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Competitive endogenous RNA

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https://www.readbyqxmd.com/read/28475648/hiv-1-competition-experiments-in-humanized-mice-show-that-apobec3h-imposes-selective-pressure-and-promotes-virus-adaptation
#1
Yusuke Nakano, Naoko Misawa, Guillermo Juarez-Fernandez, Miyu Moriwaki, Shinji Nakaoka, Takaaki Funo, Eri Yamada, Andrew Soper, Rokusuke Yoshikawa, Diako Ebrahimi, Yuuya Tachiki, Shingo Iwami, Reuben S Harris, Yoshio Koyanagi, Kei Sato
APOBEC3 (A3) family proteins are DNA cytosine deaminases recognized for contributing to HIV-1 restriction and mutation. Prior studies have demonstrated that A3D, A3F, and A3G enzymes elicit a robust anti-HIV-1 effect in cell cultures and in humanized mouse models. Human A3H is polymorphic and can be categorized into three phenotypes: stable, intermediate, and unstable. However, the anti-viral effect of endogenous A3H in vivo has yet to be examined. Here we utilize a hematopoietic stem cell-transplanted humanized mouse model and demonstrate that stable A3H robustly affects HIV-1 fitness in vivo...
May 5, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28470264/reconstruction-and-analysis-of-the-lncrna-mirna-mrna-network-based-on-competitive-endogenous-rna-reveal-functional-lncrnas-in-rheumatoid-arthritis
#2
Hui Jiang, Rong Ma, Shubiao Zou, Yongzhong Wang, Zhuqing Li, Weiping Li
Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology, occurring in approximately 1.0% of general population. More and more studies have suggested that long non-coding RNAs (lncRNAs) could play important roles in various biological processes and be associated with the pathogenesis of different kinds of diseases including RA. Although a large number of lncRNAs have been found, our knowledge of their function and physiological/pathological significance is still in its infancy. In order to reveal functional lncRNAs and identify the key lncRNAs in RA, we reconstructed a global triple network based on the competitive endogenous RNA (ceRNA) theory using the data from National Center for Biotechnology Information Gene Expression Omnibus and our previous paper...
May 4, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28444368/simultaneous-targeting-of-multiple-gene-homeologues-to-alter-seed-oil-production-in-camelina-sativa
#3
J A Aznar-Moreno, T P Durrett
The ability to easily transform Camelina sativa with biosynthetic enzymes derived from other plants has made this oil seed crop an ideal platform for the production of unusual lipids valuable for different applications. However, in addition to expressing transgenic enzymes, the suppression of endogenous enzyme activity to reduce competition for common substrates or cofactors is also required to enhance the production of target compounds. As camelina possesses a relatively undifferentiated hexaploid genome, up to three gene homeologues can encode for any particular enzymatic activity, complicating efforts to alter endogenous biosynthetic pathways...
April 21, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28440616/discovery-and-characterization-of-a-eukaryotic-initiation-factor-4a-3-selective-inhibitor-that-suppresses-nonsense-mediated-mrna-decay
#4
Misa Iwatani-Yoshihara, Masahiro Ito, Yoshihiro Ishibashi, Hideyuki Oki, Toshio Tanaka, Daisuke Morishita, Takashi Ito, Hiromichi Kimura, Yasuhiro Imaeda, Samuel Aparicio, Atsushi Nakanishi, Tomohiro Kawamoto
Eukaryotic initiation factor 4A-3 (eIF4A3) is an Asp-Glu-Ala-Asp (DEAD) box-family adenosine triphosphate (ATP)-dependent RNA helicase. Subtypes eIF4A1 and eIF4A2 are required for translation initiation, but eIF4A3 participates in the exon junction complex (EJC) and functions in RNA metabolism including nonsense-mediated RNA decay (NMD). No small molecules for NMD inhibition via selective inhibition of eIF4A3 have been discovered. Here, we identified allosteric eIF4A3 inhibitors from a high-throughput screening campaign...
May 10, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28406715/competitive-endogenous-rna-network-potential-implication-for-systemic-lupus-erythematosus
#5
Lian-Ju Li, Wei Zhao, Sha-Sha Tao, Rui-Xue Leng, Yin-Guang Fan, Hai-Feng Pan, Dong-Qing Ye
Competitive endogenous RNA (ceRNA) hypothesis proposes that RNA transcripts, both coding and non-coding, crosstalk with and coregulate each other using microRNA response elements (MREs). CeRNA analysis tremendously expands functional information of coding and non-coding RNAs. Mounting evidence have shown that various types of RNAs, including pseudogenes, long non-coding RNAs, circular RNAs, and messenger RNAs, can function as ceRNAs in distinct physiological and pathophysiological states. Many validated ceRNA pairs participate in the initiation and progression of cancers, and systemic ceRNA network analyses revealing potential of ceRNAs in diagnosis, therapy, and prognosis of cancers have also been performed...
