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Rna Interactions

Haroon Kalam, Kartikeya Singh, Komal Chauhan, Mary F Fontana, Dhiraj Kumar
Previously, we reported that infection of human macrophages with Mycobacterium tuberculosis (Mtb) results in massive alterations in the pattern of RNA splicing in the host. The finding gained significance since alternate spliced variants of a same gene may have substantially different structure, function, stability, interaction partners, localization, and so forth, owing to inclusion or exclusion of specific exons. To establish a proof-of-concept; on how infection-induced RNA splicing could impact protein functions, here we used RNA-seq data from THP-1 macrophages that were infected with clinical isolate of Mtb...
August 18, 2018: IUBMB Life
Chao Chen, Yonghua Zhang, Pan Ye, Xiaofeng Ma, Chaoxing Zheng, Genfa Zhang
There is a growing awareness that some dual-function enzymes may provide a directly evidence that metabolism could feed into the regulation of gene expression via metabolic enzymes. However, the mechanism by which metabolic enzymes control gene expression to optimize plant stress responses remains largely unknown in Arabidopsis thaliana. LOS2/ENO2 is a bifunctional gene transcribed a functional RNA that translates a full-length version of the ENO2 protein and a truncated version of the MBP-1 protein. Here, we report that eno2 negatively regulates plant tolerance to salinity stress...
August 17, 2018: Molecular Biology Reports
Antonella Minutolo, Marina Potestà, Angelo Gismondi, Stefano Pirrò, Marco Cirilli, Fabiano Gattabria, Andrea Galgani, Libera Sessa, Maurizio Mattei, Antonella Canini, Rosario Muleo, Vittorio Colizzi, Carla Montesano
Functional foods include compounds with nutritional and health properties. The human diet could play a stronger role in cancer prevention. Only a few studies have described the presence of plant small RNA, in humans who were fed with plant foods, which demonstrated the ability of these molecules to modulate consumer's genes and evidenced the existence of a plant-animal regulation. Through in silico prediction, Olea europaea small RNAs (sRs), which had been previously reported as miRNAs, were identified, each with functional homology to hsa-miR34a...
August 17, 2018: Scientific Reports
Sameer Dixit, Julius Lukes
MRP1/2 is a heteromeric protein complex that functions in the trypanosomatid mitochondrion as part of the RNA editing machinery, which facilitates multiple targeted insertions and deletions of uridines. MRP1/2 was shown to interact with MRB8170, which initiates RNA editing by marking pre-edited mRNAs, while TbRGG2 is required for its efficient progression on pan-edited mRNAs. Both MRP1/2 and TbRGG2 are capable of modulating RNA-RNA interactions in vitro. As determined by using iCLIP and RIP-qPCR, RNAs bound to MRP1/2 are characterized and compared with those associated with MRB8170 and TbRGG2...
August 17, 2018: RNA
Max Darnell, Alison O'Neil, Angelo Mao, Luo Gu, Lee L Rubin, David J Mooney
Variations in a multitude of material microenvironmental properties have been observed across tissues in vivo, and these have profound effects on cell phenotype. Phenomenological experiments have suggested that certain of these features of the physical microenvironment, such as stiffness, could sensitize cells to other features; meanwhile, mechanistic studies have detailed a number of biophysical mechanisms for this sensing. However, the broad molecular consequences of these potentially complex and nonlinear interactions bridging from biophysical sensing to phenotype have not been systematically characterized, limiting the overall understanding and rational deployment of these biophysical cues...
August 17, 2018: Proceedings of the National Academy of Sciences of the United States of America
Rajashekar Varma Kadumuri, Sarath Chandra Janga
Innovations in epitranscriptomics have resulted in the identification of more than 160 RNA modifications to date. These developments, together with the recent discovery of writers, readers, and erasers of modifications occurring across a wide range of RNAs and tissue types, have led to a surge in integrative approaches for transcriptome-wide mapping of modifications and protein-RNA interaction profiles of epitranscriptome players. RNA modification maps and crosstalk between them have begun to elucidate the role of modifications as signaling switches, entertaining the notion of an epitranscriptomic code as a driver of the post-transcriptional fate of RNA...
August 14, 2018: Trends in Molecular Medicine
Yanbo Yu, Mengye Zhu, Yong Zhao, Mu Xu, Mizhen Qiu
OBJECTIVE: The aim of this study was to investigate the mechanisms of TUSC7/miR-449a/PPAR-γ axis on the inflammation induced by microglia activation. METHODS: A compressive spinal cord injury (SCI) model was established. The expressions of TUSC7, miR-449a PPAR-γ, TNF-α and IL-1β in spinal cord tissues of SCI rats and HAPI cells were determined. The interaction of TUSC7 and miR-449a was tested by RIP and RNA pull-down assays. The regulatory relationship between miR-449a and PPAR-γ was tested by dual luciferase reporter gene assay...
