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Gebhardt Marie L ML Max Delbrück Center for Molecular Medicine, Berlin 13125, - - 2014
There are groups of genes that need coordinated repression in multiple contexts, for example if they code for proteins that work together in a pathway or in a protein complex. Redundancy of biological regulatory networks implies that such coordinated repression might occur at both the pre- and post-transcriptional level, though ...
Li Caili - - 2014
MYB is the largest plant transcription factor gene family playing vital roles in plant growth and development. However, it has not been systematically studied in Salvia miltiorrhiza, an economically important medicinal plant. Here we report the genome-wide identification and characterization of 110 R2R3-MYBs, the largest subfamily of MYBs in S. ...
Wang Shufen S Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, - - 2014
The tomato (Solanum lycopersicum) protein MADS-RIN plays important roles in fruit ripening. In this study, the functions of two homologous tomato proteins, FUL1 and FUL2, which contain conserved MIKC domains that typify plant MADS-box proteins, and which interact with MADS-RIN, were analysed. Transgenic functional analysis showed that FUL1 and FUL2 ...
Marquardt Sebastian S Department of Cell & Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, - - 2014
Antisense transcription is widespread in many genomes; however, how much is functional is hotly debated. We are investigating functionality of a set of long noncoding antisense transcripts, collectively called COOLAIR, produced at Arabidopsis FLOWERING LOCUS C (FLC). COOLAIR initiates just downstream of the major sense transcript poly(A) site and terminates either ...
Song Xiaodong X Medicine Research Center, Binzhou Medical University, Yantai, - - 2014
Long non-coding RNAs (lncRNAs) are involved in various pathophysiologic processes and human diseases. However, their dynamics and corresponding functions in pulmonary fibrosis remain poorly understood. In this study, portions of lncRNAs adjacent or homologous to protein-coding genes were determined by searching the UCSC genome bioinformatics database. This was found to ...
Marano Robert J RJ Ear Science Institute Australia (R.J.M.), Subiaco, Western Australia, 6008, Australia; Ear Sciences Centre, School of Surgery (R.J.M.), The University of Western Australia, Nedlands, Western Australia, 6009, Australia; and Department of Cancer Biology (N.B-J.), University of Cincinnati Medical School, Cincinnati, Ohio - - 2014
Prolactin (PRL) is an important hormone with many diverse functions. Although it is predominantly produced by lactrotrophs of the pituitary there are a number of other organs, cells, and tissues in which PRL is expressed and secreted. The impact of this extrapituitary PRL (ePRL) on localized metabolism and cellular functions ...
Celton Jean-Marc JM INRA, UMR1345 Institut de Recherche en Horticulture et Semences, 49071, Beaucouzé, - - 2014
Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of ...
Ramakrishnan Kalpana K Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Avenue (MC567), Chicago, IL 60607, - - 2014
M4 is a multifunctional neuron in the C. elegans pharynx that can both stimulate peristaltic contractions of the muscles in the pharyngeal isthmus and function systemically to regulate an enhanced sensory response under hypoxic conditions. Here we identify a third function for M4 that depends on activation of the TGF-ß ...
Moore Ashleigh E AE Alexandria Center for Life Sciences, New York University School of Medicine, New York, NY, - - 2014
Regulated messenger RNA (mRNA) decay is an essential mechanism that governs proper control of gene expression. In fact, many of the most physiologically potent proteins are encoded by short-lived mRNAs, many of which contain AU-rich elements (AREs) in their 3'-untranslated region (3'-UTR). AREs target mRNAs for post-transcriptional regulation, generally rapid ...
Ruby Plant Tissue Culture Division, National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, Maharashtra, - - 2014
Health related benefits of isoflavones such as genistein are well known. Glycosylation of genistein yields different glycosides like genistein 7-O-glycoside (genistin) and genistein 4'-O-glycoside (sophoricoside). This is the first report on isolation, cloning and functional characterization of a glycosyltransferase specific for genistein 4'-O-glucoside from Bacopa monniera, an important Indian medicinal ...
