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Bateman A.,Wellcome Trust Sanger Institute | Agrawal S.,Institute of Bioinformatics and Applied Biotechnology IBAB | Agrawal S.,BioCOS Life science Private Ltd | Birney E.,European Bioinformatics Institute | And 28 more authors.
RNA | Year: 2011

During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. Source


Das S.,Ecole Normale Superieure de Lyon | Cong R.,Ecole Normale Superieure de Lyon | Shandilya J.,Jawaharlal Nehru Centre for Advanced Scientific Research | Senapati P.,Jawaharlal Nehru Centre for Advanced Scientific Research | And 7 more authors.
FEBS Letters | Year: 2013

Nucleolin is a multifunctional protein that carries several post-translational modifications. We characterized nucleolin acetylation and developed antibodies specific to nucleolin K88 acetylation. Using this antibody we show that nucleolin is acetylated in vivo and is not localized in the nucleoli, but instead is distributed throughout the nucleoplasm. Immunofluorescence studies indicate that acetylated nucleolin is co-localized with the splicing factor SC35 and partially with Y12. Acetylated nucleolin is expressed in all tested proliferating cell types. Our findings show that acetylation defines a new pool of nucleolin which support a role for nucleolin in the regulation of mRNA maturation and transcription by RNA polymerase II. Structured summary of protein interactions: SC35 physically interacts with Nucleolin by anti bait coimmunoprecipitation (View interaction) Nucleolin and SC35 colocalize by fluorescence microscopy (View interaction). © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Source


Prakash A.,Institute of Bioinformatics and Applied Biotechnology | Yogeeshwari S.,Institute of Bioinformatics and Applied Biotechnology | Sircar S.,Institute of Bioinformatics and Applied Biotechnology | Agrawal S.,Institute of Bioinformatics and Applied Biotechnology | Agrawal S.,BioCOS Life science Private Ltd
PLoS ONE | Year: 2011

Vibrio cholerae, the enteropathogenic gram negative bacteria is one of the main causative agents of waterborne diseases like cholera. About 1/3rd of the organism's genome is uncharacterised with many protein coding genes lacking structure and functional information. These proteins form significant fraction of the genome and are crucial in understanding the organism's complete functional makeup. In this study we report the general structure and function of a family of hypothetical proteins, Domain of Unknown Function 3233 (DUF3233), which are conserved across gram negative gammaproteobacteria (especially in Vibrio sp. and similar bacteria). Profile and HMM based sequence search methods were used to screen homologues of DUF3233. The I-TASSER fold recognition method was used to build a three dimensional structural model of the domain. The structure resembles the transmembrane beta-barrel with an axial N-terminal helix and twelve antiparallel beta-strands. Using a combination of amphipathy and discrimination analysis we analysed the potential transmembrane beta-barrel forming properties of DUF3233. Sequence, structure and phylogenetic analysis of DUF3233 indicates that this gram negative bacterial hypothetical protein resembles the beta-barrel translocation unit of autotransporter Va secretory mechanism with a gene organisation that differs from the conventional Va system. © 2011 Prakash et al. Source


Cong R.,Ecole Normale Superieure de Lyon | Cong R.,East China Normal University | Das S.,Ecole Normale Superieure de Lyon | Ugrinova I.,Ecole Normale Superieure de Lyon | And 5 more authors.
Nucleic Acids Research | Year: 2012

Nucleolin is a multi-functional nucleolar protein that is required for ribosomal RNA gene (rRNA) transcription in vivo, but the mechanism by which nucleolin modulates RNA polymerase I (RNAPI) transcription is not well understood. Nucleolin depletion results in an increase in the heterochromatin mark H3K9me2 and a decrease in H4K12Ac and H3K4me3 euchromatin histone marks in rRNA genes. ChIP-seq experiments identified an enrichment of nucleolin in the ribosomal DNA (rDNA) coding and promoter region. Nucleolin is preferentially associated with unmethylated rRNA genes and its depletion leads to the accumulation of RNAPI at the beginning of the transcription unit and a decrease in UBF along the coding and promoter regions. Nucleolin is able to affect the binding of transcription termination factor-1 on the promoter-proximal terminator T0, thus inhibiting the recruitment of TIP5 and HDAC1 and the establishment of a repressive heterochromatin state. These results reveal the importance of nucleolin for the maintenance of the euchromatin state and transcription elongation of rDNA. © 2012 The Author(s). Source

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