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https://www.readbyqxmd.com/read/29458013/ago2-rna-immunoprecipitation-reveals-distinct-mirna-targetomes-of-primary-burkitt-lymphoma-tumors-and-normal-b-cells
#1
Agnieszka Dzikiewicz-Krawczyk, Arjan Diepstra, Bea Rutgers, Gertrud Kortman, Debora de Jong, Jasper Koerts, Marian Bulthuis, Tineke van der Sluis, Annika Seitz, Lydia Visser, Klaas Kok, Joost Kluiver, Anke van den Berg
MicroRNAs (miRNAs) are small noncoding RNAs involved in the posttranscriptional regulation of gene expression. Deregulated miRNA levels have been linked to Burkitt lymphoma (BL) pathogenesis. To date, the number of known pathogenesis-related miRNA-target gene interactions is limited. Here, we determined for the first time the miRNA targetomes of primary BL tumors and normal B cells. AGO2-RNA immunoprecipitation (AGO2-RIP) of two frozen diagnostic BL tissue samples and three CD19+ B-cell samples isolated from routinely removed tonsils revealed distinct miRNA targetomes of BL and normal B cells...
February 16, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29444957/p38-activation-induces-the-dissociation-of-tristetraprolin-from-argonaute-2-to-increase-are-mrna-stabilization
#2
Mei-Yan Qi, Jing-Wen Song, Zhuo Zhang, Shuang Huang, Qing Jing
Tristetraprolin (TTP) destabilizes AU-rich element (ARE)-containing mRNA by directly binding with their 3'UTR. P38 stimulation substantially increases ARE-mRNA stability, at least through repressing TTP. However, the mechanism by which P38 keeps TTP inactive has not been fully understood. TTP and ARE-mRNA localize to processing bodies (PBs), the mRNA granules associated with mRNA silencing. Here, we detected the influence of P38 upon TTP localization within PBs and found that P38 regulates TTP localization within PBs...
February 14, 2018: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29442415/thrombin-reduced-mir-27b-attenuates-platelet-angiogenic-activities-in-vitro-via-enhancing-platelet-synthesis-of-anti-angiogenic-thrombospondin-1
#3
Xinyan Miao, Mohammed Ferdous-Ur Rahman, Lei Jiang, Yanan Min, Shuai Tan, Hong Xie, Linkiat Lee, Miao Wang, Rickard E Malmström, Weng-Onn Lui, Nailin Li
BACKGROUND: Platelets can synthesize proteins upon activation. Platelets contain a number of microRNAs (miRNA) and a fully functional miRNA effector machinery. It is, however, unclear if platelet miRNAs can regulate protein synthesis of platelets, and whether the regulation may produce a physiological impact. OBJECTIVES: To investigate if and how platelet miRNAs regulate de novo syntheses of angiogenic regulators and subsequently modulate platelet angiogenic activities...
February 14, 2018: Journal of Thrombosis and Haemostasis: JTH
https://www.readbyqxmd.com/read/29435920/target-mrna-driven-biogenesis-of-cognate-micrornas-in-vitro
#4
Mainak Bose, Suvendra N Bhattacharyya
miRNAs are 20-22 nucleotide long noncoding RNAs that act as post-transcriptional regulators of gene expression controlling more than half of protein coding genes in humans. Being the critical modulators of the mRNA translation process, biogenesis, function, and turnover of these small RNAs are tightly regulated in cells. We have reported that target mRNAs induce increased biogenesis of cognate miRNAs from pre-miRNAs by increased activity of Ago-associated Dicer endonuclease that processes precursor miRNAs to their mature form...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29432194/structurally-modulated-codelivery-of-sirna-and-argonaute-2-for-enhanced-rna-interference
#5
Jiahe Li, Connie Wu, Wade Wang, Yanpu He, Elad Elkayam, Leemor Joshua-Tor, Paula T Hammond
Small interfering RNA (siRNA) represents a promising class of inhibitors in both fundamental research and the clinic. Numerous delivery vehicles have been developed to facilitate siRNA delivery. Nevertheless, achieving highly potent RNA interference (RNAi) toward clinical translation requires efficient formation of RNA-induced gene-silencing complex (RISC) in the cytoplasm. Here we coencapsulate siRNA and the central RNAi effector protein Argonaute 2 (Ago2) via different delivery carriers as a platform to augment RNAi...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29428901/fragile-x-mental-retardation-protein-participates-in-non-coding-rna-pathways
#6
En-Hui Li, Xin Zhao, Ce Zhang, Wei Liu
Fragile X syndrome is one of the most common forms of inherited intellectual disability. It is caused by mutations of the Fragile X mental retardation 1(FMR1) gene, resulting in either the loss or abnormal expression of the Fragile X mental retardation protein (FMRP). Recent research showed that FMRP participates in non-coding RNA pathways and plays various important roles in physiology, thereby extending our knowledge of the pathogenesis of the Fragile X syndrome. Initial studies showed that the Drosophila FMRP participates in siRNA and miRNA pathways by interacting with Dicer, Ago1 and Ago2, involved in neural activity and the fate determination of the germline stem cells...
