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N Max Schabla, Greg A Perry, Victoria L Palmer, Patrick C Swanson
The assembly of Ig genes in developing B lymphocytes by V(D)J recombination is initiated by the RAG1-RAG2 endonuclease complex. We previously identified an interaction between RAG1 and viral protein R binding protein (VprBP) (also known as DNA damage binding protein 1 cullin 4-associated factor 1 [DCAF1]), a substrate receptor for the cullin 4-really interesting new gene (RING) E3 ubiquitin ligase (CRL4). We report in this article that in mice, B cell-intrinsic loss of VprBP increases RAG1 protein levels and disrupts expression of the endoribonuclease Dicer, which is essential for microRNA maturation...
June 20, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
Jakub Dolata, Michał Taube, Mateusz Bajczyk, Artur Jarmolowski, Zofia Szweykowska-Kulinska, Dawid Bielewicz
MicroRNAs are small molecules (∼21 nucleotides long) that are key regulators of gene expression. They originate from long stem-loop RNAs as a product of cleavage by a protein complex called Microprocessor. The core components of the plant Microprocessor are the RNase type III enzyme Dicer-Like 1 (DCL1), the zinc finger protein Serrate (SE), and the double-stranded RNA binding protein Hyponastic Leaves 1 (HYL1). Microprocessor assembly and its processing of microRNA precursors have been reported to occur in discrete nuclear bodies called Dicing bodies...
2018: Frontiers in Plant Science
Sophie Atkinson, Samuel Marguerat, Danny Bitton, Francois Bachand, Maria Rodriguez-Lopez, Charalampos Rallis, Jean-Francois Lemay, Cristina Cotobal, Michal Malecki, Pawel Smialowski, Juan Mata, Philipp Korber, Jurg Bahler
Long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides but often unstable, contribute a substantial and diverse portion to pervasive non-coding transcriptomes. Most lncRNAs are poorly annotated and understood, although several play important roles in gene regulation and diseases. Here we systematically uncover and analyse lncRNAs in Schizosaccharomyces pombe. Based on RNA-seq data from twelve RNA-processing mutants and nine physiological conditions, we identify 5775 novel lncRNAs, nearly 4-times the previously annotated lncRNAs...
June 18, 2018: RNA
Qing Wang, Qian He, Yifei Chen, Wei Shao, Chao Yuan, Yizheng Wang
BACKGROUND: Amplified inflammation is important for the progression of Parkinson's disease (PD). However, how this enhanced inflammation is regulated remains largely unknown. Deletion of DICER leads to progressive dopamine neuronal loss and induces gliosis. We hypothesized that the homeostasis of microglial DICER would be responsible for the amplified inflammation in the mouse model of PD. METHODS: The microglia or C57BL/6 mice were treated or injected with l-methyl-4-phenyl-l,2,3,6-tetrahydropyridine (MPTP) or 1-methyl-4-phenylpyridinium (MPP+ ), respectively, for the model establishment...
June 15, 2018: Journal of Neuroinflammation
Kevin Tsai, David G Courtney, Edward M Kennedy, Bryan R Cullen
While the issue of whether RNA interference (RNAi) ever forms part of the antiviral innate immune response in mammalian somatic cells remains controversial, there is considerable evidence demonstrating that few, if any, viral small interfering RNAs (siRNAs) are produced in infected cells. Moreover, inhibition of RNAi by mutational inactivation of key RNAi factors, such as Dicer or Argonaute 2, fails to enhance virus replication. One potential explanation for this lack of inhibitory effect is that mammalian viruses encode viral suppressors of RNAi (VSRs) that are so effective that viral siRNAs are not produced in infected cells...
June 14, 2018: RNA
Aditya Kiran Gatta, Raghu Chandrashekhar Hariharapura, Nayanabhirama Udupa, Meka Sreenivasa Reddy, Venkata Rao Josyula
RNA interference has become a tool of choice in the development of drugs in various therapeutic areas of Post Transcriptional Gene Silencing (PTGS). The critical element in developing successful RNAi therapeutics lies in designing small interfering RNA (siRNA) using an efficient algorithm satisfying the designing criteria. Further, translation of siRNA from bench-side to bedside needs an efficient delivery system and/or chemical modification. Areas covered: This review emphasizes the importance of dicer, the criteria for efficient siRNA design, the currently available algorithms and strategies to overcome off-target effects, immune stimulatory effects and endosomal trap...
June 14, 2018: Expert Opinion on Drug Discovery
Carolina Camargo, Ke Wu, Elane Fishilevich, Kenneth E Narva, Blair D Siegfried
The use of transgenic crops that induce silencing of essential genes using double-stranded RNA (dsRNA) through RNA interference (RNAi) in western corn rootworm, Diabrotica virgifera virgifera, is likely to be an important component of new technologies for the control of this important corn pest. Previous studies have demonstrated that the dsRNA response in D. v. virgifera depends on the presence of RNAi pathway genes including Dicer-2 and Argonaute 2, and that downregulation of these genes limits the lethality of environmental dsRNA...
