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rna stability

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https://www.readbyqxmd.com/read/29236251/par-clip-for-discovering-target-sites-of-rna-binding-proteins
#1
Aitor Garzia, Pavel Morozov, Marcin Sajek, Cindy Meyer, Thomas Tuschl
RNA-binding proteins (RBPs) establish posttranscriptional gene regulation (PTGR) by coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. A variety of experimental approaches have been developed to characterize the RNAs associated with RBPs in vitro as well as in vivo. Our laboratory developed Photoactivatable-Ribonucleoside-Enhanced Cross-Linking and Immunoprecipitation (PAR-CLIP), which in combination with next-generation sequencing enables the identification of RNA targets of RBPs at a nucleotide-level resolution...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29236247/5-bromouridine-ip-chase-bric-seq-to-determine-rna-half-lives
#2
Toshimichi Yamada, Naoto Imamachi, Rena Onoguchi-Mizutani, Katsutoshi Imamura, Yutaka Suzuki, Nobuyoshi Akimitsu
Analysis of RNA stability at genome-wide level is an advanced method in RNA biology that examines the half-life of each transcript. In particular, a pulse-labeling method using uridine analogs enables the determination of half-life of each transcript under physiologically undisturbed conditions. The technique involves pulse labeling of endogenous RNAs in mammalian cells with 5'-bromouridine (BrU), followed by measuring the chronological decrease of BrU-labeled RNAs using deep sequencing (BRIC-seq). Here, we describe a detailed protocol and technical tips for BRIC-seq...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29235471/ctcf-driven-terra-transcription-facilitates-completion-of-telomere-dna-replication
#3
Kate Beishline, Olga Vladimirova, Stephen Tutton, Zhuo Wang, Zhong Deng, Paul M Lieberman
Telomere repeat DNA forms a nucleo-protein structure that can obstruct chromosomal DNA replication, especially under conditions of replication stress. Transcription of telomere repeats can initiate at subtelomeric CTCF-binding sites to generate telomere repeat-encoding RNA (TERRA), but the role of transcription, CTCF, and TERRA in telomere replication is not known. Here, we have used CRISPR/Cas9 gene editing to mutate CTCF-binding sites at the putative start site of TERRA transcripts for a class of subtelomeres...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233978/an-oomycete-plant-pathogen-reprograms-host-pre-mrna-splicing-to-subvert-immunity
#4
Jie Huang, Lianfeng Gu, Ying Zhang, Tingxiu Yan, Guanghui Kong, Liang Kong, Baodian Guo, Min Qiu, Yang Wang, Maofeng Jing, Weiman Xing, Wenwu Ye, Zhe Wu, Zhengguang Zhang, Xiaobo Zheng, Mark Gijzen, Yuanchao Wang, Suomeng Dong
The process of RNA splicing influences many physiological processes, including plant immunity. However, how plant parasites manipulate host RNA splicing process remains unknown. Here we demonstrate that PsAvr3c, an avirulence effector from oomycete plant pathogen Phytophthora sojae, physically binds to and stabilizes soybean serine/lysine/arginine-rich proteins GmSKRPs. The SKRPs are novel proteins that associate with a complex that contains plant spliceosome components, and are negative regulators of plant immunity...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233846/ve-cadherin-mediated-epigenetic-regulation-of-endothelial-gene-expression
#5
Marco F Morini, Costanza Giampietro, Monica Corada, Federica Pisati, Elisa Lavarone, Sara I Cunha, Lei L Conze, Nicola J O'Reilly, Dhira Joshi, Svend Kjaer, Roger George, Emma Nye, Anqi Ma, Jian Jin, Richard Mitter, Michela Lupia, Ugo Cavallaro, Diego Pasini, Dinis P Calado, Elisabetta Dejana, Andrea Taddei
Rationale: The mechanistic foundation of vascular maturation is still largely unknown. Several human pathologies are characterized by deregulated angiogenesis and unstable blood vessels. Solid tumours, for instance, get their nourishment from newly formed structurally abnormal vessels which present wide and irregular inter-endothelial junctions. Expression and clustering of the main endothelial-specific adherens junction protein, vascular endothelial (VE)-cadherin (VEC), upregulate genes with key roles in endothelial differentiation and stability...
