pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes

Wen-Ling Chan, Wen-Kuang Yang, Hsien-Da Huang, Jan Gowth Chang

Research output: Contribution to journalArticle

6 Scopus citations

Abstract

RNA interference (RNAi) is a gene silencing process within living cells, which is controlled by the RNA-induced silencing complex with a sequence-specific manner. In flies and mice, the pseudogene transcripts can be processed into short interfering RNAs (siRNAs) that regulate protein-coding genes through the RNAi pathway. Following these findings, we construct an innovative and comprehensive database to elucidate siRNA-mediated mechanism in human transcribed pseudogenes (TPGs). To investigate TPG producing siRNAs that regulate protein-coding genes, we mapped the TPGs to small RNAs (sRNAs) that were supported by publicly deep sequencing data from various sRNA libraries and constructed the TPG-derived siRNA-target interactions. In addition, we also presented that TPGs can act as a target for miRNAs that actually regulate the parental gene. To enable the systematic compilation and updating of these results and additional information, we have developed a database, pseudoMap, capturing various types of information, including sequence data, TPG and cognate annotation, deep sequencing data, RNA-folding structure, gene expression profiles, miRNA annotation and target prediction. As our knowledge, pseudoMap is the first database to demonstrate two mechanisms of human TPGs: encoding siRNAs and decoying miRNAs that target the parental gene. pseudoMap is freely accessible at http://pseudomap.mbc.nctu.edu.tw/.

Database URL: http://pseudomap.mbc.nctu.edu.tw/

Keywords

  • EMBRYONIC STEM-CELLS; HUMAN GENOME; GENE-EXPRESSION; MESSENGER-RNAS; ENDOGENOUS SIRNAS; INTERFERING RNAS; NONCODING RNAS; SOMATIC-CELLS; MOUSE OOCYTES; PROTEIN

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