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RNA Biology

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https://www.readbyqxmd.com/read/30422048/transformation-of-nad7-into-the-nuclear-genome-rescues-the-slow-growth3-mutant-in-arabidopsis
#1
Wei-Yu Hsieh, Sang-Chu Lin, Ming-Hsiun Hsieh
Plant pentatricopeptide repeat (PPR) proteins are mostly involved in chloroplast or mitochondrial RNA metabolism. However, direct evidence that correction of the molecular defects in the organelles can restore the plant phenotypes has yet to be demonstrated in a ppr mutant. Arabidopsis slow growth3 (slo3), a ppr mutant, is impaired in the splicing of mitochondrial nad7 intron 2. Here, we have used slo3 as an example to demonstrate that transformation of correctly spliced nad7 into the nuclear genome and targeting the Nad7 subunit into mitochondria can restore complex I activity and plant phenotypes in the mutant...
November 13, 2018: RNA Biology
https://www.readbyqxmd.com/read/30381990/correction
#2
(no author information available yet)
No abstract text is available yet for this article.
November 1, 2018: RNA Biology
https://www.readbyqxmd.com/read/30381983/a-potential-role-of-extended-simple-sequence-repeats-in-competing-endogenous-rna-crosstalk
#3
Tomasz M Witkos, Wlodzimierz J Krzyzosiak, Agnieszka Fiszer, Edyta Koscianska
MicroRNA (miRNA)-mediated crosstalk between coding and non-coding RNAs of various types is known as the competing endogenous RNA (ceRNA) concept. Here, we propose that there is a specific variant of the ceRNA language that takes advantage of simple sequence repeat (SSR) wording. We applied bioinformatics tools to identify human transcripts that may be regarded as repeat-associated ceRNAs (raceRNAs). Multiple protein-coding transcripts, transcribed pseudogenes, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) showing this potential were identified, and numerous miRNAs were predicted to bind to SSRs...
November 1, 2018: RNA Biology
https://www.readbyqxmd.com/read/30362859/luteolin-inhibits-musashi1-binding-to-rna-and-disrupts-cancer-phenotypes-in-glioblastoma-cells
#4
Caihong Yi, Guiming Li, Dmitri N Ivanov, Zhonghua Wang, Mitzli Velasco, Greco Hernandez, Soni Kaundal, Johanna Villarreal, Yogesh K Gupta, Mei Qiao, Christopher G Hubert, Matthew J Hart, Luiz O F Penalva
RNA binding proteins have emerged as critical oncogenic factors and potential targets in cancer therapy. In this study, we evaluated Musashi1 (Msi1) targeting as a strategy to treat glioblastoma (GBM); the most aggressive brain tumor type. Msi1 expression levels are often high in GBMs and other tumor types and correlate with poor clinical outcome. Moreover, Msi1 has been implicated in chemo- and radio-resistance. Msi1 modulates a range of cancer relevant processes and pathways and regulates the expression of stem cell markers and oncogenic factors via mRNA translation/stability...
October 26, 2018: RNA Biology
https://www.readbyqxmd.com/read/30332908/superior-cellular-activities-of-azido-over-amino-functionalized-ligands-for-engineered-preq-1-riboswitches-in-e-coli
#5
Eva Neuner, Marina Frener, Alexandra Lusser, Ronald Micura
For this study, we utilized class-I and class-II preQ1 -sensing riboswitches as model systems to decipher the structure-activity relationship of rationally designed ligand derivatives in vitro and in vivo. We found that synthetic preQ1 ligands with amino-modified side chains that protrude from the ligand-encapsulating binding pocket, and thereby potentially interact with the phosphate backbone in their protonated form, retain or even increase binding affinity for the riboswitches in vitro. They, however, led to significantly lower riboswitch activities in a reporter system in vivo in E...
