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https://www.readbyqxmd.com/read/29774630/the-emerging-roles-of-long-non-coding-rna-in-cancer
#1
Anna Sanchez Calle, Yumi Kawamura, Yusuke Yamamoto, Fumitaka Takeshita, Takahiro Ochiya
Since comprehensive analysis of the mammalian genome has revealed that the vast majority of genomic products are transcribed in long non-coding RNAs (lncRNAs), increasing attention has been paid towards these transcripts. The applied next-generation sequencing technologies have provided accumulating evidence of dysregulated lncRNAs in cancer. The implication of this finding may be seen in many forms and at multiple levels. With impacts ranging from integrating chromatin remodeling complexes to regulating transcription and post-transcriptional processes, aberrant expression of lncRNAs may have repercussions in cell proliferation, tumor progression or metastasis...
May 17, 2018: Cancer Science
https://www.readbyqxmd.com/read/29772275/5c-id-increased-resolution-chromosome-conformation-capture-carbon-copy-with-in-situ-3c-and-double-alternating-primer-design
#2
Ji Hun Kim, Katelyn R Titus, Wanfeng Gong, Jonathan A Beagan, Zhendong Cao, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs, and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C can generate genome-wide maps of looping interactions but is intractable for high-throughput comparison of loops across multiple conditions due to the enormous number of reads (>6 Billion) required per library...
May 14, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29755580/finding-local-genome-rearrangements
#3
Pijus Simonaitis, Krister M Swenson
Background: The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been devoted to the understanding of minimum length scenarios transforming one genome into another. In this paper we search instead for rearrangement scenarios that minimize the number of rearrangements whose breakpoints are unlikely due to some biological criteria. One such criterion has recently become accessible due to the advent of the Hi-C experiment, facilitating the study of 3D spacial distance between breakpoint regions...
2018: Algorithms for Molecular Biology: AMB
https://www.readbyqxmd.com/read/29744889/higher-order-genomic-organization-and-regulatory-compartmentalization-for-cell-cycle-control-at-the-g1-s-phase-transition
#4
REVIEW
Prachi N Ghule, David J Seward, Andrew J Fritz, Joseph R Boyd, Andre J van Wijnen, Jane B Lian, Janet L Stein, Gary S Stein
Fidelity of histone gene regulation, and ultimately of histone protein biosynthesis, is obligatory for packaging of newly replicated DNA into chromatin. Control of histone gene expression within the 3-dimensional context of nuclear organization is reflected by two well documented observations. DNA replication-dependent histone mRNAs are synthesized at specialized subnuclear domains designated histone locus bodies (HLBs), in response to activation of the growth factor dependent Cyclin E/CDK2/HINFP/NPAT pathway at the G1/S transition in mammalian cells...
May 10, 2018: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29741506/recent-advances-in-the-cellular-and-molecular-understanding-of-myelodysplastic-syndromes-implications-for-new-therapeutic-approaches
#5
Andrew M Brunner, David P Steensma
It has been more than 10 years since any new disease-modifying therapies have received regulatory approval for indications related to myelodysplastic syndromes (MDS). Advances in our collective biological understanding of MDS in the last decade, however, have made it possible to hope that effective therapeutics can be designed to improve MDS-associated cytopenias and patients' quality of life, and perhaps even delay clonal progression and extend survival. Classes of MDS-associated mutations and disordered biological pathways targeted by developmental therapeutics include the following: aberrant messenger RNA splicing, neomorphic enzymes in the citric acid cycle with oncogenic activity, overactivated tyrosine and serine-threonine kinases, epigenetic and chromatin remodeling alterations, abnormal telomere dynamics, and failed protection of DNA integrity...
January 2018: Clinical Advances in Hematology & Oncology: H&O
https://www.readbyqxmd.com/read/29734873/whole-exome-sequencing-of-sinonasal-small-cell-carcinoma-arising-within-a-papillary-schneiderian-carcinoma-in-situ
#6
Joshua Smith, Aditi Kulkarni, Andrew C Birkeland, Jonathan B McHugh, J Chad Brenner
Objective The pathogenetic underpinnings of extrapulmonary small cell carcinomas (EPSCCs) of the head and neck are poorly understood. We sought to describe the clinical case and whole-exome DNA sequencing data of a patient with sinonasal Schneiderian carcinoma in situ whose tumor progressed to small cell carcinoma (SCC). Study Design Case report and whole-exome sequencing of tumor DNA. Setting Academic medical center. Subjects and Methods A 52-year-old man with sinonasal Schneiderian carcinoma in situ whose tumor progressed to small cell carcinoma...