April 23, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/28400279/snhg1-lncrna-negatively-regulates-mir-199a-3p-to-enhance-cdk7-expression-and-promote-cell-proliferation-in-prostate-cancer
#6
Jianping Li, Zhipeng Zhang, Li Xiong, Chuan Guo, Tao Jiang, Lilan Zeng, Ge Li, Juan Wang
Long noncoding RNAs (lncRNAs) have been reported to play vital roles in the development of human cancers, but our understandings of most lncRNAs in cancers are still limited. Recently, accumlating evidences have showed that many RNA transcripts could function as competing endogenous RNAs (ceRNAs) by competitively binding common microRNAs. In this study, we demonstrated that a lncRNA, Small Nucleolar RNA Host Gene 1 (SNHG1), as a ceRNA for miR-199a-3p, played a critical role in prostate cancer cell proliferation...
May 20, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28374914/overexpression-of-long-non-coding-rna-meg3-inhibits-proliferation-of-hepatocellular-carcinoma-huh7-cells-via-negative-modulation-of-mirna-664
#7
Jin-Hua He, Ze-Ping Han, Ji-Ming Liu, Jia-Bin Zhou, Mao-Xian Zou, Yu Bing Lv, Yu-Guang Li, Ming-Rong Cao
Evidence is accumulating that long non-coding RNAs (lncRNAs) are involved in human tumorigenesis and dysregulated in many cancers, including hepatocellular carcinoma (HCC). Because lncRNAs can regulate essential pathways that contribute to tumor initiation and progression with their tissue specificity, lncRNAs are valuable biomarkers and therapeutic targets. Maternally-expressed gene 3 (MEG3) is a lncRNA overexpressed in HCC cells that inhibits HCC progression, however, the mechanism remains largely unknown...
April 4, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28368292/long-coding-rna-xist-contributes-to-neuronal-apoptosis-through-the-downregulation-of-akt-phosphorylation-and-is-negatively-regulated-by-mir-494-in-rat-spinal-cord-injury
#8
Shixin Gu, Rong Xie, Xiaodong Liu, Jiajun Shou, Wentao Gu, Xiaoming Che
Recent evidence has suggested that long non-coding RNAs (lncRNAs) may play a significant role in the pathogenesis of several neurological diseases, including spinal cord injury (SCI). However, little is known about the role of lncRNAs in SCI. The aim of the present study was to evaluate the potential functions of lncRNAs in SCI and to identify the underlying mechanisms of action. We firstly analyzed Gene Expression Omnibus (GEO) datasets to investigate aberrantly-expressed lncRNAs which might be involved in the pathogenesis of SCI...
April 1, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28306719/chromosome-19q13-disruption-alters-expressions-of-cyp2a7-mia-and-mia-rab4b-lncrna-and-contributes-to-fap-like-phenotype-in-apc-mutation-negative-familial-colorectal-cancer-patients
#9
Lai Fun Thean, Yu Hui Wong, Michelle Lo, Carol Loi, Min Hoe Chew, Choong Leong Tang, Peh Yean Cheah
Familial adenomatous polyposis (FAP) is an autosomal-dominantly inherited form of colorectal cancer (CRC) caused by mutation in the adenomatous polyposis coli (APC) gene. Our ability to exhaustively screen for APC mutations identify microsatellite-stable and APC-mutation negative familial CRC patients, enabling us to search for novel genes. We performed genome-wide scan on two affected siblings of one family and 88 ethnicity- and gender-matched healthy controls to identify deletions shared by the siblings. Combined loss of heterozygosity, copy number and allelic-specific copy number analysis uncovered 5 shared deletions...
2017: PloS One
https://www.readbyqxmd.com/read/28280365/downregulation-of-long-noncoding-rna-hotairm1-promotes-monocyte-dendritic-cell-differentiation-through-competitively-binding-to-endogenous-mir-3960
#10
Jiaxuan Xin, Jing Li, Yue Feng, Liyang Wang, Yuan Zhang, Rongcun Yang
Myeloid differentiation is controlled by a multilayered regulatory circuitry consisting of various elements, including histone modifications, transcription factors, and posttranscriptional regulators such as miRNAs, long noncoding RNAs, and circular RNAs. However, the molecular mechanism underlying this biological process remains unclear. In this study, through epigenetic profiling analysis using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq), we identified an lncRNA, HOTAIRM1, with a critical role in myeloid development...
