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https://www.readbyqxmd.com/read/29224147/comprehensive-whole-dna-methylome-analysis-by-integrating-medip-seq-and-mre-seq
#1
Xiaoyun Xing, Bo Zhang, Daofeng Li, Ting Wang
Understanding the role of DNA methylation often requires accurate assessment and comparison of these modifications in a genome-wide fashion. Sequencing-based DNA methylation profiling provides an unprecedented opportunity to map and compare complete DNA CpG methylomes. These include whole genome bisulfite sequencing (WGBS), Reduced-Representation Bisulfite-Sequencing (RRBS), and enrichment-based methods such as MeDIP-seq, MBD-seq, and MRE-seq. An investigator needs a method that is flexible with the quantity of input DNA, provides the appropriate balance among genomic CpG coverage, resolution, quantitative accuracy, and cost, and comes with robust bioinformatics software for analyzing the data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224140/whole-genome-bisulfite-sequencing-using-the-ovation%C3%A2-ultralow-methyl-seq-protocol
#2
Christian Daviaud, Victor Renault, Florence Mauger, Jean-François Deleuze, Jörg Tost
The analysis of genome-wide epigenomic alterations including DNA methylation has become a subject of intensive research for many complex diseases. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies can be considered the gold standard for a comprehensive and quantitative analysis of cytosine methylation throughout the genome. Several approaches including tagmentation- and post bisulfite adaptor tagging (PBAT)-based WGBS have been devised. Here, we provide a detailed protocol based on a commercial kit for the preparation of libraries for WGBS from limited amounts of input DNA (50-100 ng) using the classical approach of WGBS by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224068/hi-plex-for-simple-accurate-and-cost-effective-amplicon-based-targeted-dna-sequencing
#3
Bernard J Pope, Fleur Hammet, Tu Nguyen-Dumont, Daniel J Park
Hi-Plex is a suite of methods to enable simple, accurate, and cost-effective highly multiplex PCR-based targeted sequencing (Nguyen-Dumont et al., Biotechniques 58:33-36, 2015). At its core is the principle of using gene-specific primers (GSPs) to "seed" (or target) the reaction and universal primers to "drive" the majority of the reaction. In this manner, effects on amplification efficiencies across the target amplicons can, to a large extent, be restricted to early seeding cycles. Product sizes are defined within a relatively narrow range to enable high-specificity size selection, replication uniformity across target sites (including in the context of fragmented input DNA such as that derived from fixed tumor specimens (Nguyen-Dumont et al...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224019/the-mir-495-annexin-a3-p53-axis-inhibits-the-invasion-and-emt-of-colorectal-cancer-cells
#4
Zhigang Bai, Jin Wang, Tingting Wang, Yuan Li, Xiaomu Zhao, Guocong Wu, Yingchi Yang, Wei Deng, Zhongtao Zhang
BACKGROUND/AIMS: More and more reports have shown that the dysregulation of miRNAs can contribute to the progression and metastasis of human cancers. Many studies have shown that the down-regulation of the miR-495 level occurs in a variety of cancers, including colorectal cancer (CRC). However, the precise molecular mechanisms of miR-495 in CRC have not been well clarified. In the current study, we investigated the biological functions and molecular mechanisms of miR-495 in CRC cell lines...
December 8, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29224010/microrna-195-suppresses-the-progression-of-pancreatic-cancer-by-targeting-dclk1
#5
Bin Zhou, Chuandong Sun, Xiao Hu, Hanxiang Zhan, Hao Zou, Yujie Feng, Fabo Qiu, Shun Zhang, Liqun Wu, Bingyuan Zhang
BACKGROUND/AIMS: Doublecortin-like kinase 1 (DCLK1) is emerging as a tumor-specific stem cell marker in pancreatic cancer (PC). MicroRNA-195 (miR-195) plays an important role in many types of tumors. However, the roles of DCLK1 in cancer and miRNAs that directly regulate DCLK1 have not been elucidated. The goal of this study is to assess the effects of miR-195 on inhibiting DCLK1 and to clarify the regulating mechanism of miR-195-DCLK1 in PC cells. METHODS: The expression of DCLK1 protein and miR-195 in PC tissues and adjacent healthy pancreatic tissues was detected by Western blot and quantitative reverse transcription polymerase chain reaction (qRT-PCR), respectively and the correlation between overall survival of PC patients and expression of DCLK1 was measured by Kaplan-Meier analysis...
