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RNA binding proteins

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https://www.readbyqxmd.com/read/28092440/molecular-interactions-between-graphene-and-biological-molecules
#1
Xingquan Zou, Shuai Wei, Joshua Jasensky, Minyu Xiao, Qiuming Wang, Charles L Brooks, Zhan Chen
Applications of graphene have extended into areas of nanobio-technology such as nanobio-medicine, nanobio-sensing, as well as nanoelectronics with biomolecules. These applications involve interactions between proteins, peptides, DNA, RNA etc. and graphene, therefore understanding such molecular interactions is essential. For example, many applications based on using graphene and peptides require peptides to interact with (e.g., noncovalently bind to) graphene at one end, while simultaneously exposing the other end to the surrounding medium (e...
January 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28092367/molecular-architecture-and-dynamics-of-ash1-mrna-recognition-by-its-mrna-transport-complex
#2
Franziska Theresia Edelmann, Andreas Schlundt, Roland Gerhard Heym, Andreas Jenner, Annika Niedner-Boblenz, Muhammad Ibrahim Syed, Jean-Christophe Paillart, Ralf Stehle, Robert Janowski, Michael Sattler, Ralf-Peter Jansen, Dierk Niessing
mRNA localization is an essential mechanism of gene regulation and is required for processes such as stem-cell division, embryogenesis and neuronal plasticity. It is not known which features in the cis-acting mRNA localization elements (LEs) are specifically recognized by motor-containing transport complexes. To the best of our knowledge, no high-resolution structure is available for any LE in complex with its cognate protein complex. Using X-ray crystallography and complementary techniques, we carried out a detailed assessment of an LE of the ASH1 mRNA from yeast, its complex with its shuttling RNA-binding protein She2p, and its highly specific, cytoplasmic complex with She3p...
January 16, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28091569/epigenetic-regulation-of-plasmodium-falciparum-clonally-variant-gene-expression-during-development-in-anopheles-gambiae
#3
Elena Gómez-Díaz, Rakiswendé S Yerbanga, Thierry Lefèvre, Anna Cohuet, M Jordan Rowley, Jean Bosco Ouedraogo, Victor G Corces
P. falciparum phenotypic plasticity is linked to the variant expression of clonal multigene families such as the var genes. We have examined changes in transcription and histone modifications that occur during sporogonic development of P. falciparum in the mosquito host. All var genes are silenced or transcribed at low levels in blood stages (gametocyte/ring) of the parasite in the human host. After infection of mosquitoes, a single var gene is selected for expression in the oocyst, and transcription of this gene increases dramatically in the sporozoite...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28089630/the-aspergillus-nidulans-pbp1-homolog-is-required-for-normal-sexual-development-and-secondary-metabolism
#4
Alexandra A Soukup, Gregory J Fischer, Jerry Luo, Nancy P Keller
P bodies and stress granules are RNA-containing structures governing mRNA degradation and translational arrest, respectively. Saccharomyces cerevisiae Pbp1protein localizes to stress granules and promotes their formation and is involved in proper polyadenylation, suppression of RNA-DNA hybrids, and preventing aberrant rDNA recombination. A genetic screen for Aspergillus nidulans mutants aberrant in secondary metabolism identified the Pbp1 homolog, PbpA. Using Dcp1 (mRNA decapping) as a marker for P-body formation and FabM (Pab1, poly-A binding protein) to track stress granule accumulation, we examine the dynamics of RNA granule formation in A...
January 9, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28088441/resveratrol-limits-epithelial-to-mesenchymal-transition-through-modulation-of-khsrp-hnrnpa1-dependent-alternative-splicing-in-mammary-gland-cells
#5
Arfa Moshiri, Margherita Puppo, Martina Rossi, Roberto Gherzi, Paola Briata
Resveratrol (RESV) is a natural polyphenolic compound endowed with anti-inflammatory, anti-proliferative, as well as pro-apoptotic activities that make it a potential anti-tumor compound. Here we show that RESV counteracts the TGF-β-induced Epithelial to Mesenchymal Transition (EMT) phenotype in mammary gland cells and affects the alternative exon usage of pre-mRNAs that encode crucial factors in adhesion and migration -including CD44, ENAH, and FGFR2- in a panel of immortalized and transformed mammary gland cells...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088354/uncovering-oxysterol-binding-protein-osbp-as-a-target-of-the-anti-enteroviral-compound-ttp-8307
#6
Lucian Albulescu, Joëlle Bigay, Bishyajit Biswas, Marion Weber-Boyvat, Cristina M Dorobantu, Leen Delang, Hilde M van der Schaar, Young-Sik Jung, Johan Neyts, Vesa M Olkkonen, Frank J M van Kuppeveld, Jeroen R P M Strating
The genus Enterovirus (e.g. poliovirus, coxsackievirus, rhinovirus) of the Picornaviridae family of positive-strand RNA viruses includes many important pathogens linked to a range of acute and chronic diseases for which no approved antiviral therapy is available. Targeting a step in the life cycle that is highly conserved provides an attractive strategy for developing broad-range inhibitors of enterovirus infection. A step that is currently explored as a target for the development of antivirals is the formation of replication organelles, which support replication of the viral genome...