2017: OncoTargets and Therapy
https://www.readbyqxmd.com/read/28266541/cerna-crosstalk-stabilizes-protein-expression-and-affects-the-correlation-pattern-of-interacting-proteins
#11
Araks Martirosyan, Andrea De Martino, Andrea Pagnani, Enzo Marinari
Gene expression is a noisy process and several mechanisms, both transcriptional and post-transcriptional, can stabilize protein levels in cells. Much work has focused on the role of miRNAs, showing in particular that miRNA-mediated regulation can buffer expression noise for lowly expressed genes. Here, using in silico simulations and mathematical modeling, we demonstrate that miRNAs can exert a much broader influence on protein levels by orchestrating competition-induced crosstalk between mRNAs. Most notably, we find that miRNA-mediated cross-talk (i) can stabilize protein levels across the full range of gene expression rates, and (ii) modifies the correlation pattern of co-regulated interacting proteins, changing the sign of correlations from negative to positive...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28238937/sp1-is-a-competitive-endogenous-rna-of-klf4-during-odontoblast-differentiation
#12
Jie Zhang, Huan Liu, Heng Lin, Shuchen Li, Huangheng Tao, Lu Zhang, Guohua Yuan, Zhi Chen
Our previous studies have demonstrated that KLF4 is a critical transcription factor that promotes the odontoblastic differentiation of dental papilla cells. Klf4 mRNA was found to be regulated by multiple microRNAs (miRNAs). Competitive endogenous RNAs (ceRNAs) are a group of transcripts post-transcriptionally regulating each other by competing for their common miRNAs. However, the regulation of Klf4 by ceRNAs in odontoblastic differentiation remains unknown. In this study, we predicted a group of potential Klf4 ceRNAs with bioinformatics approach, and examined the expression of Klf4 and five interested potential ceRNAs including Sp1 using real-time PCR during odontoblastic differentiation of mDPC6T...
February 24, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28228215/hnrnpk-regulated-ptov1-as1-modulates-heme-oxygenase-1-expression-via-mir-1207-5p
#13
Chang Hoon Shin, Seongho Ryu, Hyeon Ho Kim
Antisense transcripts were initially identified as transcriptional noise, but have since been reported to play an important role in the quality control of miRNA functions. In this report, we tested the hypothesis that heterogeneous nuclear ribonucleoprotein K (hnRNPK) regulates miRNA function via competitive endogenous RNAs, such as pseudogenes, long non-coding RNAs, and antisense transcripts. Based on analyses of RNA sequencing data, the knockdown of hnRNPK decreased the antisense PTOV1-AS1 transcript which harbors five binding sites for miR-1207-5p...
April 2017: BMB Reports
https://www.readbyqxmd.com/read/28205334/long-non-coding-rna-tug1-promotes-migration-and-invasion-by-acting-as-a-cerna-of-mir-335-5p-in-osteosarcoma-cells
#14
Yong Wang, Tao Yang, Zhen Zhang, Ming Lu, Wei Zhao, Xiandong Zeng, Weiguo Zhang
Long non-coding RNAs (lncRNAs) have now become the new hotspots in an ocean of diseases including osteosarcoma. The function of taurine up-regulated gene 1 (TUG1) and its working mechanism in osteosarcoma remain unclear. In our research, we found that TUG1 was elevated and correlated with a poor prognosis in osteosarcoma patients. Also, the following functional experiment showed that decreased TUG1 could remarkably inhibit osteosarcoma cell migration and invasion, indicating that TUG1 functioned as an oncogene in osteosarcoma...
February 15, 2017: Cancer Science
https://www.readbyqxmd.com/read/28187158/role-of-the-long-non-coding-rna-pvt1-in-the-dysregulation-of-the-cerna-cerna-network-in-human-breast-cancer
#15
Federica Conte, Giulia Fiscon, Matteo Chiara, Teresa Colombo, Lorenzo Farina, Paola Paci
Recent findings have identified competing endogenous RNAs (ceRNAs) as the drivers in many disease conditions, including cancers. The ceRNAs indirectly regulate each other by reducing the amount of microRNAs (miRNAs) available to target messenger RNAs (mRNAs). The ceRNA interactions mediated by miRNAs are modulated by a titration mechanism, i.e. large changes in the ceRNA expression levels either overcome, or relieve, the miRNA repression on competing RNAs; similarly, a very large miRNA overexpression may abolish competition...
