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https://www.readbyqxmd.com/read/29149906/forebrain-specific-conditional-silencing-of-staufen2-alters-synaptic-plasticity-learning-and-memory-in-rats
#1
Stefan M Berger, Iván Fernández-Lamo, Kai Schönig, Sandra M Fernández Moya, Janina Ehses, Rico Schieweck, Stefano Clementi, Thomas Enkel, Sascha Grothe, Oliver von Bohlen Und Halbach, Inmaculada Segura, José María Delgado-García, Agnès Gruart, Michael A Kiebler, Dusan Bartsch
BACKGROUND: Dendritic messenger RNA (mRNA) localization and subsequent local translation in dendrites critically contributes to synaptic plasticity and learning and memory. Little is known, however, about the contribution of RNA-binding proteins (RBPs) to these processes in vivo. RESULTS: To delineate the role of the double-stranded RBP Staufen2 (Stau2), we generate a transgenic rat model, in which Stau2 expression is conditionally silenced by Cre-inducible expression of a microRNA (miRNA) targeting Stau2 mRNA in adult forebrain neurons...
November 17, 2017: Genome Biology
https://www.readbyqxmd.com/read/29142127/epstein-barr-virus-protein-eb2-stimulates-translation-initiation-of-mrnas-through-direct-interactions-with-both-pabp-and-eif4g
#2
Fabrice Mure, Baptiste Panthu, Isabelle Zanella-Cléon, Frédéric Delolme, Evelyne Manet, Théophile Ohlmann, Henri Gruffat
Epstein-Barr virus (EBV) expresses several mRNAs produced from intronless genes that could potentially be unfavorably translated compared to cellular spliced mRNAs. To overcome this situation, the virus encodes an RNA-binding protein (RBP) called EB2, previously found to both facilitate the export of nuclear mRNAs and increase their translational yield. Here, we show that EB2 binds both nuclear and cytoplasmic cap-binding complexes (respectively, CBC and eIF4F) as well as the poly(A)-binding protein (PABP) to enhance translation initiation of a given mRNP...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29140459/rbm45-competes-with-hdac1-for-binding-to-fus-in-response-to-dna-damage
#3
Juanjuan Gong, Min Huang, Fengli Wang, Xiaolu Ma, Hongmei Liu, Yingfeng Tu, Lingyu Xing, Xuefei Zhu, Hui Zheng, Junjie Fang, Xiaoling Li, Qiaochu Wang, Jiuqiang Wang, Zhongshuai Sun, Xi Wang, Yun Wang, Caixia Guo, Tie-Shan Tang
DNA damage response (DDR) is essential for genome stability and human health. Recently, several RNA binding proteins (RBPs), including fused-in-sarcoma (FUS), have been found unexpectedly to modulate this process. The role of FUS in DDR is closely linked to the pathogenesis of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease that affects nerve cells in the brain and the spinal cord. Given that RBM45 is also an ALS-associated RBP, we wondered whether RBM45 plays any function during this process...
November 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29134320/artificial-intelligence-in-neurodegenerative-disease-research-use-of-ibm-watson-to-identify-additional-rna-binding-proteins-altered-in-amyotrophic-lateral-sclerosis
#4
Nadine Bakkar, Tina Kovalik, Ileana Lorenzini, Scott Spangler, Alix Lacoste, Kyle Sponaugle, Philip Ferrante, Elenee Argentinis, Rita Sattler, Robert Bowser
Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease with no effective treatments. Numerous RNA-binding proteins (RBPs) have been shown to be altered in ALS, with mutations in 11 RBPs causing familial forms of the disease, and 6 more RBPs showing abnormal expression/distribution in ALS albeit without any known mutations. RBP dysregulation is widely accepted as a contributing factor in ALS pathobiology. There are at least 1542 RBPs in the human genome; therefore, other unidentified RBPs may also be linked to the pathogenesis of ALS...