December 8, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29223543/metagenomic-sequencing-of-environmental-dna-reveals-marine-faunal-assemblages-from-the-west-antarctic-peninsula
#6
Dominique A Cowart, Katherine R Murphy, C-H Christina Cheng
The West Antarctic Peninsula (WAP) is the fastest warming region in Antarctica where climate impact on the cold-adapted marine ecosystem is already visible. To monitor faunal changes in remote vast bodies of Antarctic waters, efficient and informative tools are essential. High-throughput sequencing of environmental DNA (eDNA) has emerged as one such tool for monitoring biodiversity and ecosystems, as it increases detection sensitivity of taxa, and sampling is often simpler and less costly than traditional collection methods...
December 6, 2017: Marine Genomics
https://www.readbyqxmd.com/read/29222900/comparisons-of-proteomic-profiles-of-whey-protein-between-donor-human-milk-collected-earlier-than-3-months-and-6-months-after-delivery
#7
Won-Ho Hahn, Joon-Hwan Song, Jong-Bok Seo, Jung Eun Lee, Jeong-Sang Lee, Seunghyun Song, Joohyun Lee, Nam Mi Kang
BACKGROUND AND OBJECTIVES: Human milk has nutritional, protective, and developmental advantages for premature infants. However, proteomic information of low abundant protein of donor milk is insufficient. The purpose of this study is to analyze and compare the proteome of low abundant protein of donor milk obtained at different postpartum ages other than the colostrum. METHODS AND STUDY DESIGN: Donor breast milk from 12 healthy mothers was collected 15 days, 2 months and 6 months after delivery and stored by medically approved methods...
2018: Asia Pacific Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/29222758/differential-proteomics-based-on-2d-difference-in-gel-electrophoresis-and-tandem-mass-spectrometry-for-the-elucidation-of-biological-processes-in-antibiotic-producer-bacterial-strains
#8
Giuseppe Gallo, Andrea Scaloni
Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a "gold standard" to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29222118/purine-and-pyrimidine-triple-helix-forming-oligonucleotides-recognize-qualitatively-different-target-sites-at-the-ribosomal-dna-locus
#9
Rodrigo Maldonado, Michael Filarsky, Ingrid Grummt, Gernot Längst
Triplexes are non-canonical DNA structures, which are functionally associated with regulation of gene expression through ncRNA targeting to chromatin. Based on the rules of Hoogsteen base pairing, poly-purine sequences of a duplex can potentially form triplex structures with single-stranded oligonucleotides. Prediction of triplex-forming sequences by bioinformatics analyses have revealed enrichment of potential triplex targeting sites (TTS) at regulatory elements, mainly in promoters and enhancers, suggesting a potential function of RNA-DNA triplexes in transcriptional regulation...
December 8, 2017: RNA
https://www.readbyqxmd.com/read/29222086/genome-wide-dna-methylation-profiling-using-the-methylation-dependent-restriction-enzyme-lpnpi
#10
Ruben Boers, Joachim Boers, Bas de Hoon, Christel Kockx, Zeliha Ozgur, Anco Molijn, Wilfred van IJcken, Joop Laven, Joost Gribnau
DNA methylation is a well-known epigenetic modification that plays a crucial role in gene regulation, but genome-wide analysis of DNA methylation remains technically challenging and costly. DNA methylation-dependent restriction enzymes can be used to restrict CpG methylation analysis to methylated regions of the genome only, which significantly reduces the required sequencing depth and simplifies subsequent bioinformatics analysis. Unfortunately, this approach has been hampered by complete digestion of DNA in CpG methylation-dense regions, resulting in fragments that are too small for accurate mapping...
