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King Isabelle I Gladstone Institutes, United - - 2014
microRNA (miRNA) maturation is regulated by interaction of particular miRNA precursors with specific RNA-binding proteins. Following their biogenesis, mature miRNAs are incorporated into the RNA-Induced Silencing Complex (RISC) where they interact with mRNAs to negatively regulate protein production. However, little is known about how mature miRNAs are regulated at the ...
Holcman D D Applied Mathematics and Computational Biology, IBENS, Ecole Normale Supérieure, 46 rue d'Ulm, 75005 , Paris, France, - - 2014
Messenger RNAs (mRNAs) can be repressed and degraded by small non-coding RNA molecules. In this paper, we formulate a coarsegrained Markov-chain description of the post-transcriptional regulation of mRNAs by either small interfering RNAs (siRNAs) or microRNAs (miRNAs). We calculate the probability of an mRNA escaping from its domain before it ...
Saramago Margarida M Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, 2781-901 Oeiras, - - 2014
Ribonucleases (RNases) are key factors in the control of biological processes, since they modulate the processing, degradation and quality control of RNAs. This review gives many illustrative examples of the role of RNases in the regulation of small RNAs (sRNAs). RNase E and PNPase have been shown to degrade the ...
Griseri Paola P 1 U.O.C Medical Genetics, Institute Giannina Gaslini , Genoa, Italy - - 2014
Control of mRNA half-life plays a central role in normal development and disease. Several pathological conditions, such as inflammation and cancer, tightly correlate with deregulation in mRNA stability of pro-inflammatory genes. Among these, pro-angiogenesis cytokines, which play a crucial role in the formation of new blood vessels, normally show rapid ...
Vreeland Amanda C AC Departments of - - 2014
The RNA-binding protein HuR binds at 3' UTR regions of target transcripts thereby protecting them against degradation. We show that HuR directly interacts with cellular retinoic acid-binding protein 2 (CRABP2), a protein known to transport RA from the cytosol to the nuclear receptor RAR. Association with CRABP2 dramatically increases the ...
Jha Bhaskar Anand BA Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D69120 Heidelberg. - - 2014
Pumilio domain RNA-binding proteins are known mainly as post-transcriptional repressors of gene expression which reduce mRNA translation and stability. Trypanosoma brucei has 11 PUF proteins. We show here that PUF2 is in the cytosol, with roughly the same number of molecules per cell as there are mRNAs. Although PUF2 exhibits ...
Baghban Roghayyeh R Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran-Qom Express Way Tehran, - - 2014
Botulinum neurotoxins (BoNTs) result in severe and often fatal disease, botulism. Common remedial measures such as equine antitoxin and human botulism immunoglobulin in turn are problematic and time-consuming. Therefore diagnosis and therapy of BoNTs are vital. The Variable domain of heavy-chain antibodies(VHH) has unique features such as ability to identify, ...
Takahashi Melissa K - - 2014
RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on timescales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this ...
Kumar Santosh - - 2014
MiRNAs are one of the key epigenetic regulators of the gene expression. They act through hybridization with their target mRNA and modulate the level of respective proteins via different mechanisms. Various cancer conditions are known to be associated with up or down regulation of the oncogenic and tumor suppressor miRNAs ...
Shi Lihua L Division of Allergy Immunology, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA - - 2014
Noncoding RNAs have been implicated in the regulation of expression of numerous genes; however, the mechanism is not fully understood. We identified bidirectional, long noncoding RNAs upstream of the TNF gene using five different methods. They arose in a region where the repressors LRRFIP1, EZH2, and SUZ12 were demonstrated to ...
Mao Yuanhui Y College of Life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, China, Bioinformatics Center, Northwest A&F University, Yangling, Shaanxi 712100, China and College of Enology, Northwest A&F University, Yangling, Shaanxi 712100, - - 2014
Messenger RNA (mRNA) secondary structure decreases the elongation rate, as ribosomes must unwind every structure they encounter during translation. Therefore, the strength of mRNA secondary structure is assumed to be reduced in highly translated mRNAs. However, previous studies in vitro reported a positive correlation between mRNA folding strength and protein ...
Chawla Geetanjali G Department of Biology, Indiana University, Bloomington, IN 47405, - - 2014
Adenosine deaminases acting on RNAs (ADARs) convert adenosine residues to inosines in primary microRNA (pri-miRNA) transcripts to alter the structural conformation of these precursors and the subsequent functions of the encoded microRNAs (miRNAs). Here we show that RNA editing by Drosophila ADAR modulates the expression of three co-transcribed miRNAs encoded ...