February 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29425832/small-activating-rna-induced-expression-of-vhl-gene-in-renal-cell-carcinoma
#7
Moo Rim Kang, Ki Hwan Park, Chang Woo Lee, Myeong Youl Lee, Sang-Bae Han, Long-Cheng Li, Jong Soon Kang
Recent studies have reported that chemically synthesized double-stranded RNAs (dsRNAs), also known as small activating RNA (saRNAs), can specifically induce gene expression by targeting promoter sequences by a mechanism termed RNA activation (RNAa). In the present study, we designed 4 candidate saRNAs targeting the Von Hippel-Lindau (VHL) gene promoter. Among these saRNAs, dsVHL-821 significantly inhibited cell growth by up-regulating VHL at both the mRNA and protein levels in renal cell carcinoma 769-P cells...
February 6, 2018: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/29396181/argonaute-2-is-required-for-extra-embryonic-endoderm-differentiation-of-mouse-embryonic-stem-cells
#8
Richard Patryk Ngondo, Daniel Cirera-Salinas, Jian Yu, Harry Wischnewski, Maxime Bodak, Sandrine Vandormael-Pournin, Anna Geiselmann, Rahel Wettstein, Janina Luitz, Michel Cohen-Tannoudji, Constance Ciaudo
In mouse, although four Argonaute (AGO) proteins with partly overlapping functions in small-RNA pathways exist, only Ago2 deficiency causes embryonic lethality. To investigate the role of AGO2 during mouse early development, we generated Ago2-deficient mouse embryonic stem cells (mESCs) and performed a detailed characterization of their differentiation potential. Ago2 disruption caused a global reduction of microRNAs, which resulted in the misregulation of only a limited number of transcripts. We demonstrated, both in vivo and in vitro, that AGO2 is dispensable for the embryonic germ-layer formation...
January 24, 2018: Stem Cell Reports
https://www.readbyqxmd.com/read/29392316/mesenchymal-stem-cell-derived-small-extracellular-vesicles-promote-neuroprotection-in-rodent-models-of-glaucoma
#9
Ben Mead, Juan Amaral, Stanislav Tomarev
Purpose: To investigate the benefit of bone marrow mesenchymal stem cell (BMSC)-derived small extracellular vesicles (sEV) as an intravitreal (ivit) therapy in two rat models of glaucoma and to determine and identify candidate miRNA involved in the mechanism. Methods: sEV were isolated from human BMSC and fibroblasts and ivit injected into adult rats after induction of elevated IOP. IOP was elevated using either intracameral injection of microbeads or laser photocoagulation of circumferential limbal vessels and the trabecular meshwork...
February 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29351846/dual-strategies-for-argonaute2-mediated-biogenesis-of-erythroid-mirnas-underlie-conserved-requirements-for-slicing-in-mammals
#10
David Jee, Jr-Shiuan Yang, Sun-Mi Park, D'Juan T Farmer, Jiayu Wen, Timothy Chou, Arthur Chow, Michael T McManus, Michael G Kharas, Eric C Lai
While Slicer activity of Argonaute is central to RNAi, conserved roles of slicing in endogenous regulatory biology are less clear, especially in mammals. Biogenesis of erythroid Dicer-independent mir-451 involves Ago2 catalysis, but mir-451-KO mice do not phenocopy Ago2 catalytic-dead (Ago2-CD) mice, suggesting other needs for slicing. Here, we reveal mir-486 as another dominant erythroid miRNA with atypical biogenesis. While it is Dicer dependent, it requires slicing to eliminate its star strand. Thus, in Ago2-CD conditions, miR-486-5p is functionally inactive due to duplex arrest...