November 13, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/29130215/individual-nucleotide-resolution-uv-cross-linking-and-immunoprecipitation-iclip-to-determine-protein-rna-interactions
#5
Christopher R Sibley
RNA-binding proteins (RBPs) interact with and determine the fate of many cellular RNA transcripts. In doing so they help direct many essential roles in cellular physiology, while their perturbed activity can contribute to disease etiology. In this chapter we detail a functional genomics approach, termed individual nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP), that can determine the interactions of RBPs with their RNA targets in high throughput and at nucleotide resolution. iCLIP achieves this by exploiting UV-induced covalent cross-links formed between RBPs and their target RNAs to both purify the RBP-RNA complexes under stringent conditions, and to cause reverse transcription stalling that then identifies the direct cross-link sites in the high throughput sequenced cDNA libraries...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29130213/systematic-detection-of-poly-a-rna-interacting-proteins-and-their-differential-binding
#6
Miha Milek, Markus Landthaler
RNA-binding proteins are dynamic posttranscriptional regulators of gene expression. Identification of mRNA-binding proteins in a given experimental setting is thus of great importance. We describe a procedure to enrich for direct poly(A)(+) RNA protein binders by 4-thiouridine-enhanced UV cross-linking and oligo(dT) purification. Subsequent nuclease-mediated release of RNA-binding proteins (RBPs) from mRNA allows for detection of eluted proteins by mass spectrometry. In addition, we provide a comparative approach to detect differences in RBP binding activity upon a biological stimulus...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29130207/rna-live-imaging-in-the-model-microorganism-ustilago-maydis
#7
Sabrina Zander, Kira Müntjes, Michael Feldbrügge
An essential feature of protein expression is the tight regulation of when and where a protein is translated from its cognate mRNA. This spatiotemporal expression is particularly important in guaranteeing the correct and efficient targeting of proteins to defined subcellular sites. In order to achieve local translation, mRNAs must be deposited at specific locations. A common mechanism is the active transport of mRNAs along the actin or microtubule cytoskeleton. To study such dynamic transport processes in vivo RNA live imaging is the method of choice...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29127290/ksrp-specifies-monocytic-and-granulocytic-differentiation-through-regulating-mir-129-biogenesis-and-runx1-expression
#8
Hongmei Zhao, Xiaoshuang Wang, Ping Yi, Yanmin Si, Puwen Tan, Jinrong He, Shan Yu, Yue Ren, Yanni Ma, Junwu Zhang, Dong Wang, Fang Wang, Jia Yu
RNA-binding proteins (RBPs) integrate the processing of RNAs into post-transcriptional gene regulation, but the direct contribution of them to myeloid cell specification is poorly understood. Here, we report the first global RBP transcriptomic analysis of myeloid differentiation by combining RNA-seq analysis with myeloid induction in CD34(+) hematopoietic progenitor cells. The downregulated expression of the KH-Type Splicing Regulatory Protein (KSRP) during monocytopoiesis and up-regulated expression during granulopoiesis suggests that KSRP has divergent roles during monocytic and granulocytic differentiation...
November 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/29127211/mechanistic-implications-of-enhanced-editing-by-a-hypertribe-rna-binding-protein
#9
Weijin Xu, Reazur Rahman, Michael Rosbash
We previously developed TRIBE, a method for the identification of cell-specific RNA binding protein targets. TRIBE expresses an RBP of interest fused to the catalytic domain (cd) of the RNA editing enzyme ADAR and performs Adenosine-to-Inosine editing on RNA targets of the RBP. However, target identification is limited by the low editing efficiency of the ADARcd. Here we describe HyperTRIBE, which carries a previously characterized hyperactive mutation (E488Q) of the ADARcd. HyperTRIBE identifies dramatically more editing sites, many of which are also edited by TRIBE but at a much lower editing frequency...
November 10, 2017: RNA
https://www.readbyqxmd.com/read/29122885/c-ebp%C3%AE-is-regulated-by-the-rank-cytoplasmic-ivvy535-538-motif-and-stimulates-osteoclastogenesis-more-strongly-than-c-fos
#10
Joel Jules, Wei Chen, Xu Feng, Yi-Ping Li
Binding of RANKL to its receptor RANK on osteoclast (OC) precursors upregulates c-Fos and C/EBPα, two critical OC transcription factors. However, the effects of c-Fos and C/EBPα on osteoclastogenesis have not been compared. Herein, we demonstrate that overexpression of c-Fos or C/EBPα in OC precursors upregulates OC genes and initiates osteoclastogenesis independently of RANKL. However, while C/EBPα upregulated c-Fos, c-Fos failed to upregulate C/EBPα in OC precursors. Consistently, C/EBPα overexpression more strongly promoted OC differentiation than did c-Fos overexpression...