Salmanidis Marika M Centre for Cancer Biology, University of South Australia, Adelaide, - - 2014
The function of microRNAs are well characterised in the cytoplasm, where they direct an Argonaute-containing complex to target and repress mRNAs. More recently, regulatory roles for microRNAs and Argonaute have also been reported in the nucleus where microRNAs guide Argonaute to target gene promoters and directly regulate transcription in either ...
Lam Michael T Y MT Department of Cellular and Molecular Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, - - 2014
A large portion of the human genome is transcribed into RNAs without known protein-coding functions, far outnumbering coding transcription units. Extensive studies of long noncoding RNAs (lncRNAs) have clearly demonstrated that they can play critical roles in regulating gene expression, development, and diseases, acting both as transcriptional activators and repressors. ...
Kagias Konstantinos - - 2014
Quantitative real-time PCR (qPCR) has become the "gold standard" for measuring expression levels of individual miRNAs. However, little is known about the validity of reference miRNAs, the improper use of which can result in misleading interpretation of data. Here we undertook a systematic approach to identify highly stable miRNAs in ...
Magnani Enrico E 1 Institut Jean-Pierre Bourgin, INRA, Centre de - - 2014
Truncated transcription factor-like proteins called microProteins can modulate transcription factor activities, thereby increasing transcriptional regulatory complexity. To understand their prevalence, evolution, and function, we predicted over 400 genes that encode putative microProteins from Arabidopsis thaliana using a bioinformatics pipeline, and validated two novel microProteins involved in flowering time and response ...
Micale Valeria V Istituto per l'Ambiente Marino Costiero, Consiglio Nazionale delle Ricerche, Messina, Italy. Electronic address: - - 2014
A short overview on the regional distribution of the gastro-intestinal peptide hormone cholecystokin (CCK) in fish is presented. In particular, the results of molecular and immunological studies on seabreams, Diplodus puntazzo and Diplodus sargus, are reported, which, by demonstrating CCK in the hindgut, open new questions regarding the functional role ...
Li Yue Y Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, - - 2014
Aberrant microRNA (miRNA) expression is implicated in tumorigenesis. The underlying mechanisms are unclear because the regulations of each miRNA on potentially hundreds of mRNAs are sample specific. We describe a novel approach to infer Probabilistic MiRNA-mRNA Interaction Signature ('ProMISe') from a single pair of miRNA-mRNA expression profile. Our model considers mRNA and ...
Sawada Reiko R The Hakubi Project, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan. Electronic address: - - 2014
Behavioral studies have shown that emotional facial expressions are detected more rapidly and accurately than are neutral expressions. However, the neural mechanism underlying this efficient detection has remained unclear. To investigate this mechanism, we measured event-related potentials (ERPs) during a visual search task in which participants detected the normal emotional ...
Takeuchi Takahiro T Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University (TWIns), Tokyo, - - 2014
CRY proteins can be classified into several groups based on their phylogenetic relationships, and they function as a photoreceptor, a photolyase, and/or a transcriptional repressor of the circadian clock. In order to elucidate the expression profile and functional diversity of CRYs in vertebrates, we focused on XtCRY4, a member of ...
Minenko Ekaterina E Gregor-Mendel-Straße 4, 85350 Freising, - - 2014
Hydrophobins are small secreted proteins ubiquitously found in filamentous fungi. Some hydrophobins were shown to have functions in fungal development, while others lack known function. Class II hydrophobins from Fusarium graminearum and Fusarium culmorum are characterized by formation of low stability aggregates and their solubility in organic solvents. They are ...
Beketaev Ilimbek I Center for Stem Cell Engineering, Department of Basic Research Laboratories, Texas Heart Institute at St. Luke's Episcopal Hospital, 6770 Bertner Avenue, MC 2-255, Houston, TX - - 2014
The role of the T-box transcription factor Tbx5 in heart and limb development has been well documented; however, how posttranslational modification is involved in mediating its activity is unknown. Here we report that Tbx5 is a novel target by SUMO conjugation, a posttranslational modification that is involved in a variety ...
