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Small rna

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https://www.readbyqxmd.com/read/28734806/snora21-an-oncogenic-small-nucleolar-rna-with-a-prognostic-biomarker-potential-in-human-colorectal-cancer
#1
Kazuhiro Yoshida, Shusuke Toden, Wenhao Weng, Kunitoshi Shigeyasu, Jinsei Miyoshi, Jacob Turner, Takeshi Nagasaka, Yanlei Ma, Tetsuji Takayama, Toshiyoshi Fujiwara, Ajay Goel
BACKGROUND: Emerging evidence indicates that small nucleolar RNAs (snoRNAs) play a central role in oncogenesis. Herein, we systematically evaluated expression profiles of snoRNAs in colorectal cancer (CRC) and investigated their clinical and functional role in this malignancy. METHODS: We compared expression levels of snoRNAs between cancer and normal tissues using publicly available datasets and identified the most differentially expressed and commonly upregulated snoRNAs in CRC...
July 12, 2017: EBioMedicine
https://www.readbyqxmd.com/read/28733670/brd3-and-brd4-bet-bromodomain-proteins-differentially-regulate-skeletal-myogenesis
#2
Thomas C Roberts, Usue Etxaniz, Alessandra Dall'Agnese, Shwu-Yuan Wu, Cheng-Ming Chiang, Paul E Brennan, Matthew J A Wood, Pier Lorenzo Puri
Myogenic differentiation proceeds through a highly coordinated cascade of gene activation that necessitates epigenomic changes in chromatin structure. Using a screen of small molecule epigenetic probes we identified three compounds which inhibited myogenic differentiation in C2C12 myoblasts; (+)-JQ1, PFI-1, and Bromosporine. These molecules target Bromodomain and Extra Terminal domain (BET) proteins, which are epigenetic readers of acetylated histone lysine tail residues. BETi-mediated anti-myogenic effects were also observed in a model of MYOD1-mediated myogenic conversion of human fibroblasts, and in primary mouse and human myoblasts...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733293/androgen-responsive-non-coding-small-rnas-extend-the-potential-use-of-hcg-stimulation-as-a-bioassay-of-androgen-sufficiency
#3
Martina Rodie, Manikhandan Av Mudaliar, Pawel Herzyk, M McMillan, Massoud Boroujerdi, Sandra Chudleigh, Edward S Tobias, S Faisal Ahmed
BACKGROUND: It is unclear whether a short-term change in circulating androgens is associated with changes in the transcriptome of the peripheral blood mononuclear cells (PBMC). AIMS & METHODS: To explore the effect of hCG-stimulation on the PBMC-transcriptome, 12 boys with a median age (range) of 0.7yrs (0.3, 11.2) who received intramuscular hCG 1500u on 3 consecutive days as part of their investigations underwent transcriptomic array analysis on RNA extracted from peripheral blood mononuclear cells before and after hCG stimulation...
July 21, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28733163/rnai-mediated-knockdown-of-spook-reduces-ecdysteroid-titers-and-causes-precocious-metamorphosis-in-the-desert-locust-schistocerca-gregaria
#4
Ryohei Sugahara, Seiji Tanaka, Takahiro Shiotsuki
The Halloween gene SPOOK (SPO) is involved in the production of the active metabolite of ecdysteroid, 20-hydroxyecdysone (20E), in insects. A previous study showed that RNAi-mediated knockdown of SPO in Schistocerca gregaria last instar nymphs markedly reduced the hemolymph 20E titer, but did not affect metamorphosis. In the present study, the effects of SPO interference on development were re-examined in this locust. Injections of SPO double-stranded RNA (dsSPO) into nymphs at mid and late instars significantly delayed nymphal development and interfered with molting...
July 18, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28733144/the-spliceosome-a-protein-directed-metalloribozyme
#5
REVIEW
Yigong Shi
Pre-mRNA splicing is executed by the ribonucleoprotein machinery spliceosome. Nearly forty years after the discovery of pre-mRNA splicing, the atomic structure of the spliceosome has finally come to light. Four distinct conformational states of the yeast spliceosome have been captured at atomic or near-atomic resolutions. Two catalytic metal ions at the active site are specifically coordinated by the U6 small nuclear RNA (snRNA) and catalyze both the branching reaction and the exon ligation. Of the three snRNAs in the fully-assembled spliceosome, U5 and U6, along with 30 contiguous nucleotides of U2 at its 5'-end, remain structurally rigid throughout the splicing reaction...