October 26, 2018: RNA Biology
https://www.readbyqxmd.com/read/30345881/dual-dna-rulers-reveal-an-mrna-looping-intermediate-state-during-ribosome-translocation
#6
Heng Yin, Shoujun Xu, Yuhong Wang
The precise 3-nucleotide movement of mRNA is critical for translation fidelity. One mRNA translocation error propagates to all of the following codons, which is detrimental to the cell. However, none of the current methods can reveal the mRNA dynamics near the ribosome entry site, which limits the understanding of this important issue. We have developed an assay of dual DNA rulers that provides such capability. By uniquely probing both the 3'- and 5'-ends of mRNA, we observed an antibiotic-trapped intermediate state that is consistent with a ribosomal conformation containing mRNA asymmetric partial displacements at its entry and exit sites...
October 22, 2018: RNA Biology
https://www.readbyqxmd.com/read/30339041/rna-accessibility-impacts-potency-of-tough-decoy-microrna-inhibitors
#7
Marjolein J G Hooykaas, Jasper A Soppe, Hendrik M De Buhr, Elisabeth Kruse, Emmanuel J H J Wiertz, Robert J Lebbink
MicroRNAs (miRNAs) are small RNA molecules that post-transcriptionally regulate gene expression through silencing of complementary target mRNAs. miRNAs are involved in many biological processes, including cell proliferation, differentiation, cell signaling and cellular defense responses to infection. Strategies that allow for strong and stable suppression of specific microRNA activity are needed to study miRNA functions and to develop therapeutic intervention strategies aimed at interfering with miRNA activity in vivo...
October 19, 2018: RNA Biology
https://www.readbyqxmd.com/read/30336727/recent-progress-in-single-molecule-studies-of-mrna-localization-in-vivo
#8
Songhee H Kim, Melissa Vieira, Jae Youn Shim, Hongyoung Choi, Hye Yoon Park
From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules...
October 19, 2018: RNA Biology
https://www.readbyqxmd.com/read/30290721/rnase-y-mediated-regulation-of-the-streptococcal-pyrogenic-exotoxin-b
#9
Laura Broglia, Solange Materne, Anne-Laure Lécrivain, Karin Hahnke, Anaïs Le Rhun, Emmanuelle Charpentier
Endoribonuclease Y (RNase Y) is a crucial regulator of virulence in Gram-positive bacteria. In the human pathogen Streptococcus pyogenes, RNase Y is required for the expression of the major secreted virulence factor streptococcal pyrogenic exotoxin B (SpeB), but the mechanism involved in this regulation remains elusive. Here, we demonstrate that the 5' untranslated region of speB mRNA is processed by several RNases including RNase Y. In particular, we identify two RNase Y cleavage sites located downstream of a guanosine (G) residue...
October 18, 2018: RNA Biology
https://www.readbyqxmd.com/read/30328748/kinetics-coming-into-focus-single-molecule-microscopy-of-riboswitch-dynamics
#10
Sujay Ray, Adrien Chauvier, Nils G Walter
Riboswitches are dynamic RNA motifs that are mostly embedded in the 5'-untranslated regions of bacterial mRNAs, where they regulate gene expression transcriptionally or translationally by undergoing conformational changes upon binding of a small metabolite or ion. Due to the small size of typical ligands, relatively little free energy is available from ligand binding to overcome the often high energetic barrier of reshaping RNA structure. Instead, most riboswitches appear to take advantage of the directional and hierarchical folding of RNA by employing the ligand as a structural 'linchpin' to adjust the kinetic partitioning between alternate folds...
October 17, 2018: RNA Biology
https://www.readbyqxmd.com/read/30328747/observation-of-preq-1-ii-riboswitch-dynamics-using-single-molecule-fret
#11
Chandani Warnasooriya, Clarence Ling, Ivan A Belashov, Mohammad Salim, Joseph E Wedekind, Dmitri N Ermolenko
PreQ1 riboswitches regulate the synthesis of the hypermodified tRNA base queuosine by sensing the pyrrolopyrimidine metabolite preQ1 . Here, we use single-molecule FRET to interrogate the structural dynamics of apo and preQ1 -bound states of the preQ1 -II riboswitch from Lactobacillus rhamnosus. We find that the apo-form of the riboswitch spontaneously samples multiple conformations. Magnesium ions and preQ1  stabilize conformations that sequester the ribosome-binding site of the mRNA within the pseudoknotted structure, thus inhibiting translation initiation...