Leidner Julia J Institute of Physiological Chemistry, University of Ulm, Albert-Einstein-Allee 23, 89070, Ulm, - - 2014
The NF-κB subunit RelB is known to act either as an activator or repressor of NF-κB-dependent gene expression. The RelB-p52 heterodimer, for instance, is the key element of the alternative NF-κB signaling pathway supporting the expression of a subset of NF-κB target genes. By contrast, RelB is crucial for the ...
Brousse Cécile C INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France, AgroParisTech, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France and Department of Biology and Plant Biology Ph.D. Program, Pennsylvania State University, University Park, PA 16802, - - 2014
Plant microRNAs (miRNAs) typically form near-perfect duplexes with their targets and mediate mRNA cleavage. Here, we describe an unconventional miRNA target of miR398 in Arabidopsis, an mRNA encoding the blue copper-binding protein (BCBP). BCBP mRNA carries an miR398 complementary site in its 5'-untranslated region (UTR) with a bulge of six ...
Gomes Ana S - - 2014
Flatfish metamorphosis is a hormone regulated post-embryonic developmental event that transforms a symmetric larva into an asymmetric juvenile. In altricial-gastric teleost fish, differentiation of the stomach takes place after the onset of first feeding, and during metamorphosis dramatic molecular and morphological modifications of the gastrointestinal (GI-) tract occur. Here we ...
Capella Matías M Instituto de Agrobiotecnología del Litoral, CONICET-UNL, CC 242 Ciudad Universitaria, 3000, Santa Fe, - - 2014
Different members of the HD-Zip I family of transcription factors exhibit differential AHA-like activation motifs, able to interact with proteins of the basal transcriptional machinery. Homeodomain-leucine zipper proteins are transcription factors unique to plants, classified in four subfamilies. Subfamily I members have been mainly associated to abiotic stress responses. Several ...
Yan Yong-Bin YB State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing, - - 2014
Lengths of the eukaryotic messenger RNA (mRNA) poly(A) tails are dynamically changed by the opposing effects of poly(A) polymerases and deadenylases. Modulating poly(A) tail length provides a highly regulated means to control almost every stage of mRNA lifecycle including transcription, processing, quality control, transport, translation, silence, and decay. The existence ...
Takahashi Paula P Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo - USP. Av. Bandeirantes, 3900 - Monte Alegre - 14049-900, Ribeirão Preto, SP, - - 2014
Type 1 diabetes mellitus (T1DM) results from an autoimmune attack against the insulin-producing pancreatic β-cells, leading to elimination of insulin production. The exact cause of this disorder is still unclear. Although the differential expression of microRNAs (miRNAs), small non-coding RNAs that control gene expression in a post-transcriptional manner, has been ...
Pandey Shree P - - 2014
Conceptual parallels exist between bacterial and eukaryotic small-RNA (sRNA) pathways, yet relatively little is known about which protein may recognize and recruit bacterial sRNAs to interact with targets. In eukaryotes, Argonaute (AGO) proteins discharge such functions. The highly conserved bacterial YbeY RNase has structural similarities to the MID domain of ...
Sabbatini Maria Eugenia ME Department of Biological Sciences, Georgia Regents University,. Electronic address: - - 2014
Adenylyl cyclases (ACs) are a group of widely distributed enzymes whose functions are very diverse. There are nine known transmembrane AC isoforms activated by Gαs. Each has its own pattern of expression in the digestive system and differential regulation of function by Ca(2+) and other intracellular signals. In addition to ...
Tiruppathi Chinnaswamy C Department of Pharmacology and the Center for Lung and Vascular Biology, University of Illinois, Chicago, Illinois, - - 2014
Here we found that the transcription repressor DREAM bound to the promoter of the gene encoding A20 to repress expression of this deubiquitinase that suppresses inflammatory NF-κB signaling. DREAM-deficient mice displayed persistent and unchecked A20 expression in response to endotoxin. DREAM functioned by transcriptionally repressing A20 through binding to downstream ...