November 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29122359/prognostic-impact-of-rita-expression-in-patients-with-anal-squamous-cell-carcinoma-treated-with-chemoradiotherapy
#11
Franz Rödel, Kerstin Steinhäuser, Nina-Naomi Kreis, Alexandra Friemel, Daniel Martin, Ulrike Wieland, Margret Rave-Fränk, Panagiotis Balermpas, Emmanouil Fokas, Frank Louwen, Claus Rödel, Juping Yuan
BACKGROUND: RBP-J interacting and tubulin-associated protein (RITA) has been identified as a negative regulator of the Notch signalling pathway and its deregulation is involved in the pathogenesis of several tumour entities. RITA's impact on the response of anal squamous cell carcinoma (SCC) to anticancer treatment, however, remains elusive. MATERIALS AND METHODS: In our retrospective study immunohistochemical evaluation of RITA was performed on 140 pre-treatment specimens and was correlated with clinical and histopathologic characteristics and clinical endpoints cumulative incidence of local control (LC), distant recurrence (DC), disease-free survival (DFS) and overall survival (OS)...
November 6, 2017: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
https://www.readbyqxmd.com/read/29109951/rna-binding-protein-regulation-and-cross-talk-in-the-control-of-au-rich-mrna-fate
#12
REVIEW
Sofía M García-Mauriño, Francisco Rivero-Rodríguez, Alejandro Velázquez-Cruz, Marian Hernández-Vellisca, Antonio Díaz-Quintana, Miguel A De la Rosa, Irene Díaz-Moreno
mRNA metabolism is tightly orchestrated by highly-regulated RNA Binding Proteins (RBPs) that determine mRNA fate, thereby influencing multiple cellular functions across biological contexts. Here, we review the interplay between six well-known RBPs (TTP, AUF-1, KSRP, HuR, TIA-1, and TIAR) that recognize AU-rich elements (AREs) at the 3' untranslated regions of mRNAs, namely ARE-RBPs. Examples of the links between their cross-regulations and modulation of their targets are analyzed during mRNA processing, turnover, localization, and translational control...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29080175/investigating-ornithine-decarboxylase-posttranscriptional-regulation-via-a-pulldown-assay-using-biotinylated-transcripts
#13
Anh Mai, Shannon L Nowotarski
Ornithine decarboxylase (ODC) is the first rate-limiting enzyme in the polyamine biosynthetic pathway. It has been well documented that ODC is tightly regulated at the levels of transcription, posttranscriptional changes in RNA, and protein degradation during normal conditions and that these processes are dysregulated during tumorigenesis. Moreover, it has been recently shown that ODC is posttranscriptionally regulated by RNA binding proteins (RBPs) which can bind to the ODC mRNA transcript and alter its stability and translation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29079670/the-levels-of-adipokines-and-hormonal-changes-during-the-menstrual-cycle-in-normal-weight-women
#14
Katarzyna Wyskida, Grzegorz Franik, Tomasz Wikarek, Aleksander Owczarek, Alham Delroba, Jerzy Chudek, Jerzy Sikora, Magdalena Olszanecka-Glinianowicz
CONTEXT: The aim of this study was to assess plasma leptin, adiponectin, resistin, visfatin/NAMPT, omentin-1, vaspin, apelin, TNF-α, IL-6 and RBP4 levels in relation to hormonal changes during the menstrual cycle in young, healthy, normal-weight women. METHODS: The study involved 52 young, healthy, normal-weight women. Anthropometric parameters, body composition and levels of plasma leptin, adiponectin, resistin, visfatin/NAMPT, omentin-1, vaspin, apelin, TNF-α, IL-6 and RBP4 in addition to serum FSH, LH, estradiol, progesterone, 17-OH progesterone, androgens, SHBG and insulin concentrations were measured during a morning in fasting state three times: between days 2-4, days 12-14 and days 24-26 of the menstrual cycle...
October 27, 2017: Endocrine Connections
https://www.readbyqxmd.com/read/29076943/computational-parametric-study-of-the-axial-and-radial-clearances-in-a-centrifugal-rotary-blood-pump
#15
Mohammad Amin Rezaienia, Gordon Paul, Eldad Avital, Martin T Rothman, Theodosios Korakianitis
In centrifugal rotary blood pumps (RBP), clearances are a critical parameter in determining blood trauma. This study investigates the effect of axial clearance (Cax) and radial clearance (Crad) on the hydrodynamic and hemolytic performance of a centrifugal RBP. A centrifugal pump was parameterized so that it could be defined by geometric variables Cax and Crad. Optimal Latin hypercube sampling was used to determine design points based on Cax, Crad, and rotor speed (ω). For each design point, a computational simulation was conducted to determine efficiency (η) and normalized index of hemolysis (NIH)...