July 18, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28731988/roles-of-mitogen-activating-protein-kinase-kinase-kinase-kinase-3-map4k3-in-preterm-skeletal-muscle-satellite-cell-myogenesis-and-mammalian-target-of-rapamycin-complex-1-mtorc1-activation-regulation
#6
Chu-Yi Guo, Mu-Xue Yu, Jie-Min Dai, Si-Nian Pan, Zhen-Tong Lu, Xiao-Shan Qiu, Si-Qi Zhuang
BACKGROUND Preterm skeletal muscle genesis is a paradigm for myogenesis. The role of mitogen-activating protein kinase kinase kinase kinase-3 (MAP4K3) in preterm skeletal muscle satellite cells myogenesis or its relationship to mammalian target of rapamycin complex 1 (mTORC1) activity have not been previously elaborated. MATERIAL AND METHODS Small interfering RNA (siRNA) interference technology was used to inhibit MAP4K3 expression. Leucine stimulation experiments were performed following MAP4K3-siRNA interference...
July 21, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28731225/decreased-levels-of-pdi-and-p5-in-oligodendrocytes-in-alzheimer-s-disease
#7
Yasuyuki Honjo, Takashi Ayaki, Takami Tomiyama, Tomohisa Horibe, Hidefumi Ito, Hiroshi Mori, Ryosuke Takahashi, Koji Kawakami
Protein disulfide isomerase (PDI) is a chaperone protein located in the endoplasmic reticulum (ER). Nitric oxide-induced S-nitrosylation of PDI inhibits its enzymatic activity, leading to protein accumulation and activation of the unfolded protein response. Protein disulfide isomerase P5 (P5) is a member of the PDI family that mostly localizes to the ER lumen. Both S-nitrosylated PDI and S-nitrosylated P5 are found in Alzheimer's disease (AD) brain. Previously, we showed that expression of the ER stress marker, growth arrest, and DNA damage protein (GADD34) was significantly increased in neurons and oligodendrocytes in AD brain...
July 21, 2017: Neuropathology: Official Journal of the Japanese Society of Neuropathology
https://www.readbyqxmd.com/read/28731195/inhibition-of-arc-promoting-the-apoptosis-of-rat-pulmonary-arterial-smooth-muscle-cells-after-serum-deprivation-in%C3%A2-vitro
#8
Jie Zhang, Zeyu Wu, Ming Guan, Hongyan Lu, Xuming Mo
Apoptosis has important pathophysiological consequences contributing to pulmonary arterial hypertension (PAH). However, the mechanism underlying apoptosis in PAH remains unknown. Apoptosis repressor with caspase recruitment domain (ARC) is an essential factor in cell apoptosis, and regulates intrinsic and extrinsic apoptosis signaling pathways. It is hypothesized that ARC may be involved in the apoptotic responses of pulmonary arterial smooth muscle cells (PASMCs) following mild chronic injury. In the present study, serum deprivation (SD) was used to induce apoptosis of PASMCs...
July 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28731158/the-long-non-coding-rna-snhg3-functions-as-a-competing-endogenous-rna-to-promote-malignant-development-of-colorectal-cancer
#9
Weizhen Huang, Yunming Tian, Shaoting Dong, Yinlian Cha, Jun Li, Xiaohong Guo, Xia Yuan
Accumulating evidence has revealed that aberrantly expressed long non-coding transcripts are involved in the development and progression of colorectal cancer (CRC). Small nucleolar RNA host gene 3 (SNHG3) is a newly identified lncRNA, and little is known about its clinical significance and biological functions in the development of CRC. In the present study, we found that the expression of SNHG3 was significantly upregulated in CRC, and upregulation of SNHG3 predicted poor prognosis for patients with CRC as determined through analysis of the data obtained from TCGA database...
