IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites

Internal Ribosome Entry Sites (IRESs) are functional RNA elements that can directly recruit ribosomes to an internal position of the mRNA in a cap-independent manner to initiate translation. Recently, IRES elements have attracted much attention for their critical roles in various processes including translation initiation of a new type of RNA, circular RNA, with no 5′ cap to support classical cap-dependent translation. Thus, an integrative data resource of IRES elements with experimental evidences will be useful for further studies. In this study, we present a comprehensive database of IRESs (IRESbase) by curating the experimentally validated functional minimal IRES elements from literature and annotating their host linear and circular RNA information. The current version of IRESbase contains 1328 IRESs, including 774 eukaryotic IRESs and 554 viral IRESs from 11 eukaryotic organisms and 198 viruses. As our database collected only IRES of minimal length with functional evidences, the median length of IRESs in IRESbase is 174 nucleotides. By mapping IRESs to human circRNAs and lncRNAs, 2191 circRNAs and 168 lncRNAs were found to contain at least one entire or partial IRES sequences. The IRESbase is available at http://reprod.njmu.edu.cn/iresbase/index.php.

[1]  N. Sonenberg,et al.  Internal initiation of translation of eukaryotic mRNA directed by a sequence derived from poliovirus RNA , 1988, Nature.

[2]  Wen J. Li,et al.  Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation , 2015, Nucleic Acids Res..

[3]  Elspeth A. Bruford,et al.  Genenames.org: the HGNC resources in 2015 , 2014, Nucleic Acids Res..

[4]  R. Siliciano,et al.  The Human Immunodeficiency Virus Type 1gag Gene Encodes an Internal Ribosome Entry Site , 2001, Journal of Virology.

[5]  Qi Zhang,et al.  Translation of the circular RNA circβ-catenin promotes liver cancer cell growth through activation of the Wnt pathway , 2019, Genome Biology.

[6]  R. Korneluk,et al.  Distinct Regulation of Internal Ribosome Entry Site-mediated Translation following Cellular Stress Is Mediated by Apoptotic Fragments of eIF4G Translation Initiation Factor Family Members eIF4GI and p97/DAP5/NAT1* , 2003, The Journal of Biological Chemistry.

[7]  Mark Johnson,et al.  NCBI BLAST: a better web interface , 2008, Nucleic Acids Res..

[8]  Liu Ming,et al.  A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis , 2018, Oncogene.

[9]  Sameer Velankar,et al.  PDBe: Protein Data Bank in Europe , 2010, Nucleic Acids Res..

[10]  Suyun Huang,et al.  Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis , 2017, Journal of the National Cancer Institute.

[11]  Sameer Velankar,et al.  PDBe: Protein Data Bank in Europe , 2009, Nucleic Acids Res..

[12]  J. Kocher,et al.  CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model , 2013, Nucleic acids research.

[13]  Yan Li,et al.  circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations , 2016, Scientific Reports.

[14]  N. Rajewsky,et al.  Translation of CircRNAs , 2017, Molecular cell.

[15]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[16]  Michel Krempf,et al.  IRES-dependent translation of the long non coding RNA meloe in melanoma cells produces the most immunogenic MELOE antigens , 2016, Oncotarget.

[17]  M. MacFarlane,et al.  Initiation of Apaf-1 translation by internal ribosome entry , 2000, Oncogene.

[18]  R. Korneluk,et al.  Functional Characterization of the X-Linked Inhibitor of Apoptosis (XIAP) Internal Ribosome Entry Site Element: Role of La Autoantigen in XIAP Translation , 2000, Molecular and Cellular Biology.

[19]  Beth Walters,et al.  Cap-Independent Translational Control of Carcinogenesis , 2016, Front. Oncol..

[20]  Shun Liu,et al.  RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data , 2017, Nucleic Acids Res..

[21]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[22]  Petar Glažar,et al.  circBase: a database for circular RNAs , 2014, RNA.

[23]  Adi Kimchi,et al.  A Novel Form of DAP5 Protein Accumulates in Apoptotic Cells as a Result of Caspase Cleavage and Internal Ribosome Entry Site-Mediated Translation , 2000, Molecular and Cellular Biology.

[24]  A. Komar,et al.  Cellular IRES-mediated translation , 2011, Cell cycle.

[25]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[26]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[27]  M. Bushell,et al.  Internal ribosome entry segment-mediated translation during apoptosis: the role of IRES-trans-acting factors , 2005, Cell Death and Differentiation.

[28]  M. Holcik,et al.  IRES-mediated translation of cellular messenger RNA operates in eIF2α- independent manner during stress , 2011, Nucleic acids research.

[29]  Gwendolyn M. Jang,et al.  Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. , 2015, Cell host & microbe.

[30]  Sophie Bonnal,et al.  IRESdb: the Internal Ribosome Entry Site database , 2003, Nucleic Acids Res..

[31]  P. Sarnow,et al.  Initiation of protein synthesis by the eukaryotic translational apparatus on circular RNAs. , 1995, Science.

[32]  Robert D. Finn,et al.  Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families , 2017, Nucleic Acids Res..

[33]  F. Zhao,et al.  Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals. , 2019, Cell reports.

[34]  N. Rajewsky,et al.  Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis , 2017, Molecular cell.

[35]  E. Beck,et al.  Functional analysis of the internal translation initiation site of foot-and-mouth disease virus , 1990, Journal of virology.

[36]  N. Sonenberg,et al.  Suppression of cap-dependent translation in mitosis. , 2001, Genes & development.

[37]  Elizabeth M. Smigielski,et al.  dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..

[38]  Chris Mungall,et al.  AmiGO: online access to ontology and annotation data , 2008, Bioinform..

[39]  E. Wimmer,et al.  A segment of the 5' nontranslated region of encephalomyocarditis virus RNA directs internal entry of ribosomes during in vitro translation , 1988, Journal of virology.

[40]  Gong Zhang,et al.  A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma , 2018, Nature Communications.

[41]  Daling Zhu,et al.  RE: Novel Role of FBXW7 Circular RNA in Repressing Glioma Tumorigenesis. , 2018, Journal of the National Cancer Institute.

[42]  Martin Mokrejs,et al.  IRESite: the database of experimentally verified IRES structures () , 2005, Nucleic Acids Res..

[43]  Akira R. Kinjo,et al.  Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format , 2011, Nucleic Acids Res..

[44]  R. Grover,et al.  Two internal ribosome entry sites mediate the translation of p53 isoforms , 2006, EMBO reports.