within the Peg3-controlling DMR is also provided...
June 9, 2017: Nucleic Acids Research
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