December 12, 2017: Circulation Research
https://www.readbyqxmd.com/read/29230895/dissecting-and-analyzing-key-residues-in-protein-dna-complexes
#6
A Kulandaisamy, Ambuj Srivastava, R Nagarajan, M Michael Gromiha
Protein-DNA interactions are involved in various fundamental biological processes such as replication, transcription, DNA repair, and gene regulation. To understand the interaction in protein-DNA complexes, the integrative study of binding and stabilizing residues is important. In the present study, we have identified key residues that play a dual role in both binding and stability from a nonredundant dataset of 319 protein-DNA complexes. We observed that key residues are identified in very less number of complexes (29%) and only about 4% of stabilizing/binding residues are identified as key residues...
December 12, 2017: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29230368/stem-loop-structure-preference-for-site-specific-rna-editing-by-apobec3a-and-apobec3g
#7
Shraddha Sharma, Bora E Baysal
APOBEC3A and APOBEC3G cytidine deaminases inhibit viruses and endogenous retrotransposons. We recently demonstrated the novel cellular C-to-U RNA editing function of APOBEC3A and APOBEC3G. Both enzymes deaminate single-stranded DNAs at multiple TC or CC nucleotide sequences, but edit only a select set of RNAs, often at a single TC or CC nucleotide sequence. To examine the specific site preference for APOBEC3A and -3G-mediated RNA editing, we performed mutagenesis studies of the endogenous cellular RNA substrates of both proteins...
2017: PeerJ
https://www.readbyqxmd.com/read/29229736/comparison-of-salmonella-enterica-serovars-typhi-and-typhimurium-reveals-typhoidal-specific-responses-to-bile
#8
Rebecca Johnson, Matt Ravenhall, Derek Pickard, Gordon Dougan, Alexander Byrne, Gad Frankel
Salmonella enterica serovars Typhi and Typhimurium cause typhoid fever and gastroenteritis respectively. A unique feature of typhoid infection is asymptomatic carriage within the gallbladder, which is linked with S Typhi transmission. Despite this, S Typhi responses to bile have been poorly studied. RNA-Seq of S Typhi Ty2 and a clinical S Typhi isolate belonging to the globally dominant H58 lineage (129-0238), as well as S Typhimurium 14028, revealed that 249, 389 and 453 genes respectively were differentially expressed in the presence of 3% bile compared to control cultures lacking bile...
December 11, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29229605/mir-204-5p-and-mir-211-5p-contribute-to-braf-inhibitor-resistance-in-melanoma
#9
Marta Díaz-Martínez, Lucía Benito-Jardón, Lola Alonso, Lisa Koetz-Ploch, Eva Hernando, Joaquin Teixido
Melanoma treatment with the BRAF V600E inhibitor vemurafenib (VMF) provides therapeutic benefits but the common emergence of drug resistance remains a challenge. We generated A375 melanoma cells resistant to VMF with the goal of investigating changes in miRNA expression patterns that might contribute to resistance. Increased expression of miR-204-5p and miR-211-5p occurring in VMF-resistant cells was determined to impact VMF response. Their expression was rapidly affected by VMF treatment through RNA stabilization...
December 11, 2017: Cancer Research
https://www.readbyqxmd.com/read/29229300/c-myc-g-quadruplex-binding-by-the-rna-polymerase-i-inhibitor-bmh-21-and-analogues-revealed-by-a-combined-nmr-and-biochemical-approach
#10
Loana Musso, Stefania Mazzini, Anna Rossini, Lorenzo Castagnoli, Leonardo Scaglioni, Roberto Artali, Massimo Di Nicola, Franco Zunino, Sabrina Dallavalle
BACKGROUND: Pyridoquinazolinecarboxamides have been reported as RNA polymerase I inhibitors and represent a novel class of potential antitumor agents. BMH-21, was reported to intercalate with GC-rich rDNA, resulting in nucleolar stress as a primary mechanism of cytotoxicity. METHODS: The interaction of BMH-21 and analogues with DNA G-quadruplex structures was studied by NMR and molecular modelling. The cellular response was investigated in a panel of human tumor cell lines and protein expression was examined by Western Blot analysis...