October 17, 2018: RNA Biology
https://www.readbyqxmd.com/read/30321100/altered-levels-of-long-ncrnas-meg3-and-neat1-in-cell-and-animal-models-of-huntington-s-disease
#12
Kaushik Chanda, Srijit Das, Joyeeta Chakraborty, Sudha Bucha, Arindam Maitra, Raghunath Chatterjee, Debashis Mukhopadhyay, Nitai P Bhattacharyya
Altered expression levels of protein-coding genes and microRNAs have been implicated in the pathogenesis of Huntington's disease (HD). The involvement of other ncRNAs, especially long ncRNAs (lncRNA), is being realized recently and the related knowledge is still rudimentary. Using small RNA sequencing and PCR arrays we observed perturbations in the levels of 12 ncRNAs in HD mouse brain, eight of which had human homologs. Of these, Meg3, Neat1, and Xist showed a consistent and significant increase in HD cell and animal models...
October 15, 2018: RNA Biology
https://www.readbyqxmd.com/read/30321081/snd1-acts-as-an-anti-apoptotic-factor-via-regulating-the-expression-of-lncrna-uca1-in-hepatocellular-carcinoma
#13
Xiaoteng Cui, Chunyan Zhao, Xuyang Yao, Baoxin Qian, Chao Su, Yuanyuan Ren, Zhi Yao, Xingjie Gao, Jie Yang
Multifunctional SND1 (staphylococcal nuclease and tudor domain containing 1) protein is reportedly associated with different types of RNA molecules, including mRNA, miRNA, pre-miRNA, and dsRNA. SND1 has been implicated in a number of biological processes in eukaryotic cells, including cell cycle, DNA damage repair, proliferation, and apoptosis. However, the specific molecular mechanism regarding the anti-apoptotic role of SND1 in mammalian cells remains largely elusive. In this study, the analysis of the online HPA (human protein atlas) and TCGA (the cancer genome atlas) databases showed the significantly high expression of SND1 in liver cancer patients...
October 15, 2018: RNA Biology
https://www.readbyqxmd.com/read/30295127/rbm-5-modulates-u2af-large-subunit-dependent-alternative-splicing-in-c-elegans
#14
Chuanman Zhou, Xiaoyang Gao, Surong Hu, Wenjing Gan, Jing Xu, Yongchao C Ma, Long Ma
A key step in pre-mRNA splicing is the recognition of 3' splicing sites by the U2AF large and small subunits, a process regulated by numerous trans-acting splicing factors. How these trans-acting factors interact with U2AF in vivo is unclear. From a screen for suppressors of the temperature-sensitive (ts) lethality of the C. elegans U2AF large subunit gene uaf-1(n4588) mutants, we identified mutations in the RNA binding motif gene rbm-5, a homolog of the tumor suppressor gene RBM5. rbm-5 mutations can suppress uaf-1(n4588) ts-lethality by loss of function and neuronal expression of rbm-5 was sufficient to rescue the suppression...
October 13, 2018: RNA Biology
https://www.readbyqxmd.com/read/30252595/the-francisella-novicida-cas12a-is-sensitive-to-the-structure-downstream-of-the-terminal-repeat-in-crispr-arrays
#15
Chunyu Liao, Rebecca A Slotkowski, Tatjana Achmedov, Chase L Beisel
The Class 2 Type V-A CRISPR effector protein Cas12a/Cpf1 has gained widespread attention in part because of the ease in achieving multiplexed genome editing, gene regulation, and DNA detection. Multiplexing derives from the ability of Cas12a alone to generate multiple guide RNAs from a transcribed CRISPR array encoding alternating conserved repeats and targeting spacers. While array design has focused on how to optimize guide-RNA sequences, little attention has been paid to sequences outside of the CRISPR array...