June 2018: Pesticide Biochemistry and Physiology
Thomas A Reh, Robert Hindges
The small RNA regulatory molecules called microRNAs (miRNAs) play key roles in the development of most organisms. The expression of many different miRNAs has been described in the developing and mature vertebrate retina. The ability of miRNAs to regulate a diversity of messenger RNA targets allows them to have effects on many different developmental processes, but the functions of only a few miRNAs have been documented to date. Developmental transitions between cell states appear to be particularly sensitive to miRNA loss of function, as evidenced by specific miRNA knockdowns or from global perturbations in miRNA levels (e...
June 11, 2018: Annual Review of Vision Science
Joanna Miskiewicz, Marta Szachniuk
A small non-coding molecule of microRNA (19⁻24 nt) controls almost every biological process, including cellular and physiological, of various organisms’ lives. The amount of microRNA (miRNA) produced within an organism is highly correlated to the organism’s key processes, and determines whether the system works properly or not. A crucial factor in plant biogenesis of miRNA is the Dicer Like 1 (DCL1) enzyme. Its responsibility is to perform the cleavages in the miRNA maturation process...
June 6, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Rafaella Nascimento Ferreira, Gustavo Moraes Holanda, Eliana Vieira Pinto Silva, Samir Mansour Moraes Casseb, Karla Fabiane Lopes Melo, Carlos Alberto Marques Carvalho, Juliana Abreu Lima, Pedro Fernando Costa Vasconcelos, Ana Cecília Ribeiro Cruz
Zika virus (ZIKV) is an arbovirus belonging to the genus Flavivirus (Flaviviridae). ZIKV infection is associated with alterations in various organs, including the liver, lungs, and kidneys. Studies on the influence of posttranscriptional control on viral infections have demonstrated that microRNAs (miRNAs) interfere with different stages of the replicative cycle of several viruses and may influence the disease outcome. To shed light on ZIKV-induced regulation of host miRNA-processing machinery in the above organs, we analyzed the expression of genes encoding key proteins of the miRNA pathway in different ZIKV-infected continuous primate cell lineages (HepG2, A549, and MA104) by reverse-transcription quantitative polymerase chain reaction (RT-qPCR)...
June 7, 2018: Viral Immunology
Y-H Taguchi
MicroRNA (miRNA) transfection is known to degrade target mRNAs and to decrease mRNA expression. In contrast to the notion that most of the gene expression alterations caused by miRNA transfection involve downregulation, they often involve both up- and downregulation; this phenomenon is thought to be, at least partially, mediated by sequence-nonspecific off-target effects. In this study, I used tensor decomposition-based unsupervised feature extraction to identify genes whose expression is likely to be altered by miRNA transfection...
June 4, 2018: Cells
Bora Jang, Boyoung Kim, Hyunsook Kim, Hyokyoung Kwon, Minjeong Kim, Yunmi Seo, Marion Colas, Hansaem Jeong, Eun Hye Jeong, Kyuri Lee, Hyukjin Lee
Enzymatic synthesis of RNA nanostructures is achieved by isothermal rolling circle transcription (RCT). Each arm of RNA nanostructures provides a functional role of Dicer substrate RNA inducing sequence specific RNA interference (RNAi). Three different RNAi sequences (GFP, RFP, and BFP) are incorporated within the three-arm junction RNA nanostructures (Y-RNA). The template and helper DNA strands are designed for the large-scale in vitro synthesis of RNA strands to prepare self-assembled Y-RNA. Interestingly, Dicer processing of Y-RNA is highly influenced by its physical structure and different gene silencing activity is achieved depending on its arm length and overhang...
June 4, 2018: Nano Letters
Tsz-Lun Yeung, Jianting Sheng, Cecilia S Leung, Fuhai Li, Jaeyeon Kim, Samuel Y Ho, Martin M Matzuk, Karen H Lu, Stephen T C Wong, Samuel C Mok
Background: Bulk tumor tissue samples are used for generating gene expression profiles in most research studies, making it difficult to decipher the stroma-cancer crosstalk networks. In the present study, we describe the use of microdissected transcriptome profiles for the identification of cancer-stroma crosstalk networks with prognostic value, which presents a unique opportunity for developing new treatment strategies for ovarian cancer. Methods: Transcriptome profiles from microdissected ovarian cancer-associated fibroblasts (CAFs) and ovarian cancer cells from patients with high-grade serous ovarian cancer (n = 70) were used as input data for the computational systems biology program CCCExplorer to uncover crosstalk networks between various cell types within the tumor microenvironment...