January 11, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28088346/msi1-promotes-tumor-progression-by-epithelial-to-mesenchymal-transition-in-cervical-cancer
#7
Pijun Gong, Yidong Wang, Yane Gao, Mei Gao, Lixia Liu, Ping Qu, Xinxing Jin, Qing Gao
Musashi1 (Msi1) is an RNA-binding protein that has been reported to be a pivotal regulator in tumorigenesis and progression in several cancers. However, its function and mechanism in cervical cancer is still unknown. In this study, Msi1 expression was found elevated in cervical cancers by immunohistochemistry and correlated with poor outcomes. Then, endogenous Msi1 was silenced in cervical cancer cell lines by short hairpin RNA (shRNA), and its function and mechanism were determined. The results showed that the silencing of Msi1 in SiHa and HeLa cells inhibited the cells' migratory and invasive abilities in vitro and tumor progression in vivo...
January 11, 2017: Human Pathology
https://www.readbyqxmd.com/read/28087991/an-exceptionally-selective-dna-cooperatively-binding-two-ca2-ions
#8
Wenhu Zhou, Runjhun Saran, Po-Jung Jimmy Huang, Jinsong Ding, Juewen Liu
Ca2+ is a highly important metal ion in biology and in the environment, leading to extensive work in developing sensors for Ca2+ detection. While many Ca2+ binding proteins are known, few nucleic acids can selectively bind Ca2+. DNA-based biosensors are attractive for its high stability and excellent programmability. Herein, we report a RNA-cleaving DNAzyme named EtNa cooperatively binding two Ca2+ ions but only one Mg2+. Four DNAzymes with known Ca2+-dependent activity were compared, and the EtNa has the best selectivity...
January 14, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28087642/stxbp4-drives-tumor-growth-and-is-associated-with-poor-prognosis-through-pdgf-receptor-signaling-in-lung-squamous-cell-carcinoma
#9
Yukihiro Otaka, Susumu Rokudai, Kyoichi Kaira, Michiru Fujieda, Ikuko Horikoshi, Reika Kawabata, Shinji Yoshiyama, Takehiko Yokobori, Yoichi Ohtaki, Kimihiro Shimizu, Tetsunari Oyama, Jun'ichi Tamura, Carol Prives, Masahiko Nishiyama
PURPOSE: Expression of the ΔN isoform of p63 (ΔNp63) is a diagnostic marker highly specific for lung squamous cell carcinoma (SCC). We previously found that Syntaxin Binding Protein 4 (STXBP4) regulates ΔNp63 ubiquitination, suggesting that STXBP4 may also be a SCC biomarker. To address this issue, we investigated the role of STXBP4 expression in SCC biology and the impact of STXBP4 expression on SCC prognosis. EXPERIMENTAL DESIGN: We carried out a clinicopathological analysis of STXBP4 expression in 87 lung SCC patients...
January 13, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28087229/disease-associated-mutations-identify-a-novel-region-in-human-sting-necessary-for-the-control-of-type-i-interferon-signaling
#10
Isabelle Melki, Yoann Rose, Carolina Uggenti, Lien Van Eyck, Marie-Louise Frémond, Naoki Kitabayashi, Gillian I Rice, Emma M Jenkinson, Anaïs Boulai, Nadia Jeremiah, Marco Gattorno, Sefano Volpi, Olivero Sacco, Suzanne W J Terheggen-Lagro, Harm A W M Tiddens, Isabelle Meyts, Marie-Anne Morren, Petra De Haes, Carine Wouters, Eric Legius, Anniek Corveleyn, Frederic Rieux-Laucat, Christine Bodemer, Isabelle Callebaut, Mathieu P Rodero, Yanick J Crow
BACKGROUND: Gain-of-function mutations in transmembrane protein 173 (TMEM173) encoding stimulator of interferon genes (STING) underlie a recently described type I interferonopathy called STING-associated vasculopathy with onset in infancy (SAVI). OBJECTIVES: We sought to define the molecular and cellular pathology relating to 3 individuals variably exhibiting the core features of the SAVI phenotype including systemic inflammation, destructive skin lesions, and interstitial lung disease...