December 8, 2017: Genome Research
https://www.readbyqxmd.com/read/29221754/up-regulation-of-ypel1-and-ypel5-and-down-regulation-of-itga2-in-erlotinib-treated-egfr-mutant-non-small-cell-lung-cancer-a-bioinformatic-analysis
#11
Xiaoli Wu
PURPOSE: This study aimed to identify genes with significant alteration following treatment of epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) with tyrosine kinase inhibitors (TKIs). METHODS: We downloaded microarray data of GSE67051 from the Gene Expression Omnibus (GEO) database. Genes with differential expression were identified in two groups: erlotinib-treated versus DMSO-treated PC9 cells and erlotinib-treated versus DMSO-treated HCC827 cells...
December 5, 2017: Gene
https://www.readbyqxmd.com/read/29221726/mirna-495-suppresses-proliferation-and-migration-of-colorectal-cancer-cells-by-targeting-fam83d
#12
Likun Yan, Jianfeng Yao, Jian Qiu
microRNAs (miRNAs) have been reported to play crucial roles in malignant tumor progression, including cell development, proliferation, and progression. Increasing evidence suggests that miR-495 functions as either an oncogene or tumor suppressor in several tumor types. However, its biological role in the development of colorectal cancer (CRC) still remains unclear. In this study, we found that miR-495 expression level was remarkably down-regulated in CRC tissues samples and cell lines when compared to adjacent normal tissues and cell line by using qRT-PCR detection...
December 5, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29221465/yale-school-of-public-health-symposium-on-lifetime-exposures-and-human-health-the-exposome-summary-and-future-reflections
#13
REVIEW
Caroline H Johnson, Toby J Athersuch, Gwen W Collman, Suraj Dhungana, David F Grant, Dean P Jones, Chirag J Patel, Vasilis Vasiliou
The exposome is defined as "the totality of environmental exposures encountered from birth to death" and was developed to address the need for comprehensive environmental exposure assessment to better understand disease etiology. Due to the complexity of the exposome, significant efforts have been made to develop technologies for longitudinal, internal and external exposure monitoring, and bioinformatics to integrate and analyze datasets generated. Our objectives were to bring together leaders in the field of exposomics, at a recent Symposium on "Lifetime Exposures and Human Health: The Exposome," held at Yale School of Public Health...
December 8, 2017: Human Genomics
https://www.readbyqxmd.com/read/29221215/dnmt1-overexpression-predicting-gastric-carcinogenesis-subsequent-progression-and-prognosis-a-meta-and-bioinformatic-analysis
#14
Tianmiao Ma, Hao Li, Mingjun Sun, Yuan Yuan, Li-Ping Sun
DNMT1 is important in maintaining DNA methylation, and participates in the oncogenesis via up- or down-regulation leading to hyper-methylation or hypo-methylation. In the meta and bioinformatic analysis, we found that DNMT1 expression was higher in gastric cancer, compared with normal (p < 0.00001), para-cancerous (p = 0.0004) and dysplasia (p < 0.00001) tissues. DNMT1 up-regulation was associated with gender (OR = 2.27, p = 0.006), differentiation (OR = 0.21, p = 0.01) and TNM stage (OR = 0.31, p = 0...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221202/ezh2-alteration-driven-by-microrna-524-5p-and-microrna-324-5p-promotes-cell-proliferation-and-temozolomide-resistance-in-glioma
#15
Tongle Zhi, Tianfu Yu, Minhong Pan, Er Nie, Weining Wu, Xiefeng Wang, Ning Liu, Yongping You, Yingyi Wang, Junxia Zhang
Recent data have been shown that EZH2 is a critical oncogene via the repression of tumor suppressor genes in human cancers. In our study, we performed a genome-wide miRNA screen with a bioinformatics analysis to identify EZH2 specific miRNAs. Of these miRNAs, miR-524-5p and miR-324-5p were decreased in glioma tissues, and confered poor prognosis for glioma patients. Upregulation of miR-524-5p and miR-324-5p reduced glioma cell proliferation and increased temozolomide (TMZ) chemosensitivity by targeting EZH2...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221196/identification-of-cellular-genes-and-pathways-important-for-tumorigenicity-of-hepatocellular-carcinoma-cell-lines-by-proteomic-profiling