Geach Timothy J TJ Department of Cell and Developmental Biology, University College London, Anatomy Building, Gower Street, London, WC1E 6BT, - - 2014
Lysophosphatidic acid (LPA) has wide-ranging effects on many different cell types, acting through G-protein-coupled receptors such as LPAR6. We show that Xenopus lpar6 is expressed from late blastulae and is enriched in the mesoderm and dorsal ectoderm of early gastrulae. Expression in gastrulae is an early response to FGF signalling. ...
Han Yi-Qiang YQ College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China; The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, - - 2014
Objective: MicroRNAs (miRNAs) are genome-encoded, small non-coding RNAs that play important functions in development, biotic and abiotic stress responses, and other processes. Our aim was to explore the regulation of miRNA expression. Methods: We used bioinformatics methods to predict the core promoters of 440 miRNAs identified from a soybean (Glycine ...
Rule D M - - 2014
Commercial field corn (Zea mays L.) hybrids transformed to express some or all of the lepidopteran insect-resistant traits present in SmartStax corn hybrids were evaluated for insecticidal efficacy against a wide range oflepidopteran corn pests common to the northern United States, during 2008 to 2011 at locations in 15 states. ...
Vance Keith W KW MRC Functional Genomics Unit, University of Oxford, Oxford - - 2014
Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis. Here, we describe the genomically local and more distal functions of Paupar, a ...
Liu Yan Y Department of Ophthalmology, Huashan Hospital Affiliated to Fudan University, Shanghai, 200040, People's Republic of - - 2014
Pituitary homeobox 2 (PITX2), a Paired-like homeodomain transcription factor and a downstream effector of Wnt/β-catenin signaling, plays substantial roles in embryonic development and human disorders. The mechanism of its functions, however, is not fully understood. In this study, we demonstrated that PITX2 associated with histone H3 lysine 4 (H3K4) methyltransferase ...
Li Zhenye Z Beijing Neurosurgical Institute, Capital Medical University, 6 Tiantan Xili, Dongcheng District, Beijing, 10050, People's Republic of - - 2014
It is becoming evident that long non-coding RNAs (lncRNAs) participate in diverse biological processes via distinct mechanisms. Many lncRNAs have altered expression and likely to have functional roles in tumorigenesis. Although loss of maternally-expressed gene 3 (MEG3) expression has been detected in non-functioning pituitary adenomas (NFPAs), there are no published ...
Coego Alberto A Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, - - 2014
Transcription factors (TFs) are key regulators of gene expression in all organisms. In eukaryotes, TFs are often represented by functionally redundant members of large gene families. Overexpression might prove a means to unveil the biological functions of redundant TFs. However, constitutive overexpression of TFs frequently causes severe developmental defects preventing ...
Dogar Afzal M AM Institute of Pharmaceutical Sciences , Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland - - 2014
Thrombospondin 1 (THBS1) is a secreted protein with a variety of biological functions, including a potent anti-angiogenic activity and activation of latent transforming growth factor beta (TGF-β). In many human cancers it is expressed at low levels, although mutations in the THBS1 gene have been rarely reported. Instead, the loss ...
Ou Zhao Z College of Life Sciences, Zhejiang University, Hangzhou 310058, - - 2014
Zebrafish Δ113p53, an N-terminal truncated p53 isoform, is a p53-target gene that antagonises p53-mediated apoptotic activity. Interestingly, Δ113p53 does not act on p53 in a dominant-negative manner, but rather interferes with the p53 function by differentially modulating p53-target gene expression to protect cells from apoptosis. Previous studies showed that over-expressed ...
Necsulea Anamaria A 1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland [3] Laboratory of Developmental Genomics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland (A.N.); Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA, and Broad Institute, Cambridge, Massachusetts 02142, USA - - 2014
Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, ...
Hsieh C-L CL Department of Biomedical Sciences, Graduate Institute of Biomedical Sciences, College of Medicine, Tao-Yuan, - - 2014
Adenosine deaminases acting on RNA 1 (ADAR1) catalyzes cellular RNA adenosine-to-inosine editing events on structured RNA molecules. In line with this critical role, ADAR1 exhibits ubiquitous expression and is essential for embryonic development. However, regulation and developmental significance of this RNA editor in a spatiotemporal context are largely elusive. Here ...