September 5, 2018: Biochemical and Biophysical Research Communications
Wenfei Gu, Enfeng Zhang, Lijun Song, Laiyong Tu, Zhenbin Wang, Feng Tian, Kahaer Aikenmu, Ge Chu, Jiang Zhao
Osteosarcoma is the most common primary malignant bone tumor and long non-coding RNAs (lncRNAs) have been proved to epigenetically regulate the oncogenesis of osteosarcoma. In this research, we investigate the role of lncRNA HOXD-AS1 on the osteosarcoma oncogenesis. Results revealed that HOXD-AS1 expression level was significantly up-regulated in osteosarcoma tissue and cells, moreover, the aberrant overexpression predicted the poor prognosis of osteosarcoma patients. Loss-of-functional experiments indicated that HOXD-AS1 silencing inhibited the osteosarcoma cells proliferation and induced G1/G0 phase arrest in vitro, and repressed tumor cell growth in vivo...
July 11, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Yu Wang, Chuanqiang Wu, Chao Zhang, Zhaoqing Li, Tingting Zhu, Jinliang Chen, Yu Ren, Xudong Wang, Lun Zhang, Xuan Zhou
Aberrant signal transducer and activator of transcription 3 (STAT3) signaling is a critical factor that drives the invasion and metastasis of head and neck squamous cell carcinoma (HNSCC). However, the underlying mechanisms of STAT3 overexpression and regulation of HNSCC metastasis remain unknown. In the current study, we demonstrated that upregulated TGF-β may promote epithelial-mesenchymal transition (EMT) through STAT3 activation. In addition, we explored the contributions of STAT3 to HNSCC with a specific focus on its transcriptional regulation and its interaction with the long noncoding RNA (lncRNA) metastasis associated lung adenocarcinoma transcript 1 (malat1)...
August 14, 2018: Cancer Letters
Jana R Jenquin, Leslie A Coonrod, Quinn A Silverglate, Natalie A Pellitier, Melissa A Hale, Guangbin Xia, Masayuki Nakamori, J Andrew Berglund
Myotonic dystrophy type 1 (DM1) is an autosomal dominant, CTG•CAG microsatellite expansion disease. Expanded CUG repeat RNA sequester the muscleblind-like (MBNL) family of RNA-binding proteins, thereby disrupting their normal cellular function leading to global mis-regulation of RNA processing. Previously, the small molecule furamidine was shown to reduce CUG foci and rescue mis-splicing in a DM1 HeLa cell model and rescue mis-splicing in the HSALR DM1 mouse model, but furamidine's mechanism of action was not explored...
August 17, 2018: ACS Chemical Biology
Rebekah C Gullberg, J Jordan Steel, Venugopal Pujari, Joel Rovnak, Dean C Crick, Rushika Perera
Positive strand RNA viruses, such as dengue virus type 2 (DENV2) expand and structurally alter ER membranes to optimize cellular communication pathways that promote viral replicative needs. These complex rearrangements require significant protein scaffolding as well as changes to the ER chemical composition to support these structures. We have previously shown that the lipid abundance and repertoire of host cells are significantly altered during infection with these viruses. Specifically, enzymes in the lipid biosynthesis pathway such as fatty acid synthase (FAS) are recruited to viral replication sites by interaction with viral proteins and displayed enhanced activities during infection...
August 17, 2018: PLoS Pathogens
Vengamanaidu Modepalli, Arie Fridrich, Maayan Agron, Yehu Moran
Small non-coding RNAs (sRNAs) such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and piwi-interacting RNAs (piRNAs) regulate the levels of endogenous, viral and transposable element RNA in plants (excluding piRNAs) and animals. These pathways are explored mainly in bilaterian animals, such as vertebrates, arthropods and nematodes, where siRNAs and piRNAs, but not miRNAs bind their targets with a perfect match and mediate the cleavage of the target RNA. Methylation of the 3' ends of piRNAs and siRNAs by the methyltransferase HEN1 protects these sRNAs from degradation...
August 17, 2018: PLoS Genetics
Xiaolei Liu, Peter S Klein
Glycogen synthase kinase-3 (GSK-3) is a highly conserved negative regulator of receptor tyrosine kinase, cytokine, and Wnt signaling pathways. Stimulation of these pathways inhibits GSK-3 to modulate diverse downstream effectors that include transcription factors, nutrient sensors, glycogen synthesis, mitochondrial function, circadian rhythm, and cell fate. GSK-3 also regulates alternative splicing in response to T-cell receptor activation, and recent phosphoproteomic studies have revealed that multiple splicing factors and regulators of RNA biosynthesis are phosphorylated in a GSK-3-dependent manner...