January 3, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28081465/biological-function-and-mechanism-of-lncrna-meg3-in-tenon-s-capsule-fibroblasts-proliferation-by-meg3-nrf2-protein-interaction
#11
Yuan Wang, Jing Wang, Li-Juan Wei, Dong-Mei Zhu, Jin-Song Zhang
OBJECTIVE: The proliferation of Tenon's capsule fibroblasts after glaucoma filtration surgery is a harmful element for operation failure. However, the underlying mechanism remains unclear. In this study, we evaluated the role of long non-coding RNA (lncRNA)-MEG3 in the proliferation of Glaucoma Tenon's capsule fibroblasts (GTFs) with a model of transforming growth factor-β (TGF-β)-induced proliferation which has been used in previous studies to explore the mechanism underlying glaucoma surgery failure...
January 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28079881/translational-upregulation-of-aurora-a-by-hnrnp-q1-contributes-to-cell-proliferation-and-tumorigenesis-in-colorectal-cancer
#12
Chien-Hsien Lai, Yu-Chuan Huang, Jenq-Chang Lee, Joseph Ta-Chien Tseng, Kung-Chao Chang, Yen-Ju Chen, Nai-Jhu Ding, Pao-Hsuan Huang, Wen-Chang Chang, Bo-Wen Lin, Ruo-Yu Chen, Yu-Chu Wang, Yi-Chien Lai, Liang-Yi Hung
By using RNA-immunoprecipitation assay following next-generation sequencing, a group of cell cycle-related genes targeted by hnRNP Q1 were identified, including Aurora-A kinase. Overexpressed hnRNP Q1 can upregulate Aurora-A protein, but not alter the mRNA level, through enhancing the translational efficiency of Aurora-A mRNA, either in a cap-dependent or -independent manner, by interacting with the 5'-UTR of Aurora-A mRNA through its RNA-binding domains (RBDs) 2 and 3. By ribosomal profiling assay further confirmed the translational regulation of Aurora-A mRNA by hnRNP Q1...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28078810/anti-hcv-activity-from-semi-purified-methanolic-root-extracts-of-valeriana-wallichii
#13
Krishna Kumar Ganta, Anirban Mandal, Sukalyani Debnath, Banasri Hazra, Binay Chaubey
Hepatitis C virus (HCV) is a serious global health problem affecting approximately 130-150 million individuals. Presently available direct-acting anti-HCV drugs have higher barriers to resistance and also improved success rate; however, cost concerns limit their utilization, especially in developing countries like India. Therefore, development of additional agents to combat HCV infection is needed. In the present study, we have evaluated anti-HCV potential of water, chloroform, and methanol extracts from roots of Valeriana wallichii, a traditional Indian medicinal plant...
January 12, 2017: Phytotherapy Research: PTR
https://www.readbyqxmd.com/read/28077579/neuron-enriched-rna-binding-proteins-regulate-pancreatic-beta-cell-function-and-survival
#14
Jon Agraves Juan-Mateu, Tatiana H Rech, Olatz Villate, Esther Lizarraga-Mollinedo, Anna Wendt, Jean-Valery Turatsinze, Leticia A Brondani, Tarlliza R Nardelli, Tatiane C Nogueira, Jonatan L S Esguerra, Maria In Ecircs Alvelos, Piero Marchetti, Lena Eliasson, D Eacutecio L Eizirik
Pancreatic beta cell failure is the central event leading to diabetes. Beta cells share many phenotypic traits with neurons, and proper beta cell function relies on the activation of several neuronal-like transcription programs. Regulation of gene expression by alternative splicing plays a pivotal role in brain, where it affects neuronal development, function and disease. The role of alternative splicing in beta cells remains unclear, but recent data indicate that splicing alterations modulated by both inflammation and susceptibility genes for diabetes contribute to beta cell dysfunction and death...