December 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29228327/most-m6a-rna-modifications-in-protein-coding-regions-are-evolutionarily-unconserved-and-likely-nonfunctional
#11
Zhen Liu, Jianzhi Zhang
Methylation of the adenosine base at the nitrogen-6 position (m6A) is the most prevalent internal posttranscriptional modification of mRNAs in many eukaryotes. Despite the rapid progress in the transcriptome-wide mapping of m6As, identification of proteins responsible for writing, reading, and erasing m6As, and elucidation of m6A functions in splicing, RNA stability, translation, and other processes, it is unknown whether most observed m6A modifications are functional. To address this question, we respectively analyze the evolutionary conservation of yeast and human m6As in protein-coding regions...
December 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29227944/effects-of-starch-coating-of-magnetite-nanoparticles-on-cellular-uptake-toxicity-and-gene-expression-profiles-in-adult-zebrafish
#12
Min Zheng, Jianguo Lu, Dongye Zhao
Engineered magnetite nanoparticles (Fe3O4 NPs) have been used in many fields. To prevent particle agglomeration, stabilizers or coatings are often required. While such coatings have been shown to enhance performances, the environmental impact or toxicity of stabilized or coated Fe3O4 NPs remain poorly understood. In an effort to understand the impacts of such coatings on the toxicity of Fe3O4 NPs, we used the transcriptome sequencing (RNA-seq) technique to characterize the gill and liver transcriptomes from adult zebrafish when exposed to bare and starch-stabilized Fe3O4 NPs for 7days, demonstrating remarkable differences in gene expression profiles, also known as differentially expressed genes (DEGs) profiles, in both tissues...
December 8, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29226647/human-peripheral-blood-cells-mrna-levels-are-highly-sensitive-to-duration-of-ex-vivo-post-sampling-conditions-prior-to-rna-isolation
#13
Eva Bohackova, Pavlina Dankova
BACKGROUND: This study aimed to evaluate an effect of the time period between drawing the peripheral blood and specimen processing on the stability of mRNA levels of 7 selected genes. METHODS: Blood samples derived from 15 healthy volunteers were always processed at five consecutive time points 0.5, 1.5, 2, 3, and 9 hours; mRNA was quantified by real-time PCR. RESULTS: Anti-inflammatory genes CCL2 and IL10 showed a significant rise of expression between the 3rd and 9th hour after blood collection (p ≤ 0...
November 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/29226219/systematic-optimization-and-modification-of-a-dna-aptamer-with-2-o-methyl-rna-analogues
#14
George Maio, Osita Enweronye, Hasan E Zumrut, Sana Batool, Nabeela Van, Prabodhika Mallikaratchy
Nucleic acid aptamers (NAAs) are short synthetic DNA or RNA molecules that specifically fold into distinct three-dimensional structures able to specifically recognize a target. While NAAs show unprecedented promise in a variety of applications, including sensing, therapeutics and diagnostics, one major limitation involves the lack of stability towards omnipresent nucleases. Therefore, we herein report a systematic truncation and incorporation of 2'-O-methyl bases to a DNA aptamer, which results in increased stability without affecting affinity...
March 1, 2017: ChemistrySelect
https://www.readbyqxmd.com/read/29226062/interactions-of-protonated-guanidine-and-guanidine-derivatives-with-multiply-deprotonated-rna-probed-by-electrospray-ionization-and-collisionally-activated-dissociation
#15
Jovana Vušurović, Eva-Maria Schneeberger, Kathrin Breuker
Interactions of ribonucleic acid (RNA) with guanidine and guanidine derivatives are important features in RNA-protein and RNA-drug binding. Here we have investigated noncovalently bound complexes of an 8-nucleotide RNA and six different ligands, all of which have a guanidinium moiety, by using electrospray ionization (ESI) and collisionally activated dissociation (CAD) mass spectrometry (MS). The order of complex stability correlated almost linearly with the number of ligand atoms that can potentially be involved in hydrogen-bond or salt-bridge interactions with the RNA, but not with the proton affinity of the ligands...