May 1, 2018: Otolaryngology—Head and Neck Surgery
https://www.readbyqxmd.com/read/29718103/a-powerful-approach-reveals-numerous-expression-quantitative-trait-haplotypes-in-multiple-tissues
#7
Dingge Ying, Mulin Jun Li, Pak Chung Sham, Miaoxin Li
Motivation: Recently many studies showed single nucleotide polymorphisms (SNPs) affect gene expression and contribute to development of complex traits/diseases in a tissue context-dependent manner. However, little is known about haplotype's influence on gene expression and complex traits, which reflects the interaction effect between SNPs. Results: In the present study, we firstly proposed a regulatory region guided eQTL haplotype association analysis approach, and then systematically investigate the expression quantitative trait loci (eQTL) haplotypes in 20 different tissues by the approach...
April 26, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29717045/chip-chip
#8
Tae Hoon Kim, Job Dekker
ChIP-chip can be used to analyze protein-DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications...
May 1, 2018: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/29710459/inhibitory-effect-of-chidamide-on-the-growth-of-human-adenoid-cystic-carcinoma-cells
#9
Sheng Yang, Peng Nan, Chunxiao Li, Feng Lin, Hui Li, Ting Wang, Chunxia Zhou, Xueyan Zhang, Xiting Meng, Haili Qian, Haijuan Wang, Mei Dong
Adenoid cystic carcinoma (ACC) is a malignant epithelial neoplasm that limitedly responses to chemotherapy at the cost of significant toxicity. There is no single targeted drug approved by Food and Drug Administration (FDA) for ACC. Genomic landscape studies have revealed that frequently mutated pathways in ACC often involve in chromatin remodeling, which interfere multiple histone related proteins. Chidamide is a novel histone deacetylase inhibitor (HDACi) approved in clinical practice that was designed to increase the acetylation level of histone H3...
March 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29708552/rna-pull-down-procedure-to-identify-rna-targets-of-a-long-non-coding-rna
#10
Manon Torres, Denis Becquet, Séverine Guillen, Bénédicte Boyer, Mathias Moreno, Marie-Pierre Blanchard, Jean-Louis Franc, Anne-Marie François-Bellan
Long non-coding RNA (lncRNA), which are sequences of more than 200 nucleotides without a defined reading frame, belong to the regulatory non-coding RNA's family. Although their biological functions remain largely unknown, the number of these lncRNAs has steadily increased and it is now estimated that humans may have more than 10,000 such transcripts. Some of these are known to be involved in important regulatory pathways of gene expression which take place at the transcriptional level, but also at different steps of RNA co- and post-transcriptional maturation...
April 10, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29679238/identification-of-subsets-of-actionable-genetic-alterations-in-kras-mutant-lung-cancers-using-association-rule-mining
#11
Junior Tayou
BACKGROUND: Lung cancer is the leading cause of cancer-related death in both men and women. KRAS mutations occur in ~ 25% of patients with lung cancer, and the presence of these mutations is associated with a poor prognosis. Unfortunately, efforts to directly target KRAS or its associated downstream MAPK or PI3K/AKT/mTOR pathways have seen little or no benefits. Here, I hypothesize that KRAS-mutant tumors do not respond to KRAS pathway therapies due to the co-occurrence of other activated cell survival pathways and/or mechanisms...
April 20, 2018: Cellular Oncology (Dordrecht)
https://www.readbyqxmd.com/read/29678692/nucpospred-predicting-species-specific-genomic-nucleosome-positionin-g-via-four-different-modes-of-general-pseknc
#12
Cangzhi Jia, Qing Yang, Quan Zou
The nucleosome is the basic structure of chromatin in eukaryotic cells, with essential roles in the regulation of many biological processes, such as DNA transcription, replication and repair, and RNA splicing. Because of the importance of nucleosomes, the factors that determine their positioning within genomes should be investigated. High-resolution nucleosome-positioning maps are now available for organisms including Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans, enabling the identification of nucleosome positioning by application of computational tools...
April 17, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29663340/molecular-signatures-in-hepatocellular-carcinoma-a-step-toward-rationally-designed-cancer-therapy
#13
REVIEW
Derek J Erstad, Bryan C Fuchs, Kenneth K Tanabe
Molecular characterization of hepatocellular carcinoma (HCC) has greatly improved our understanding of disease pathogenesis. Mutational analysis, RNA and microRNA expression profiling, and epigenetic characterization have revealed common aberrations in oncogenes and tumor suppressors that correlate with disease biology and serve as a guide for the rational design of targeted therapies. These approaches have also led to the discovery of novel targets, including mutations in isocitrate dehydrogenase and chromatin remodeling enzymes...
April 17, 2018: Cancer
https://www.readbyqxmd.com/read/29662313/inhibition-of-h1n1-influenza-virus-induced-apoptosis-by-functionalized-selenium-nanoparticles-with-amantadine-through-ros-mediated-akt-signaling-pathways
#14
Yinghua Li, Zhengfang Lin, Min Guo, Mingqi Zhao, Yu Xia, Changbing Wang, Tiantian Xu, Bing Zhu
Introduction: As a therapeutic antiviral agent, the clinical application of amantadine (AM) is limited by the emergence of drug-resistant viruses. To overcome the drug-resistant viruses and meet the growing demand of clinical diagnosis, the use of biological nanoparticles (NPs) has increased in order to develop novel anti-influenza drugs. The antiviral activity of selenium NPs with low toxicity and excellent activities has attracted increasing attention for biomedical intervention in recent years...