January 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28077561/micrornas-stimulate-translation-initiation-mediated-by-hcv-like-ireses
#15
Chloé Mengardi, Taran Limousin, Emiliano P Ricci, Ricardo Soto-Rifo, Didier Decimo, Théophile Ohlmann
MicroRNAs (miRNAs) are small non-coding RNAs that control gene expression by recognizing and hybridizing to a specific sequence generally located in the 3' untranslated region (UTR) of targeted mRNAs. miRNA-induced inhibition of translation occurs during the initiation step, most probably at the level of ribosome scanning. In this process, the RNA-induced silencing complex interacts both with PABP and the 43S pre-initiation complex to disrupt scanning of the 40S ribosome. However, in some specific cases, miRNAs can stimulate translation...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28077174/mutant-hspb1-causes-loss-of-translational-repression-by-binding-to-pcbp1-an-rna-binding-protein-with-a-possible-role-in-neurodegenerative-disease
#16
Thomas Geuens, Vicky De Winter, Nicholas Rajan, Tilmann Achsel, Ligia Mateiu, Leonardo Almeida-Souza, Bob Asselbergh, Delphine Bouhy, Michaela Auer-Grumbach, Claudia Bagni, Vincent Timmerman
The small heat shock protein HSPB1 (Hsp27) is an ubiquitously expressed molecular chaperone able to regulate various cellular functions like actin dynamics, oxidative stress regulation and anti-apoptosis. So far disease causing mutations in HSPB1 have been associated with neurodegenerative diseases such as distal hereditary motor neuropathy, Charcot-Marie-Tooth disease and amyotrophic lateral sclerosis. Most mutations in HSPB1 target its highly conserved α-crystallin domain, while other mutations affect the C- or N-terminal regions or its promotor...
January 11, 2017: Acta Neuropathologica Communications
https://www.readbyqxmd.com/read/28077169/distinct-5-methylcytosine-profiles-in-poly-a-rna-from-mouse-embryonic-stem-cells-and-brain
#17
Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura, Alexandra Lusser
BACKGROUND: Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes...
January 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28077065/structure-alignment-based-classification-of-rna-binding-pockets-reveals-regional-rna-recognition-motifs-on-protein-surfaces
#18
Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang, Ling-Yun Wu
BACKGROUND: Many critical biological processes are strongly related to protein-RNA interactions. Revealing the protein structure motifs for RNA-binding will provide valuable information for deciphering protein-RNA recognition mechanisms and benefit complementary structural design in bioengineering. RNA-binding events often take place at pockets on protein surfaces. The structural classification of local binding pockets determines the major patterns of RNA recognition. RESULTS: In this work, we provide a novel framework for systematically identifying the structure motifs of protein-RNA binding sites in the form of pockets on regional protein surfaces via a structure alignment-based method...
January 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28076796/ribosomal-proteins-rpl22-and-rpl22l1-control-morphogenesis-by-regulating-pre-mrna-splicing
#19
Yong Zhang, Monique N O'Leary, Suraj Peri, Minshi Wang, Jikun Zha, Simon Melov, Dietmar J Kappes, Qing Feng, Jennifer Rhodes, Paul S Amieux, David R Morris, Brian K Kennedy, David L Wiest
Most ribosomal proteins (RP) are regarded as essential, static components that contribute only to ribosome biogenesis and protein synthesis. However, emerging evidence suggests that RNA-binding RP are dynamic and can influence cellular processes by performing "extraribosomal," regulatory functions involving binding to select critical target mRNAs. We report here that the RP, Rpl22, and its highly homologous paralog Rpl22-Like1 (Rpl22l1 or Like1) play critical, extraribosomal roles in embryogenesis. Indeed, they antagonistically control morphogenesis through developmentally regulated localization to the nucleus, where they modulate splicing of the pre-mRNA encoding smad2, an essential transcriptional effector of Nodal/TGF-β signaling...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28076795/hangover-links-nuclear-rna-signaling-to-camp-regulation-via-the-phosphodiesterase-4d-ortholog-dunce
#20
Manuela Ruppert, Mirjam Franz, Anastasios Saratsis, Laura Velo Escarcena, Oliver Hendrich, Li Ming Gooi, Isabell Schwenkert, Ansgar Klebes, Henrike Scholz
The hangover gene defines a cellular stress pathway that is required for rapid ethanol tolerance in Drosophila melanogaster. To understand how cellular stress changes neuronal function, we analyzed Hangover function on a cellular and neuronal level. We provide evidence that Hangover acts as a nuclear RNA binding protein and we identified the phosphodiesterase 4d ortholog dunce as a target RNA. We generated a transcript-specific dunce mutant that is impaired not only in ethanol tolerance but also in the cellular stress response...
January 10, 2017: Cell Reports
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