Giraud Matthieu M Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA - - 2014
Aire induces the expression of a large set of autoantigen genes in the thymus, driving immunological tolerance in maturing T cells. To determine the full spectrum of molecular mechanisms underlying the Aire transactivation function, we screened an AIRE-dependent gene-expression system with a genome-scale lentiviral shRNA library, targeting factors associated with ...
Frazee Alyssa C AC Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, - - 2014
RNA-sequencing (RNA-seq) is a flexible technology for measuring genome-wide expression that is rapidly replacing microarrays as costs become comparable. Current differential expression analysis methods for RNA-seq data fall into two broad classes: (1) methods that quantify expression within the boundaries of genes previously published in databases and (2) methods that ...
Cochrane Alan - - 2014
The requirement of HIV-1 and HTLV-1 to export incompletely spliced mRNAs has necessitated the evolution of Rev and Rex, respectively, to overcome host cellular mechanism that block nuclear-cytoplasmic export of incompletely processed mRNAs. Evaluating the function of these viral factors can be done at multiple levels: examining the functional consequence ...
Wirth Henry - - 2014
The systematic analysis of miRNA expression and its potential mRNA targets constitutes a basal objective in miRNA research in addition to miRNA gene detection and miRNA target prediction. In this chapter we address methodical issues of miRNA expression analysis using self-organizing maps (SOM), a neural network machine learning algorithm with ...
Pavlou Sofia S Biomedical Systems Analysis Section, Medical Developmental Genetics Section, Medical Research Council Human Genetics Unit, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United - - 2014
THE ZEBRAFISH EPITHALAMUS IS PART OF THE DIENCEPHALON AND ENCOMPASSES THREE MAJOR COMPONENTS: the pineal, the parapineal and the habenular nuclei. Using sox2 knockdown, we show here that this key transcriptional regulator has pleiotropic effects during the development of these structures. Sox2 negatively regulates pineal neurogenesis. Also, Sox2 is identified ...
Xu Qi Q Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu province, Yangzhou University, Yangzhou, People's Republic of - - 2014
Recent functional studies have demonstrated that the microRNAs (miRNAs) play critical roles in ovarian gonadal development, steroidogenesis, apoptosis, and ovulation in mammals. However, little is known about the involvement of miRNAs in the ovarian function of fowl. The goose (Anas cygnoides) is a commercially important food that is cultivated widely ...
Zhai Hong H Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, - - 2014
The major maturity gene E1 has the most prominent effect on flowering time and photoperiod sensitivity of soybean, but the pathway mediated by E1 is largely unknown. Here, we found the expression of GmFT4, a homolog of Flowering Locus T, was strongly up-regulated in transgenic soybean overexpressing E1, whereas expression ...
Peterson Sarah M SM Center for Molecular Medicine, Maine Medical Center Research Institute Scarborough, ME, USA ; Graduate School of Biomedical Sciences and Engineering, University of Maine Orono, ME, - - 2014
The human genome encodes for over 1800 microRNAs (miRNAs), which are short non-coding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one miRNA to target multiple gene transcripts, miRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction ...
Arthanari Yamini Y The Michael Smith Building, Faculty of Life Sciences, University of Manchester, Manchester, United - - 2014
The prevalence of long non-coding RNAs (lncRNA) and natural antisense transcripts (NATs) has been reported in a variety of organisms. While a consensus has yet to be reached on their global importance, an increasing number of examples have been shown to be functional, regulating gene expression at the transcriptional and ...
Hook Lauren M LM Vaccine & Gene Therapy Institute, Oregon Health and Sciences University, Beaverton, OR, - - 2014
microRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level, by binding to sites within the 3' untranslated regions of messenger RNA (mRNA) transcripts. The discovery of this completely new mechanism of gene regulation necessitated the development of a variety of techniques to further characterize miRNAs, ...
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