January 18, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29322452/identification-of-circrnas-for-mirna-targets-by-argonaute2-rna-immunoprecipitation-and-luciferase-screening-assays
#11
Yan Li, Bing Chen, Shenglin Huang
Circular RNAs from back-spliced exons (circRNAs) represent a novel class of widespread and endogenous RNAs in eukaryotes. circRNAs may bind to microRNAs (miRNAs) and inhibit the activity of miRNAs. Alternatively, miRNAs could also directly target circRNAs and regulate the expression of circRNAs. Here we describe the Argonaute2 (AGO2) RNA immunoprecipitation (RIP) and luciferase screening assays to identify the interaction between circRNAs and miRNAs. The AGO2 RIP assay evaluates the potential of the interaction between circRNAs and miRNAs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29311329/dysregulation-of-cotranscriptional-alternative-splicing-underlies-charge-syndrome
#12
Catherine Bélanger, Félix-Antoine Bérubé-Simard, Elizabeth Leduc, Guillaume Bernas, Philippe M Campeau, Seema R Lalani, Donna M Martin, Stephanie Bielas, Amanda Moccia, Anshika Srivastava, David W Silversides, Nicolas Pilon
CHARGE syndrome-which stands for coloboma of the eye, heart defects, atresia of choanae, retardation of growth/development, genital abnormalities, and ear anomalies-is a severe developmental disorder with wide phenotypic variability, caused mainly by mutations in CHD7 (chromodomain helicase DNA-binding protein 7), known to encode a chromatin remodeler. The genetic lesions responsible for CHD7 mutation-negative cases are unknown, at least in part because the pathogenic mechanisms underlying CHARGE syndrome remain poorly defined...
January 8, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29298376/a-single-amide-linkage-in-the-passenger-strand-suppresses-its-activity-and-enhances-guide-strand-targeting-of-sirnas
#13
Travis Hardcastle, Irina Novosjolova, Venubabu Kotikam, Samwel K Cheruiyot, Daniel Mutisya, Scott D Kennedy, Martin Egli, Melissa L Kelley, Anja van Brabant Smith, Eriks Rozners
Potential in vivo applications of RNA interference (RNAi) require suppression of various off-target activities. Herein we report that replacement of a single phosphate linkage between the first and second nucleosides of the passenger strand with an amide linkage almost completely abolished its undesired activity and restored the desired activity of guide strands that had been compromised by unfavorable amide modifications. Molecular modelling suggested that the observed effect was most likely due to suppressed loading of the amide-modified strand into Ago2 caused by inability of amide to adopt the conformation required for the backbone twist that docks the first nucleotide of the guide strand in the MID domain of Ago2...
January 3, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29283313/circular-rnas-are-abundantly-expressed-and-upregulated-during-human-epidermal-stem-cell-differentiation
#14
Lasse Sommer Kristensen, Trine Line Hauge Okholm, Morten Trillingsgaard Venø, Jørgen Kjems
The expression patterns of endogenous circular RNA (circRNA) molecules during epidermal stem cell (EpSC) differentiation have not previously been explored. Here, we show that circRNAs are abundantly expressed in EpSCs and that their expression change dramatically during differentiation in a coordinated manner. Overall, circRNAs are expressed at higher levels in the differentiated cells, and many upregulated circRNAs are derived from developmental genes, including four different circRNAs from DLG1. The observed changes in circRNA expression were largely independent of host gene expression, and circRNAs independently upregulated upon differentiation are more prone to AGO2 binding and have more predicted miRNA binding sites compared to stably expressed circRNAs...
December 28, 2017: RNA Biology
https://www.readbyqxmd.com/read/29282144/family-level-variation-in-wolbachia-mediated-dengue-virus-blocking-in-aedes-aegypti
#15
Gerard Terradas, Scott L Allen, Stephen F Chenoweth, Elizabeth A McGraw
BACKGROUND: The mosquito vector Aedes aegypti is responsible for transmitting a range of arboviruses including dengue (DENV) and Zika (ZIKV). The global reach of these viruses is increasing due to an expansion of the mosquito's geographic range and increasing urbanization and human travel. Vector control remains the primary means for limiting these diseases. Wolbachia pipientis is an endosymbiotic bacterium of insects that has the ability to block the replication of pathogens, including flaviviruses such as DENV or ZIKV, inside the body of the vector...