2018: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/29648779/the-role-of-membrane-curvature-in-nanoscale-topography-induced-intracellular-signaling
#15
Hsin-Ya Lou, Wenting Zhao, Yongpeng Zeng, Bianxiao Cui
Over the past decade, there has been growing interest in developing biosensors and devices with nanoscale and vertical topography. Vertical nanostructures induce spontaneous cell engulfment, which enhances the cell-probe coupling efficiency and the sensitivity of biosensors. Although local membranes in contact with the nanostructures are found to be fully fluidic for lipid and membrane protein diffusions, cells appear to actively sense and respond to the surface topography presented by vertical nanostructures...
April 12, 2018: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29620420/research-progress-of-selective-small-molecule-bromodomain-containing-protein-9-inhibitors
#16
Ma Hui, Zhang Jian, Zheng Peiyuan, Wu Zhenwei, Zhang Huibin
The bromodomain proteins, known as the key targets in epigenetics, are 'readers' of acetylated lysine of histones. As a member of bromodomain proteins, bromodomain-containing protein 9 (BRD9) is a subunit of mammalian SWI/SNF chromatin remodeling complexes. However, the biological functions and the potential application in therapeutics of BRD9 remain ambiguous due to a lack of selective small molecule inhibitors of BRD9. Recently, series of chemical ligands against BRD9 were developed by different research institutes...
April 5, 2018: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/29605855/defining-regulatory-elements-in-the-human-genome-using-nucleosome-occupancy-and-methylome-sequencing-nome-seq
#17
Suhn Kyong Rhie, Shannon Schreiner, Peggy J Farnham
NOMe-seq (nucleosome occupancy and methylome sequencing) identifies nucleosome-depleted regions that correspond to promoters, enhancers, and insulators. The NOMe-seq method is based on the treatment of chromatin with the M.CviPI methyltransferase, which methylates GpC dinucleotides that are not protected by nucleosomes or other proteins that are tightly bound to the chromatin (GpCm does not occur in the human genome and therefore there is no endogenous background of GpCm ). Following bisulfite treatment of the M...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29605634/crispcut-a-novel-tool-for-designing-optimal-sgrnas-for-crispr-cas9-based-experiments-in-human-cells
#18
Jaspreet Kaur Dhanjal, Navaneethan Radhakrishnan, Durai Sundar
The ability to direct the CRISPR/Cas9 nuclease to a unique target site within a genome would have broad use in targeted genome engineering. However, CRISPR RNA is reported to bind to other genomic locations that differ from the intended target site by a few nucleotides, demonstrating significant off-target activity. We have developed the CRISPcut tool that screens the off-targets using various parameters and predicts the ideal genomic target for -guide RNAs in human cell lines. sgRNAs for four different types of Cas9 nucleases can be designed with an option for the user to work with different PAM sequences...
March 29, 2018: Genomics
https://www.readbyqxmd.com/read/29603290/bet-ting-on-nrf2-how-nrf2-signaling-can-influence-the-therapeutic-activities-of-bet-protein-inhibitors
#19
REVIEW
Nirmalya Chatterjee, Dirk Bohmann
BET proteins such as Brd3 and Brd4 are chromatin-associated factors, which control gene expression programs that promote inflammation and cancer. The Nrf2 transcription factor is a master regulator of genes that protect the organism against xenobiotic attack and oxidative stress. Nrf2 has demonstrated anti-inflammatory activity and can support cancer cell malignancy. This review describes the discovery, mechanism and biomedical implications of the regulatory interplay between Nrf2 and BET proteins. Both Nrf2 and BET proteins are established drug targets...
March 30, 2018: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29593737/overall-downregulation-of-mrnas-and-enrichment-of-h3k4me3-change-near-genome-wide-association-study-signals-in-systemic-lupus-erythematosus-cell-specific-effects
#20
Zhe Zhang, Lihua Shi, Li Song, Kelly Maurer, Michele A Petri, Kathleen E Sullivan
This study was designed to define gene expression and H3K4me3 histone modifications in T cells, B cells, and monocytes in systemic lupus erythematosus (SLE). Array studies of total peripheral blood mononuclear cells have demonstrated gene expression signatures related to neutrophils, interferon, and other inflammatory pathways. It is not clear how consistent these effects are across different cell types. In this study, RNA-seq and chromatin immunoprecipitation-seq were utilized to identify gene expression patterns and H3K4me3 histone modifications related to promoter activation in SLE...
2018: Frontiers in Immunology
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