2017: PloS One
https://www.readbyqxmd.com/read/28177876/long-intergenic-non-protein-coding-rna-00858-functions-as-a-competing-endogenous-rna-for-mir-422a-to-facilitate-the-cell-growth-in-non-small-cell-lung-cancer
#16
Shao-Ping Zhu, Jun-Yu Wang, Xian-Guo Wang, Jin-Ping Zhao
The expression of long non-coding RNAs (lncRNAs) is dysregulated in non-small cell lung cancer (NSCLC). However, the functions and contributions of lncRNAs remain largely unknown. Here, we identified a critical role of long intergenic non-protein coding RNA 00858 (LINC00858) in NSCLC. Ectopic expression of LINC00858 in NSCLC cells promoted cell proliferation and induced cell migration and invasion. Moreover, LINC00858 functioned as a competitive endogenous RNA (ceRNA), effectively becoming sponge for miR-422a and thereby modulating the expression of kallikrein-related peptidase 4 (KLK4)...
February 6, 2017: Aging
https://www.readbyqxmd.com/read/28123636/long-noncoding-rna-mhencr-promotes-melanoma-progression-via-regulating-mir-425-489-mediated-pi3k-akt-pathway
#17
Xiangjun Chen, Hao Dong, Sha Liu, Li Yu, Dexiong Yan, Xingwei Yao, Weijing Sun, Dezhi Han, Guozhen Gao
Increasing evidences demonstrated that long noncoding RNAs (lncRNAs) are frequently dysregulated and have critical roles in many tumors. However, the roles and functional mechanisms of lncRNAs in melanoma remain largely unknown. In this study, we identified a novel lncRNA MHENCR which was upregulated in melanoma tissues and further upregulated in metastatic melanoma. Increased expression of MHENCR indicted poor survival of melanoma patients. Functional experiments revealed that MHENCR knockdown significantly inhibited melanoma cells proliferation, induced cell cycle arrest and apoptosis, and also attenuated melanoma cells migration in vitro...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28093311/long-non-coding-rna-fth1p3-facilitates-oral-squamous-cell-carcinoma-progression-by-acting-as-a-molecular-sponge-of-mir-224-5p-to-modulate-fizzled-5-expression
#18
Chen-Zheng Zhang
A growing body of evidence has indicated that long non-coding RNAs (lncRNAs) function as competing endogenous RNAs (ceRNAs) during tumorigenesis. In this study, the qRT-PCR results revealed that the lncRNA ferritin heavy chain 1 pseudogene 3 (FTH1P3) was over-expressed in oral squamous cell carcinoma (OSCC) and decreased the survival rate of OSCC patients. Ectopic expression of FTH1P3 facilitates cell proliferation and colony formation in OSCC cells. Moreover, FTH1P3 acted as a competitive endogenous RNA (ceRNA), effectively becoming sponge for miR-224-5p and thereby modulating the expression of fizzled 5...
April 5, 2017: Gene
https://www.readbyqxmd.com/read/28072746/znf148-modulates-top2a-expression-and-cell-proliferation-via-cerna-regulatory-mechanism-in-colorectal-cancer
#19
Xian Hua Gao, Juan Li, Yan Liu, Qi Zhi Liu, Li Qiang Hao, Lian Jie Liu, Wei Zhang
BACKGROUND: Competing endogenous RNA (ceRNA) regulation is a novel hypothesized mechanism that states RNA molecules share common target microRNAs (miRNAs) and may competitively combine into the same miRNA pool. METHODS: Zinc finger protein 148 (ZNF148) and TOP2A expression were analyzed in 742 colorectal cancer (CRC) tissues using immunohistochemistry (IHC). ZNF148 mRNA, TOP2A mRNA, miR101, miR144, miR335, and miR365 expression were estimated in 53 fresh frozen CRC tissues by reverse transcription polymerase chain reaction...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28053167/pcerbase-a-database-of-plant-competing-endogenous-rna
#20
Chunhui Yuan, Xianwen Meng, Xue Li, Nicola Illing, Robert A Ingle, Jingjing Wang, Ming Chen
Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants...
January 4, 2017: Nucleic Acids Research
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