Xie Ping P Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. Electronic address: - - 2014
Translocation is an essential step in the elongation cycle of protein synthesis in which mRNA that is coupled with tRNAs by codon-anticodon interaction is moved through the ribosome. It has been well documented that the kinetics of mRNA translocation generally shows biphasic character. However, the physical basis of the phenomenon ...
Chabelskaya Svetlana S Université de Rennes 1, Inserm U835-UPRES EA 2311, Biochimie Pharmaceutique, 2 avenue du Prof. Léon Bernard, 35043 Rennes, - - 2014
In pathogens, the accurate programming of virulence gene expression is essential for infection. It is achieved by sophisticated arrays of regulatory proteins and ribonucleic acids (sRNAs), but in many cases their contributions and connections are not yet known. Based on genetic, biochemical and structural evidence, we report that the expression ...
Singh Aditi A Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D69120 Heidelberg, - - 2014
The trypanosome zinc finger protein ZC3H11 binds to AU-rich elements in mRNAs. It is essential for survival of the mammalian-infective bloodstream form, where it stabilizes several mRNAs including some encoding chaperones, and is also required for stabilization of chaperone mRNAs during the heat-shock response in the vector-infective procyclic form. When ...
Schueler Markus - - 2014
RNA-binding proteins (RBPs) mediate mRNA biogenesis, translation and decay. We recently developed an approach to profile transcriptome-wide RBP contacts on polyadenylated transcripts by next-generation sequencing. A comparison of such profiles from different biological conditions has the power to unravel dynamic changes in protein-contacted cis-regulatory mRNAs regions without a priori knowledge ...
Srinivasan Sumana S Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India. - - 2014
A Gene Regulatory Network (GRN) represents complex connections between genes in a cell which interact with each other through their RNA and protein expression products, thereby determining the expression levels of mRNA and proteins required for functioning of the cell. Microarray experiments yield the log fold change in mRNA abundance ...
Webb Shaun - - 2014
Nrd1 and Nab3 are essential sequence-specific yeast RNA binding proteins that function as a heterodimer in the processing and degradation of diverse classes of RNAs. These proteins also regulate several mRNA coding genes; however, it remains unclear exactly what percentage of the mRNA component of the transcriptome these proteins control. ...
de Messieres Michel M Department of Physics, Institute for Physical Science and Technology Biophysics Program, University of Maryland, College Park, - - 2014
Secondary or tertiary structure in an mRNA, such as a pseudoknot, can create a physical barrier that requires the ribosome to generate additional force to translocate. The presence of such a barrier can dramatically increase the probability that the ribosome will shift into an alternate reading frame, in which a ...
Sharawat Surender Kumar - - 2014
Objective Quantitative assessment of BAX transcripts and protein in acute myeloid leukemia (AML). Methods We quantitatively evaluated BAX gene transcripts by real-time polymerase chain reaction (TaqMan probe chemistry) and protein expression by flow cytometry. Results Consecutive 112 AML patients with a median age of 16 (1-59) years were recruited in ...
Zhang Yan Y Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of - - 2014
Prion diseases are rare and aggressive neurodegenerative disorders caused by the accumulation of misfolded, toxic conformations of the prion protein (PrP). Therapeutic strategies directed at reducing the levels of PrP offer the best chance of delaying or halting disease progression. The challenge, though, is to define pharmacologic targets that result ...
Li Jingyi Jessica JJ Department of Statistics, University of California , Berkeley, CA , USA ; Departments of Statistics and Human Genetics, University of California , Los Angeles, CA , - - 2014
Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000-16,000 molecules per cell and that differences in mRNA expression between genes explain only 10-40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated ...
Durruthy-Durruthy Jens J Institute for Stem Cell Biology and Regenerative Medicine, Department of Obstetrics and Gynecology and Department of Genetics, Stanford University, Stanford, California, United States of - - 2014
Data suggest that clinical applications of human induced pluripotent stem cells (hiPSCs) will be realized. Nonetheless, clinical applications will require hiPSCs that are free of exogenous DNA and that can be manufactured through Good Manufacturing Practice (GMP). Optimally, derivation of hiPSCs should be rapid and efficient in order to minimize ...
Xu Enshun E University of California at - - 2013
P63, a p53 family member, plays pivotal roles in epidermal development, aging, and tumorigenesis. Thus, understanding how p63 expression is controlled has biological and clinical importance. RBM24 is an RNA-binding protein and shares a high sequence similarity with RBM38, a critical regulator of p63. In the current study, we investigated ...
Tian Rui R Rui Tian, Rui-Lan Wang, Hui Xie, Wei Jin, Kang-Long Yu, Intensive Care Unit, First People's Hospital, Shanghai Jiaotong University, Shanghai 201620, - - 2013
To investigate whether miRNA-155 (miR-155) dysregulates apical junctional complex (AJC) protein expression in experimental severe acute pancreatitis (SAP). Twenty-four male BALB/c mice were randomly assigned to two groups: the SAP group (n = 12) receiving sequential intraperitoneal injection of 50 µg/kg caerulein and 10 mg/kg lipopolysaccharide over 6 h, and ...