July 18, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28730963/increased-expression-of-ire1%C3%AE-associates-with-the-resistant-mechanism-of-osimertinib-azd9291-resistant-non-small-cell-lung-cancer-hcc827-osir-cells
#10
Zheng-Hai Tang, Min-Xia Su, Xia Guo, Xiao-Ming Jiang, Lin Jia, Xiuping Chen, Jin-Jian Lu
BACKGROUND: Osimertinib (OSI), also known as AZD9291, is a third-generation epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) that has been approved for the treatment of non-small cell lung cancer (NSCLC) patients. OBJECTIVE: Establishment of the OSI-resistant HCC827/OSIR cell line and study of its resistant mechanism. METHOD: The anti-proliferative effect was studied through MTT and colony formation assays. The protein expression was detected by Western blot assay...
July 19, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28730546/mammalian-mitochondrial-rnas-are-degraded-in-the-mitochondrial-intermembrane-space-by-rnaset2
#11
Peipei Liu, Jinliang Huang, Qian Zheng, Leiming Xie, Xinping Lu, Jie Jin, Geng Wang
Mammalian mitochondrial genome encodes a small set of tRNAs, rRNAs, and mRNAs. The RNA synthesis process has been well characterized. How the RNAs are degraded, however, is poorly understood. It was long assumed that the degradation happens in the matrix where transcription and translation machineries reside. Here we show that contrary to the assumption, mammalian mitochondrial RNA degradation occurs in the mitochondrial intermembrane space (IMS) and the IMS-localized RNASET2 is the enzyme that degrades the RNAs...
July 20, 2017: Protein & Cell
https://www.readbyqxmd.com/read/28730528/sulforaphane-promotes-mitochondrial-protection-in-sh-sy5y-cells-exposed-to-hydrogen-peroxide-by-an-nrf2-dependent-mechanism
#12
Marcos Roberto de Oliveira, Flávia de Bittencourt Brasil, Cristina Ribas Fürstenau
Sulforaphane (SFN; C6H11NOS2) is an isothiocyanate found in cruciferous vegetables, such as broccoli, kale, and radish. SFN exhibits antioxidant, anti-apoptotic, anti-tumor, and anti-inflammatory activities in different cell types. However, it was not previously demonstrated whether and how this natural compound would exert mitochondrial protection experimentally. Therefore, we investigated here the effects of a pretreatment (for 30 min) with SFN at 5 μM on mitochondria obtained from human neuroblastoma SH-SY5Y cells exposed to hydrogen peroxide (H2O2) at 300 μM for 24 h...
July 20, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28730478/high-content-imaging-and-rnai-screens-for-investigating-kinase-network-plasticity
#13
Simon R Stockwell, Sibylle Mittnacht
High-content imaging connects the information-rich method of microscopy with the systematic objective principles of software-driven analysis. Suited to automation and, therefore, considerable scale-up of study size, this approach can deliver multiparametric data over cell populations or at the level of the individual cell and has found considerable utility in reverse genetic and pharmacological screens. Here we present a method to screen small interfering RNA (siRNA) libraries allowing subsequent observation of the impact of each knockdown on two interlinked, high-content, G1-/S-phase cell cycle transition assays related to cyclin-dependent kinase (CDK) 2 activity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730449/rational-engineering-of-a-modular-group-i-ribozyme-to-control-its-activity-by-self-dimerization
#14
Takahiro Tanaka, Yoshiya Ikawa, Shigeyoshi Matsumura
We designed and constructed a dimer of the Tetrahymena group I ribozyme the activity of which is regulated by self-dimerization. This dimer was rationally designed by utilizing the P5abc and ΔP5abc domains as large RNA motifs. This strategy enabled us to install large ribozyme functions into an RNA structure. This is a step toward expanding the field of RNA nanotechnology beyond the limitation of using only relatively small functional motifs. Self-dimerization can also be rationally programmed by modular engineering of RNA interaction motifs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730443/synthesis-of-plga-lipid-hybrid-nanoparticles-for-sirna-delivery-using-the-emulsion-method-plga-peg-lipid-nanoparticles-for-sirna-delivery
#15
Lei Wang, Benjamin Griffel, Xiaoyang Xu