October 23, 2017: ASAIO Journal: a Peer-reviewed Journal of the American Society for Artificial Internal Organs
https://www.readbyqxmd.com/read/29069457/nol12-is-a-multifunctional-rna-binding-protein-at-the-nexus-of-rna-and-dna-metabolism
#16
Daniel D Scott, Christian Trahan, Pierre J Zindy, Lisbeth C Aguilar, Marc Y Delubac, Eric L Van Nostrand, Srivathsan Adivarahan, Karen E Wei, Gene W Yeo, Daniel Zenklusen, Marlene Oeffinger
To counteract the breakdown of genome integrity, eukaryotic cells have developed a network of surveillance pathways to prevent and resolve DNA damage. Recent data has recognized the importance of RNA binding proteins (RBPs) in DNA damage repair (DDR) pathways. Here, we describe Nol12 as a multifunctional RBP with roles in RNA metabolism and genome maintenance. Nol12 is found in different subcellular compartments-nucleoli, where it associates with ribosomal RNA and is required for efficient separation of large and small subunit precursors at site 2; the nucleoplasm, where it co-localizes with the RNA/DNA helicase Dhx9 and paraspeckles; as well as GW/P-bodies in the cytoplasm...
October 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29065764/recognition-and-stabilization-of-geranylgeranylated-human-rab5-by-the-gdp-dissociation-inhibitor-gdi
#17
Eileen Edler, Matthias Stein
The small GTPase Rab5 is the key regulator of early endosomal fusion. It is post-translationally modified by covalent attachment of two geranylgeranyl (GG) chains to adjacent cysteine residues of the C-terminal hypervariable region (HVR). The GDP dissociation inhibitor (GDI) recognizes membrane-associated Rab5(GDP) and serves to release it into the cytoplasm where it is kept in a soluble state. A detailed new structural and dynamic model for human Rab5(GDP) recognition and binding with human GDI at the early endosome membrane and in its dissociated state is presented...
October 25, 2017: Small GTPases
https://www.readbyqxmd.com/read/29061699/hud-and-the-survival-motor-neuron-protein-interact-in-motoneurons-and-are-essential-for-motoneuron-development-function-and-mrna-regulation
#18
Le Thi Hao, Phan Q Duy, Min An, Jared Talbot, Chitra C Iyer, Marc Wolman, Christine E Beattie
Motoneurons establish a critical link between the central nervous system and muscles. If motoneurons do not develop correctly, they cannot form the required connections resulting in movement defects or paralysis. Compromised development can also lead to degeneration since the motoneuron is not set up to function properly. Little is known, however, regarding the mechanisms that control vertebrate motoneuron development particularly the later stages of axon branch and dendrite formation. The motoneuron disease spinal muscular atrophy (SMA) is caused by low levels of the survival motor neuron (SMN) protein leading to defects in vertebrate motoneuron development and synapse formation...
October 23, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/29059375/translational-co-regulation-of-a-ligand-and-inhibitor-by-a-conserved-rna-element
#19
Andreas Zaucker, Agnieszka Nagorska, Pooja Kumari, Nikolai Hecker, Yin Wang, Sizhou Huang, Ledean Cooper, Lavanya Sivashanmugam, Shruthi VijayKumar, Jan Brosens, Jan Gorodkin, Karuna Sampath
In many organisms, transcriptional and post-transcriptional regulation of components of pathways or processes has been reported. However, to date, there are few reports of translational co-regulation of multiple components of a developmental signaling pathway. Here, we show that an RNA element which we previously identified as a dorsal localization element (DLE) in the 3'UTR of zebrafish nodal-related1/squint (ndr1/sqt) ligand mRNA, is shared by the related ligand nodal-related2/cyclops (ndr2/cyc) and the nodal inhibitors, lefty1 (lft1) and lefty2 mRNAs...
October 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29057311/targeting-rna-binding-protein-in-prostate-cancer
#20
Teng Fei
RNA binding protein (RBP) controls multiple aspects of RNA metabolism and plays crucial roles in many physiopathological contexts, including cancer. We recently identified an RBP HNRNPL as a novel prostate cancer dependency via regulation of RNA splicing, suggesting the potential to target RBP or RBP-RNA interaction to treat cancer.
2017: Molecular & Cellular Oncology
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