Hassan Tidi - - 2013
Retention of abnormal alpha-1 antitrypsin activates the unfolded protein response in alpha-1 antitrypsin deficient monocytes. The regulatory role of microRNAs in unfolded protein responses and chronic obstructive pulmonary disease pathogenesis has not been investigated. To investigate microRNA expression and function in MM and ZZ monocytes and identify microRNA(s) regulating the ...
Duval Mélodie M Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire-CNRS, Strasbourg, - - 2013
Regulation of translation initiation is well appropriate to adapt cell growth in response to stress and environmental changes. Many bacterial mRNAs adopt structures in their 5' untranslated regions that modulate the accessibility of the 30S ribosomal subunit. Structured mRNAs interact with the 30S in a two-step process where the docking ...
Liu Hui-Hui - - 2013
The C1q-domain-containing (C1qDC) proteins, which are involved in various processes of vertebrates, are important pattern recognition receptors in innate immunity of invertebrates. In present study, a novel C1qDC was identified from Mytilus coruscus (designated as McC1qDC), which was 917 bp in length encoding 236 amino acids with a typical signal ...
Lutz Benjamin - - 2013
Riboswitches are part of noncoding regions of messenger RNA (mRNA) that act as RNA sensors regulating gene expression of the downstream gene. Typically, one out of two distinct conformations is formed depending on ligand binding when the transcript leaves RNA polymerase (RNAP). Elongation of the RNA chain by RNAP, folding ...
Krishnan Ramya - - 2013
The spliceosome is a dynamic ribonucleoprotein (RNP) machine that catalyzes the removal of introns during the two transesterification steps of eukaryotic pre-mRNA splicing. Here we used single-molecule fluorescence resonance energy transfer to monitor the distance of the 5' splice site (5' SS) and branch point (BP) of pre-mRNA in affinity-purified ...
Teo Guoshou - - 2013
Protein expression varies as a result of intricate regulation of synthesis and degradation of messenger RNAs (mRNA) and proteins. Studies of dynamic regulation typically rely on time course datasets of mRNA and protein expression, yet there are no statistical methods that integrate these multi-omics data and deconvolute individual regulatory processes ...
Modrak-Wojcik Anna - - 2013
Initiation is the rate-limiting step during mRNA 5' cap-dependent translation, and thus a target of a strict control in the eukaryotic cell. It is shown here by analytical ultracentrifugation and fluorescence spectroscopy that the affinity of the human translation inhibitor, eIF4E-binding protein (4E-BP1), to the translation initiation factor 4E is ...
Kato Yumiko - - 2013
MicroRNAs (miRNAs) comprise a group of small noncoding RNA molecules thought to have contributed to the evolution of vertebrate brain homogeneity and diversity. The miRNA miR-124 is well conserved between invertebrates and vertebrates and is expressed abundantly in the central nervous system (CNS). We identified miR-124 in the medaka, Oryzias ...
Mo Sudong S State Key Laboratory of Virology; College of Life Sciences; Wuhan University; Wuhan, Hubei - - 2013
Transcription pause release from gene promoters has been recognized to be a critical point for transcriptional regulation in higher eukaryotes. Recent studies suggest that regulatory RNAs are extensively involved in transcriptional control, which may enlist various RNA binding proteins. We recently showed a key role of SRSF2, a member of ...
King H A - - 2013
Post-transcriptional control of gene expression is mediated by the interaction of RNA-binding proteins with their cognate mRNAs that specifically regulate their stability, localization and translation. mRNA-binding proteins are multifunctional and it has been proposed therefore that a combinatorial RNA-binding protein code exists that allows specific protein sub-complexes to control cytoplasmic ...
Dalton Ryan P - - 2013
Olfactory receptor (OR) expression requires the transcriptional activation of 1 out of 1,000s of OR alleles and a feedback signal that preserves this transcriptional choice. The mechanism by which olfactory sensory neurons (OSNs) detect ORs to signal to the nucleus remains elusive. Here, we show that OR proteins generate this ...
Lee Sung Ho - - 2013
Peptidyl-prolyl Isomerase 1 (Pin1) is the only enzyme known to catalyze isomerization of the pSer/Thr-Pro peptide bond. Pin1 induces conformational change of substrates and subsequently regulates diverse cellular processes. However, its role in osteoblast differentiation is not well understood. Here we show that Pin1 enhances osteoblast differentiation. Pin1 interacts and ...