The effective delivery of small interfering RNA (siRNA) to tumor cells remains a challenge for applications in cancer therapy. The development of polymeric nanoparticles with high siRNA loading efficacy has shown great potential for cancer targets. Double emulsion solvent evaporation technique is a useful tool for encapsulation of hydrophilic molecules (e.g., siRNA). Here we describe a versatile platform for siRNA delivery based on PLGA-PEG-cationic lipid nanoparticles by using the double emulsion method. The resulting nanoparticles show high encapsulation efficiency for siRNA (up to 90%) and demonstrate effective downregulation of the target genes in vitro and vivo...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730442/chitosan-nanoparticles-for-mirna-delivery
#16
Merve Denizli, Burcu Aslan, Lingegowda S Mangala, Dahai Jiang, Cristian Rodriguez-Aguayo, Gabriel Lopez-Berestein, Anil K Sood
RNA interference techniques represent a promising strategy for therapeutic applications. In addition to small interfering RNA-based approaches, which have been widely studied and translated into clinical investigations, microRNA-based approaches are attractive owing to their "one hit, multiple targets" concept. To overcome challenges with in vivo delivery of microRNAs related to stability, cellular uptake, and specific delivery, our group has developed and characterized chitosan nanoparticles for nucleotide delivery...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730440/cellular-delivery-of-sirnas-using-bolaamphiphiles
#17
Kshitij Gupta
Discovery of RNA interference (RNAi) has opened up a new arena of therapeutic intervention for the treatment of cancerous as well as noncancerous diseases. The RNAi pathway utilizes RNAi inducers such as small interfering RNAs (siRNAs) to target and silence disease causing genes. However, efficient delivery of siRNAs for eliciting efficacious RNAi has remained a daunting challenge. Nonviral vectors such as lipids have shown great promise in delivering siRNAs. Recently, a novel class of cationic lipid molecules "bolaamphiphile lipids" or "bola lipids" has been shown to deliver siRNAs to cause effective gene silencing in cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730431/protocols-for-molecular-dynamics-simulations-of-rna-nanostructures
#18
Taejin Kim, Wojciech K Kasprzak, Bruce A Shapiro
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729919/toward-understanding-non-coding-rna-roles-in-intracranial-aneurysms-and-subarachnoid-hemorrhage
#19
Fengzhen Huang, Jiping Yi, Tieqiao Zhou, Xiaoxiang Gong, Hong Jiang, Xiaoxi Yao
Subarachnoid hemorrhage (SAH) is a common and frequently life-threatening cerebrovascular disease, which is mostly related with a ruptured intracranial aneurysm. Its complications include rebleeding, early brain injury, cerebral vasospasm, delayed cerebral ischemia, chronic hydrocephalus, and also non neurological problems. Non-coding RNAs (ncRNAs), comprising of microRNAs (miRNAs), small interfering RNAs (siRNAs) and long non-coding RNAs (lncRNAs), play an important role in intracranial aneurysms and SAH. Here, we review the non-coding RNAs expression profile and their related mechanisms in intracranial aneurysms and SAH...
2017: Translational Neuroscience
https://www.readbyqxmd.com/read/28729555/inhibition-of-phosphodiesterase-5-suppresses-calcineurin-nfat-mediated-trpc6-expression-in-pulmonary-artery-smooth-muscle-cells
#20
Shaojun Li, Yilin Pan, Rui Ke, Xinming Xie, Cui Zhai, Wenhua Shi, Jian Wang, Xin Yan, Limin Chai, Qingting Wang, Qianqian Zhang, Xiaofan Su, Lan Yang, Li Gao, Manxiang Li
The up-regulation of transient receptor potential channel 6 (TRPC6) has been found to contribute to the proliferation of pulmonary artery smooth muscle cells (PASMCs), and inhibition of phosphodiesterase-5 (PDE5) has been shown to suppress TRPC6 expression in PASMCs. However, the molecular mechanisms underlying the up-regulation of TRPC6 expression and PDE5 modulation of TRPC6 expression in PASMCs remain largely unclear. The aim of this study is to address these issues. Endothelin-1 (ET-1) dose and time-dependently up-regulated TRPC6 expression in primary cultured rat PASMCs, and this was accompanied with the activation of calcineurin and subsequent translocation of NFATc4 to the nucleus...
July 20, 2017: Scientific Reports
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