August 17, 2018: Wiley Interdisciplinary Reviews. RNA
Alex Dobzanski, Syed Muaz Khalil, Andrew P Lane
BACKGROUND: While essential to the normal differentiation of ciliated airway epithelial cells, upregulated Wnt signaling in chronic rhinosinusitis with nasal polyps (CRSwNP) has been proposed to result in abnormal epithelial morphology and dysfunctional mucociliary clearance. The mechanism of epithelial Wnt signaling dysregulation in CRSwNP is unknown, and importantly cellular sources of Wnt ligands in CRSwNP have not yet been investigated. METHODS: Human sinonasal epithelial cells (hSNECs) and human sinonasal fibroblasts (hSNFs) were collected from 34 human subjects (25 control and 9 CRSwNP) and differentiated as primary air-liquid interface (ALI) and organoid co-cultures...
August 17, 2018: International Forum of Allergy & Rhinology
Hongchu Wang, Pengfei Wu
RNA-protein interactions (RPIs) play a very important role in a wide range of post-transcriptional regulations, and identifying whether a given RNA-protein pair can form interactions or not is a vital prerequisite for dissecting the regulatory mechanisms of functional RNAs. Currently, expensive and time-consuming biological assays can only determine a very small portion of all RPIs, which calls for computational approaches to help biologists efficiently and correctly find candidate RPIs. Here, we integrated a successful computing algorithm, conjoint triad feature (CTF), and another method, chaos game representation (CGR), for representing RNA-protein pairs and by doing so developed a prediction model based on these representations and random forest (RF) classifiers...
2018: Bioengineered
Duc Duy Vo, Cécile Becquart, Thi Phuong Anh Tran, Audrey Di Giorgio, Fabien Darfeuille, Cathy Staedel, Maria Duca
MicroRNAs (miRNAs) are a recently discovered category of small RNA molecules that regulate gene expression at the post-transcriptional level. Accumulating evidence indicates that miRNAs are aberrantly expressed in a variety of human cancers, thus being oncogenic. The inhibition of oncogenic miRNAs (defined as the blocking of miRNAs' production or function) would find application in the therapy of different types of cancer in which these miRNAs are implicated. In this work, we describe the design and synthesis of new small-molecule RNA ligands with the aim of inhibiting Dicer-mediated processing of oncogenic miRNAs...
August 17, 2018: Organic & Biomolecular Chemistry
Heng Li, Guofeng Tian, Feipeng Tian, Lin Shao
Taurine upregulated gene 1 (TUG1), a long non-coding RNA (lncRNA), has recently been suggested to be associated with the development of osteosarcoma (OS), but the underlying molecular mechanism still remains largely unclear. In the present study, it was revealed that TUG1 was significantly upregulated whereas miR-212-3p was significantly downregulated in OS tissues and cell lines, when compared with adjacent non-tumor tissues and normal osteoblasts cell lines, respectively. An inverse association between the TUG1 and miR-212-3p expression was also observed in OS tissues...
August 2018: Experimental and Therapeutic Medicine
Jiji T Kurup, Benjamin L Kidder
RNA has been shown to interact with various proteins to regulate chromatin dynamics and gene expression. However, it is unknown whether RNAs associate with epigenetic marks such as post-translational modifications of histones, including histone 4 lysine 20 trimethylation (H4K20me3) or trimethylated histone 3 lysine 4 (H3K4me3), to regulate chromatin and gene expression. Here, we used chromatin-associated RNA immunoprecipitation (CARIP) followed by next-generation sequencing (CARIP-Seq) to survey RNAs associated with H4K20me3 and H3K4me3-marked chromatin on a global-scale in embryonic stem (ES) cells...
August 16, 2018: Journal of Biological Chemistry
Zitai Yang, Hang Li, Juan Li, Xiaoting Lv, Min Gao, Yanhong Bi, Ziwei Zhang, Shengli Wang, Sixuan Li, Na Li, Zhigang Cui, Baosen Zhou, Zhihua Yin
Long noncoding RNA (lncRNA) maternal-expressed gene 3 (MEG3) is associated with proliferation of various tumor cells and has decreased expression in many types of cancers. In this study, we aimed at demonstrating the association between MEG3 polymorphisms and the risk of lung cancer in northeast China. There were 526 lung cancer patients and 526 healthy controls included in this hospital-based case-control study. The genotyping of two polymorphisms, rs7158663 G > A and rs4081134 G>A, was performed by the Taqman allelic discrimination method...
August 16, 2018: DNA and Cell Biology
Ye Wang, Philip D Howes, Eunjung Kim, Christopher D Spicer, Michael R Thomas, Yiyang Lin, Spencer W Crowder, Isaac J Pence, Molly M Stevens
Advances in nanotechnology have provided new opportunities for the design of next-generation nucleic acid biosensors and diagnostics. Indeed, combining advances in functional nanoparticles, DNA nanotechnology, and nuclease-enzyme-based amplification can give rise to new assays with advantageous properties. In this work, we developed a microRNA (miRNA) assay using bright fluorescent quantum dots (QDs), simple DNA probes, and the enzyme duplex-specific nuclease. We employed an isothermal target-recycling mechanism, where a single miRNA target triggers the cleavage of many DNA signal probes...
August 16, 2018: ACS Applied Materials & Interfaces
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