Yeh Yen-Hsiu - - 2013
The interferon-stimulated gene 15 (ISG15)- and ubiquitin-conjugation pathways play roles in hypoxic and inflammatory responses. To identify interaction(s) between these two tumor microenvironments, we investigated the effect of ISG15 on the activity of the master hypoxic transcription factor HIF-1α. Interferon and desferoxamine treatments were used to induce the expression of ...
De Rubeis Silvia S VIB Center for Biology of Disease, KULeuven, 3000 Leuven, Belgium; Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), KULeuven, 3000 Leuven, - - 2013
The CYFIP1/SRA1 gene is located in a chromosomal region linked to various neurological disorders, including intellectual disability, autism, and schizophrenia. CYFIP1 plays a dual role in two apparently unrelated processes, inhibiting local protein synthesis and favoring actin remodeling. Here, we show that brain-derived neurotrophic factor (BDNF)-driven synaptic signaling releases CYFIP1 ...
Orom Ulf Andersson - - 2013
Enhancer-associated long noncoding RNAs act over long distances and across chromosomes to activate transcription at distal promoters. Here, we address the latest advances made toward understanding the role of long noncoding RNA expression and the involvement of these RNAs in enhancer function through association with protein factors and modulation of ...
Livesay S Brent - - 2013
The spliceosome is a dynamic macromolecular machine that catalyzes the removal of introns from pre-mRNA, yielding mature message. Schizosaccharomyces pombe Cwf10 (homolog of Saccharomyces cerevisiae Snu114 and human U5-116K), an integral member of the U5 snRNP, is a GTPase that has multiple roles within the splicing cycle. Cwf10/Snu114 family members ...
Yang Yun - - 2013
Adenosine to inosine (A-to-I) RNA editing is the most abundant editing event in animals. It converts adenosine to inosine in double-stranded RNA regions through the action of the adenosine deaminase acting on RNA (ADAR) proteins. Editing of pre-mRNA coding regions can alter the protein codon and increase functional diversity. However, ...
Islam Rabia - - 2013
Regulation of the hematopoietic transcription factor PU.1, a member of the ETS family, plays a critical role in the development of blood cells and in leukemia. The dosage of PU.1 has been shown to cause a shift in myelomonocytic progenitor fate. Pin1 is a unique substrate-specific enzyme that can isomerize ...
Liu Zhijun - - 2013
To investigate the effect of HSV-1 infection via TLR3 on the transcriptional activity of NF-kappaB and the expression of cytokines TNF-alpha and IL-6 in astrocytes. HSV-1-infected primary astrocytes were cultured until the third passage and the mRNA and protein levels of TLR3, NF-kappaB, TNF-alpha, and IL-6 were assessed by immunofluorescence, ...
Wang Min - - 2013
MicroRNAs (miRNAs) are an important gene regulator, controlling almost all biological and metabolic processes, in both plants and animals. In this study, we investigated the effect of drought and salinity stress on the expression of miRNAs and their targets in cotton (Gossypium hirsutum L.). Our results show that the expression ...
Trotta Edoardo - - 2013
Codons that code for the same amino acid are often used with unequal frequencies. This phenomenon is termed codon bias. Here, we report a computational analysis of codon bias in yeast using experimental and theoretical genome-wide data. We show that the most used codons in highly expressed genes can be ...
Qin Jing - - 2013
MicroRNAs (miRNAs) regulate gene expression through translational repression and RNA degradation. Recently developed high-throughput proteomic methods measure gene expression changes at protein levels, and therefore can reveal the direct effects of miRNAs translational repression. Here, we present a web server, ProteoMirExpress that integrates proteomic and mRNA expression data together to ...
Zhang Yuanyuan - - 2013
Brassinosteroids (BRs) regulate many physiological processes during plant development, including flowering. However, little is known about the components of BR signaling that mediate flowering. Here, we report that BRASSINAZOLE-RESISTANT1 (BZR1), the conformation of which is altered by a cyclophilin (CYP20-2), binds cis-elements in the FLOWERING LOCUS D (FLD) promoter to ...
Silva Inês Jesus - - 2013
Small noncoding RNAs (sRNAs) are usually expressed in the cell to face a variety of stresses. In this report we disclose the first target for SraL (also known as RyjA), a sRNA present in many bacteria, which is highly induced in stationary phase. We also demonstrate that this sRNA is ...
Chen Siqi - - 2013
BACKGROUND: Guanine-rich sequence of c-myc nucleic hypersensitive element (NHE) III1 is known to fold in G-quadruplex and subsequently serves as transcriptional silencer. Cellular nucleic-acid-binding protein (CNBP), a highly conserved zinc-finger protein with multiple biological functions, could bind to c-myc NHE III1 region, specifically to the single strand G-rich sequence. METHODS: ...
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