#16
Ali Zamani, Huahao Fan, Guangxiang Luo
Hepatocellular carcinoma (HCC) is the most commonly diagnosed malignancy of the liver. A more thorough understanding of HCC pathogenesis will provide novel targets for development of cancer drugs to effectively treat HCC. To further this goal, we carried out a proteomic profiling of HCC cell lines Huh-7.4 and Huh-7.5. These two cell lines were derived from subgenomic HCV RNA-replicating Huh-7 cells upon clearance of HCV RNA by antiviral drug treatment. Initially, the tumorigenicity of each cell line was determined and compared in parallel in the same immunedeficient mice...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221188/overexpression-of-agt-promotes-bronchopulmonary-dysplasis-via-the-jak-stat-signal-pathway
#17
Lili Shen, Tiancheng Zhang, Hongyan Lu
Angiotensinogen (AGT) is involved in the production of angiotensin II which is the main mediator of action of the rennin-angiotensin system (RAS), whereas the RAS mediates the regulation of sodium homeostasis, blood pressure, and inflammation. The present study aimed to investigate the roles of the AGT in the progression of broncopulmonary dysplasia in premature newborns. By bioinformatics analysis, AGT was found to be the major node in molecular interaction networks of BPD mouse model. Quantitative PCR and western blot analyses were applied to examine AGT expression in A549 cells which were treated with the hyperoxic condition...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221168/diagnosis-prognosis-and-bioinformatics-analysis-of-lncrnas-in-hepatocellular-carcinoma
#18
Meiyu Dai, Siyuan Chen, Xiaomou Wei, Xuan Zhu, Fang Lan, Shengming Dai, Xue Qin
This study aims to comprehensively analyze the diagnosis and prognosis of lncRNAs in hepatocellular carcinoma (HCC). From the Gene Expression Omnibus database, we screened out and analyzed the differently expressed lncRNAs and related mRNAs using bioinformatics methods. The expressions of lncRNAs were validated in tumor tissues, cell lines and the Cancer Genome Atlas database. At the same time, we also conducted an exploratory analysis on the diagnostic and prognostic ability of lncRNAs in HCC. In this study, we found that most of the targeted mRNAs promote the biological process of cell division, cellular component of nucleoplasm, molecular function of protein binding, which were significantly associated with 12 KEGG pathways...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221160/circular-rna-profile-indicates-circular-rna-vrk1-is-negatively-related-with-breast-cancer-stem-cells
#19
Ningning Yan, Haiyan Xu, Jinnan Zhang, Liang Xu, Yanyun Zhang, Le Zhang, Yingchun Xu, Fengchun Zhang
Circular RNAs (circRNAs), a novel type of noncoding RNAs (ncRNAs), have been shown to be implicated in biological processes including cancer as gene expression regulators. However, the roles of circRNAs in cancer stem cells (CSCs) have been unexplored. In the present study, we screened the circRNA profile in breast cancer stem cells (BCSCs) using RNA-Sequencing. Here, 27 circRNAs were found to be aberrantly expressed. Of these, 19 circRNAs were downregulated and 8 were upregulated and some of these circRNAs were validated by Q-PCR...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221136/kif3a-and-il-4-are-disease-specific-biomarkers-for-psoriatic-arthritis-susceptibility
#20
Raffaella Cascella, Claudia Strafella, Michele Ragazzo, Laura Manzo, Gaetana Costanza, John Bowes, Ulrike Hüffmeier, Saverio Potenza, Federica Sangiuolo, André Reis, Anne Barton, Giuseppe Novelli, Augusto Orlandi, Emiliano Giardina
To date, the genes associated with Psoriatic Arthritis (PsA) are principally involved in inflammation, immune response and epidermal differentiation, without any information about the relationship between disease and bone metabolism genes. Our work was focused on 5q31 locus, which contains several genetic variants significantly associated with PsA. The study involved 1526 subjects (500 PsA, 426 PsV, 600 controls). The region was evaluated by selecting and genotyping the SNPs of interest by Real Time PCR and direct sequencing...
November 10, 2017: Oncotarget
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