May 31, 2018: Journal of the National Cancer Institute
Canan Kuscu, Pankaj Kumar, Manjari Kiran, Zhangli Su, Asrar Malik, Anindya Dutta
tRNA related RNA fragments (tRFs), also known as tRNA derived RNAs (tdRNAs), are abundant small RNAs reported to be associated with Argonaute proteins, yet their function is unclear. We show that endogenous 18 nucleotide tRFs derived from the 3' ends of tRNAs (tRF-3) post-transcriptionally repress genes in HEK293T cells in culture. tRF-3 levels increase upon parental tRNA over-expression. This represses target genes with a sequence complementary to the tRF-3 in the 3' UTR. The tRF-3-mediated repression is Dicer-independent, Argonaute-dependent and the targets are recognized by sequence complementarity...
May 29, 2018: RNA
Taichiro Iki, Cléry Antoine, Nicolas Bologna, Alexis Sarazin, Christopher Brosnan, Nathan Pumplin, Frédéric H T Allain, Olivier Voinnet
In eukaryotes, the RNase-III Dicer often produces length/sequence microRNA (miRNA) variants, called "isomiRs", owing to intrinsic structural/sequence determinants of miRNA precursors (pre-miRNAs). Here, we combined biophysics, genetics and biochemistry to study Arabidopsis miR168, the key feedback-regulator of the central plant silencing effector protein ARGONAUTE1 (AGO1). We identified a motif conserved among plant pre-miR168 orthologs that enables flexible internal base-pairing underlying at least three metastable structural configurations...
May 24, 2018: Molecular Plant
Hans Christian Høiberg, Steffen M Sparvath, Veronica L Andersen, Jørgen Kjems, Ebbe S Andersen
The fields of DNA and RNA nanotechnology have established nucleic acids as valuable building blocks for functional nanodevices with applications in nanomedicine. Here, a simple method for designing and assembling a three-dimensional (3D) scaffolded RNA origami wireframe structure with intrinsic functioning small interfering RNAs (siRNAs) embedded is introduced. Uniquely, the method uses an mRNA fragment as scaffold strand, which is folded by sequence-complementarity of nine shorter synthetic strands. High-yield production of the intended 3D structure is verified by transmission electron microscopy (TEM)...
May 26, 2018: Biotechnology Journal
Jilong Li, Subhadip Ghatak, Mohamed S El Masry, Amitava Das, Yang Liu, Sashwati Roy, Robert J Lee, Chandan K Sen
Lyophilized keratinocyte-targeted nanocarriers (TLNκ ) loaded with locked nucleic acid (LNA) modified anti-miR were developed for topical application to full thickness burn injury. TLNκ were designed to selectively deliver LNA-anti-miR-107 to keratinocytes using the peptide sequence ASKAIQVFLLAG. TLNκ employed DOTAP/DODAP combination pH-responsive lipid components to improve endosomal escape. To minimize interference of clearance by non-targeted cells, especially immune cells in the acute wound microenvironment, surface charge was neutralized...
April 27, 2018: Molecular Therapy: the Journal of the American Society of Gene Therapy
Shuxin Zhang, Yongchao Dou, Shengjun Li, Guodong Ren, David Chevalier, Chi Zhang, Bin Yu
DAWDLE (DDL) is a conserved forkhead-associated (FHA) domain-containing protein with essential roles in plant development and immunity. It acts in the biogenesis of microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs), which regulate gene expression at the transcriptional and/or post-transcriptional levels. However, the functional mechanism of DDL and its impact on exogenous siRNAs remain elusive. Here we report that DDL is required for the biogenesis of siRNAs derived from sense transgenes and inverted-repeat transgenes...
May 21, 2018: Plant Physiology
Courtney Davis-Vogel, Angel Ortiz, Lisa Procyk, Jonathan Robeson, Adane Kassa, Yiwei Wang, Emily Huang, Carl Walker, Amit Sethi, Mark E Nelson, Dipali G Sashital
Western corn rootworm (Diabrotica virgifera virgifera) is a serious agricultural pest known for its high adaptability to various management strategies, giving rise to a continual need for new control options. Transgenic maize expressing insecticidal RNAs represents a novel mode of action for rootworm management that is dependent on the RNA interference (RNAi) pathways of the insect for efficacy. Preliminary evidence suggests that western corn rootworm could develop broad resistance to all insecticidal RNAs through changes in RNAi pathway genes; however, the likelihood of field-evolved resistance occurring through this mechanism remains unclear...
May 18, 2018: Scientific Reports
Jake C Robertson, Cheryl L Jorcyk, Julia Thom Oxford
DICER1 syndrome is a rare genetic disorder that predisposes individuals to multiple cancer types. Through mutations of the gene encoding the endoribonuclease, Dicer, DICER1 syndrome disrupts the biogenesis and processing of miRNAs with subsequent disruption in control of gene expression. Since the first description of DICER1 syndrome, case reports have documented novel germline mutations of the DICER1 gene in patients with cancers as well as second site mutations that alter the function of the Dicer protein expressed...
May 15, 2018: Cancers
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