December 28, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29273203/transcriptome-wide-identification-and-validation-of-interactions-between-the-mirna-machinery-and-hur-on-mrna-targets
#16
Yahui Li, Jason A Estep, Fedor V Karginov
The 3' UTR of mRNAs is the primary regulatory region that mediates post-transcriptional control by microRNAs and RNA-binding proteins (RBPs) in the cytoplasm. Aside from individual sequence-specific binding and regulation, examples of interaction between these factors at particular 3' UTR sites have emerged. However, the whole picture of such higher-order regulatory modules across the transcriptome is lacking. Here, we investigate the interactions between HuR, a ubiquitous RBP, and Ago2, a core effector of the miRNA pathway, at the transcriptome-wide level...
December 20, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29245946/mir-483-5p-promotes-igf-ii-transcription-and-is-associated-with-poor-prognosis-of-hepatocellular-carcinoma
#17
Shaohui Tang, Yanfang Chen, Shufen Feng, Tingzhuang Yi, Xuyou Liu, Qiang Li, Zhilong Liu, Cuiping Zhu, Jianjun Hu, Xi Yu, Min Wang, Guoli Cao, Hui Tang, Caiqun Bie, Feng Ma, Huijun Tang, Gang Du, Jianwei Huang
The human insulin-like growth factor-II (IGF-II) gene transcribes four mRNAs (P1 mRNA-P4 mRNA), and P3 mRNA overexpression contributes to hepatocarcinogenesis. IGF-II-derived miR-483-5p is implicated in the development of cancers. Here, we investigated the involvement of miR-483-5p in P3 mRNA overexpression regulation and its role in hepatocellular carcinoma. Our results showed that miR-483-5p up-regulated P3 mRNA transcription by targeting the 5'-untranslated region (5'UTR) of P3 mRNA in hepatocellular carcinoma...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29236257/identifying-risc-components-using-ago2-immunoprecipitation-and-mass-spectrometry
#18
Tingfang Yi
Complex immunoprecipitation (Co-IP) is a powerful technique for precipitating an intact protein complex out of solution and cell lysates using an antibody that specifically binds to a particular protein in a large complex of proteins. Mass spectrometry (MS) is used to identify, sequence, and quantify proteins. RNA-induced silencing complexes (RISCs), Ago2 centered protein assemblies, are essential for miRNA mediated RNA decay and gene expression regulation; however, the complete list of RISCs is unknown. Here we describe methods used to combine IP and MS to identify new components of RISCs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29191172/microrna-profile-in-hbv-induced-infection-and-hepatocellular-carcinoma
#19
Guanyu Wang, Fulu Dong, Zhiyao Xu, Sherven Sharma, Xiaotong Hu, Dafang Chen, Lumin Zhang, Jinping Zhang, Qinghua Dong
BACKGROUND: MicroRNAs (miRNAs) exhibit essential regulatory functions related to cell growth, apoptosis, development and differentiation. Dysregulated expression of miRNAs is associated with a wide variety of human diseases. As such miRNA signatures are valuable as biomarkers for disease and for making treatment decisions. Hepatitis B virus (HBV) is a major risk factor for hepatocellular carcinoma (HCC). Here we screened for miRNAs in chronic HBV associated HCC. METHODS: To determine the miRNAs in HCC occurrence associated with HBV infection, we analyzed global miRNA expression profiles in 12 pairs of HCC and adjacent matched non-HCC tissues from HBV-positive and HBV-negative patients using microarray analyses...
December 1, 2017: BMC Cancer
https://www.readbyqxmd.com/read/29170131/negative-regulation-of-lncrna-gas5-by-mir-196a-inhibits-esophageal-squamous-cell-carcinoma-growth
#20
Kai Wang, Juan Li, Gang Xiong, Gang He, Xingying Guan, Kang Yang, Yun Bai
MiR-196a could play important roles in carcinogenesis by targeting many protein coding genes. However, little is known about whether miR-196a can target any long non-coding RNAs (lncRNAs). In the present study, we screen lncRNAs which are regulated by miRNA-196a in human esophageal squamous cell carcinoma (ESCC). We found that miR-196a could suppress the expression of lncRNA growth arrest-specific 5(GAS5). GAS5 is frequently down-regulated in 86 paired human ESCC tissues. Importantly, there was lower GAS5 expression in the late stage of ESCC patients...
November 20, 2017: Biochemical and Biophysical Research Communications
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