December 2017: ChemistryOpen
https://www.readbyqxmd.com/read/29225167/adenovirus-infection-induces-hur-relocalization-to-facilitate-virus-replication
#16
Jumond P Jehung, Tetsuya Kitamura, Aya Yanagawa-Matsuda, Takeshi Kuroshima, Alam Towfik, Motoaki Yasuda, Hidehiko Sano, Yoshimasa Kitagawa, Kazuyuki Minowa, Masanobu Shindoh, Fumihiro Higashino
HuR is an RNA-binding protein of the embryonic lethal abnormal vision (ELAV) family, which binds to the AU-rich element (ARE) in the 3'-untranslated region (UTR) of certain mRNAs and is involved in the nucleo-cytoplasmic export and stabilization of ARE-mRNAs. The cytoplasmic relocalization of ARE-mRNAs with several proteins such as HuR and pp32 increases in cells transformed by the adenovirus oncogene product E4orf6. Additionally, these ARE-mRNAs were stabilized and acquired the potential to transform cells...
December 7, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29225039/a-massively-parallel-reporter-assay-of-3-utr-sequences-identifies-in%C3%A2-vivo-rules-for-mrna-degradation
#17
Michal Rabani, Lindsey Pieper, Guo-Liang Chew, Alexander F Schier
The stability of mRNAs is regulated by signals within their sequences, but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here we introduce UTR-seq, a combination of massively parallel reporter assays and regression models, to survey the dynamics of tens of thousands of 3' UTR sequences during early zebrafish embryogenesis. UTR-seq revealed two temporal degradation programs: a maternally encoded early-onset program and a late-onset program that accelerated degradation after zygotic genome activation...
November 30, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29223394/islet-%C3%AE-cell-an-endocrine-cell-secreting-mirnas
#18
Aisen Zhang, Dameng Li, Yucheng Liu, Jing Li, Yujing Zhang, Chen-Yu Zhang
The pancreas is an important endocrine organ. Pancreatic beta (β) cells secrete insulin to regulate the metabolism of glucose and maintain the stability of blood glucose. MicroRNAs (miRNAs), small (20-25 nt) non-coding RNA molecules, function in target gene silencing through post-transcriptional patterns, and multiple miRNAs regulate insulin secretion, insulin signaling pathways in pancreatic β cells and islet activity. In recent years, it has been found that many types of cells can secrete regulatory miRNA, but whether islet cells can secrete miRNA has not been clarified yet...
December 6, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29222953/bacterial-community-changes-in-copper-and-pex-drinking-water-pipeline-biofilms-under-extra-disinfection-and-magnetic-water-treatment
#19
Jenni Inkinen, Balamuralikrishna Jayaprakash, Merja Ahonen, Tarja Pitkänen, Riika Mäkinen, Anna Pursiainen, Jorge W Santo Domingo, Heidi Salonen, Michael Elk, Minna M Keinänen-Toivola
AIMS: To study stability of biofilms and water quality in pilot scale drinking water copper and PEX pipes in changing conditions (extra disinfection, magnetic water treatment MWT). METHODS AND RESULTS: Next-generation sequencing (NGS) of 16S ribosomal RNA genes (rDNA) to describe total bacterial community and ribosomal RNA (rRNA) to describe active bacterial members in addition to traditional microbiological methods were applied. Biofilms from control copper and PEX pipes shared same most abundant bacteria (Methylobacterium spp...
December 9, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29222492/interaction-of-rna-binding-protein-hur-and-mir-466i-regulates-gm-csf-expression
#20
Jing Chen, William Adamiak, Ganlei Huang, Ulus Atasoy, Abdolmohamad Rostami, Shiguang Yu
Granulocyte-macrophage colony-stimulating factor (GM-CSF) produced by T helper 17 (Th17) cells plays an essential role in autoimmune diseases. Transcriptional regulation of Th17 cell differentiation has been extensively studied, but post-transcriptional regulation of Th17 cell differentiation has remained less well characterized. The RNA-binding protein HuR functions to promote the stability of target mRNAs via binding the AU-rich elements of the 3' untranslated region (3'UTR) of numerous pro-inflammatory cytokines including IL-4, IL-13, IL-17 and TNF-α...
December 8, 2017: Scientific Reports
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