October 12, 2018: RNA Biology
https://www.readbyqxmd.com/read/30306823/microrna-therapeutics-design-of-single-stranded-mir-216b-mimics-to-target-kras-in-pancreatic-cancer-cells
#16
Annalisa Ferino, Giulia Miglietta, Raffaella Picco, Stefan Vogel, Jesper Wengel, Luigi E Xodo
Datasets reporting microRNA expression profiles in normal and cancer cells show that miR-216b is aberrantly downregulated in pancreatic ductal adenocarcinoma (PDAC). We found that KRAS, whose mutant G12D allele drives the pathogenesis of PDAC, is a target of miR-216b. To suppress oncogenic KRAS in PDAC cells, we designed single-stranded (ss) miR-216b mimics with unlocked nucleic acid (UNA) modifications to enhance their nuclease resistance. We prepared variants of ss-miR-216b mimics with and without a 5' phosphate group...
October 11, 2018: RNA Biology
https://www.readbyqxmd.com/read/30293519/the-small-rna-sdsr-acts-as-a-novel-type-of-toxin-in-escherichia-coli
#17
Jee Soo Choi, Wonkyong Kim, Shinae Suk, Hongmarn Park, Geunu Bak, Junhyeok Yoon, Younghoon Lee
Most small noncoding RNAs (sRNAs) are known to base pair with target mRNAs and regulate mRNA stability or translation to trigger various changes in the cell metabolism of Escherichia coli. The SdsR sRNA is expressed specifically during the stationary phase and represses tolC and mutS expression. However, it was not previously known whether the growth-phase-dependent regulation of SdsR is important for cell growth. Here, we ectopically expressed SdsR during the exponential phase and examined cell growth and survival...
October 7, 2018: RNA Biology
https://www.readbyqxmd.com/read/30081743/lactococcus-lactis-type-iii-a-crispr-cas-system-cleaves-bacteriophage-rna
#18
Anne M Millen, Julie E Samson, Denise M Tremblay, Alfonso H Magadán, Geneviève M Rousseau, Sylvain Moineau, Dennis A Romero
CRISPR-Cas defends microbial cells against invading nucleic acids including viral genomes. Recent studies have shown that type III-A CRISPR-Cas systems target both RNA and DNA in a transcription-dependent manner. We previously found a type III-A system on a conjugative plasmid in Lactococcus lactis which provided resistance against virulent phages of the Siphoviridae family. Its naturally occurring spacers are oriented to generate crRNAs complementary to target phage mRNA, suggesting transcription-dependent targeting...
October 2, 2018: RNA Biology
https://www.readbyqxmd.com/read/30269676/identification-of-factors-that-promote-biogenesis-of-trna-cga-ser
#19
Fu Xu, Yang Zhou, Anders S Byström, Marcus J O Johansson
A wide variety of factors are required for the conversion of pre-tRNA molecules into the mature tRNAs that function in translation. To identify factors influencing tRNA biogenesis, we previously performed a screen for strains carrying mutations that induce lethality when combined with a sup61-T47:2C allele, encoding a mutant form of [Formula: see text]. Analyzes of two complementation groups led to the identification of Tan1 as a protein involved in formation of the modified nucleoside N4 -acetylcytidine (ac4 C) in tRNA and Bud13 as a factor controlling the levels of ac4 C by promoting TAN1 pre-mRNA splicing...
September 29, 2018: RNA Biology
https://www.readbyqxmd.com/read/30257600/regulatory-roles-of-vertebrate-nocturnin-insights-and-remaining-mysteries
#20
Kelsey L Hughes, Elizabeth T Abshire, Aaron C Goldstrohm
Post-transcriptional control of messenger RNA (mRNA) is an important layer of gene regulation that modulates mRNA decay, translation, and localization. Eukaryotic mRNA decay begins with the catalytic removal of the 3' poly-adenosine tail by deadenylase enzymes. Multiple deadenylases have been identified in vertebrates and are known to have distinct biological roles; among these proteins is Nocturnin, which has been linked to circadian biology, adipogenesis, osteogenesis, and obesity. Multiple studies have investigated Nocturnin's involvement in these processes; however, a full understanding of its molecular function remains elusive...
September 27, 2018: RNA Biology
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