Browsing by Author "Chan, Wen-Ling"

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IncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome
(2014-06-01)
Chan, Wen-Ling
;
Huang, Hsien-Da
;
Chang, Jan-Gowth
;
生物科技學系
;
生物資訊及系統生物研究所
Background: Recent studies have demonstrated the importance of long non-coding RNAs (IncRNAs) in chromatin remodeling, and in transcriptional and post-transcriptional regulation. However, only a few specific IncRNAs are well understood, whereas others are completely uncharacterized. To address this, there is a need for user-friendly platform to studying the putative regulatory functions of human IncRNAs. Description: IncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human IncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate IncRNAs producing siRNAs that regulate protein-coding genes, IncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed IncRNA-derived siRNA-target interactions. In addition, IncRNAMap demonstrated that IncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic IncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, IncRNAMap surveyed neighboring genes within a 1 Mb distance from the genomic location of specific IncRNAs and provided the expression profiles of IncRNA and its neighboring genes. The gene expression profiles may supply the relationship between incRNA and its neighboring genes. Conclusions: lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human IncRNAs with producing siRNAs and acting as miRNA decoy. IncRNAMap is freely available on the web at http://IncRNAMap.mbc.nctu.edu.tw/., (C) 2014 Elsevier Ltd. All rights reserved.
IncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome
(2014-06-01)
Chan, Wen-Ling
;
Huang, Hsien-Da
;
Chang, Jan-Gowth
;
生物科技學系
;
生物資訊及系統生物研究所
Background: Recent studies have demonstrated the importance of long non-coding RNAs (IncRNAs) in chromatin remodeling, and in transcriptional and post-transcriptional regulation. However, only a few specific IncRNAs are well understood, whereas others are completely uncharacterized. To address this, there is a need for user-friendly platform to studying the putative regulatory functions of human IncRNAs. Description: IncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human IncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate IncRNAs producing siRNAs that regulate protein-coding genes, IncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed IncRNA-derived siRNA-target interactions. In addition, IncRNAMap demonstrated that IncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic IncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, IncRNAMap surveyed neighboring genes within a 1 Mb distance from the genomic location of specific IncRNAs and provided the expression profiles of IncRNA and its neighboring genes. The gene expression profiles may supply the relationship between incRNA and its neighboring genes. Conclusions: lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human IncRNAs with producing siRNAs and acting as miRNA decoy. IncRNAMap is freely available on the web at http://IncRNAMap.mbc.nctu.edu.tw/., (C) 2014 Elsevier Ltd. All rights reserved.
miRTarBase: a database curates experimentally validated microRNA-target interactions
(2011-01-01)
Hsu, Sheng-Da
;
Lin, Feng-Mao
;
Wu, Wei-Yun
;
Liang, Chao
;
Huang, Wei-Chih
MicroRNAs (miRNAs), i.e. small non-coding RNA molecules (similar to 22 nt), can bind to one or more target sites on a gene transcript to negatively regulate protein expression, subsequently controlling many cellular mechanisms. A current and curated collection of miRNA-target interactions (MTIs) with experimental support is essential to thoroughly elucidating miRNA functions under different conditions and in different species. As a database, miRTarBase has accumulated more than 3500 MTIs by manually surveying pertinent literature after data mining of the text systematically to filter research articles related to functional studies of miRNAs. Generally, the collected MTIs are validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs. miRTarBase curates 3576 experimentally verified MTIs between 657 miRNAs and 2297 target genes among 17 species. miRTarBase contains the largest amount of validated MTIs by comparing with other similar, previously developed databases. The MTIs collected in the miRTarBase can also provide a large amount of positive samples to develop computational methods capable of identifying miRNA-target interactions. miRTarBase is now available on http://miRTarBase.mbc.nctu.edu.tw/, and is updated frequently by continuously surveying research articles.
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes
(2013-02-08)
Chan, Wen-Ling
;
Yang, Wen-Kuang
;
Huang, Hsien-Da
;
Chang, Jan-Gowth
;
生物科技學系
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/
Small Molecule Amiloride Modulates Oncogenic RNA Alternative Splicing to Devitalize Human Cancer Cells
(2011-06-09)
Chang, Jan-Gowth
;
Yang, Den-Mei
;
Chang, Wen-Hsin
;
Chow, Lu-Ping
;
Chan, Wen-Ling
Alternative splicing involves differential exon selection of a gene transcript to generate mRNA and protein isoforms with structural and functional diversity. Abnormal alternative splicing has been shown to be associated with malignant phenotypes of cancer cells, such as chemo-resistance and invasive activity. Screening small molecules and drugs for modulating RNA splicing in human hepatocellular carcinoma cell line Huh-7, we discovered that amiloride, distinct from four pH-affecting amiloride analogues, could "normalize" the splicing of BCL-X, HIPK3 and RON/MISTR1 transcripts. Our proteomic analyses of amiloride-treated cells detected hypo-phosphorylation of splicing factor SF2/ASF, and decreased levels of SRp20 and two un-identified SR proteins. We further observed decreased phosphorylation of AKT, ERK1/2 and PP1, and increased phosphorylation of p38 and JNK, suggesting that amiloride treatment down-regulates kinases and up-regulates phosphatases in the signal pathways known to affect splicing factor protein phosphorylation. These amiloride effects of "normalized" oncogenic RNA splicing and splicing factor hypo-phosphorylation were both abrogated by pretreatment with a PP1 inhibitor. Global exon array of amiloride-treated Huh-7 cells detected splicing pattern changes involving 584 exons in 551 gene transcripts, many of which encode proteins playing key roles in ion transport, cellular matrix formation, cytoskeleton remodeling, and genome maintenance. Cellular functional analyses revealed subsequent invasion and migration defects, cell cycle disruption, cytokinesis impairment, and lethal DNA degradation in amiloride-treated Huh-7 cells. Other human solid tumor and leukemic cells, but not a few normal cells, showed similar amiloride-altered RNA splicing with devitalized consequence. This study thus provides mechanistic underpinnings for exploiting small molecule modulation of RNA splicing for cancer therapeutics.
Transcribed pseudogene psi PPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma
(2013-04-01)
Chan, Wen-Ling
;
Yuo, Chung-Yee
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Yang, Wen-Kuang
;
Hung, Shih-Ya
;
Chang, Ya-Sian
Pseudogenes, especially those that are transcribed, may not be mere genomic fossils, but their biological significance remains unclear. Postulating that in the human genome, as in animal models, pseudogenes may function as gene regulators through generation of endo-siRNAs (esiRNAs), antisense RNAs or RNA decoys, we performed bioinformatic and subsequent experimental tests to explore esiRNA-mediated mechanisms of pseudogene involvement in oncogenesis. A genome-wide survey revealed a partial retrotranscript pseudogene psi PPM1K containing inverted repeats capable of folding into hairpin structures that can be processed into two esiRNAs; these esiRNAs potentially target many cellular genes, including NEK8. In 41 paired surgical specimens, we found significantly reduced expression of two predicted psi PPM1K-specific esiRNAs, and the cognate gene PPM1K, in hepatocellular carcinoma compared with matched non-tumour tissues, whereas the expression of target gene NEK8 was increased in tumours. Additionally, NEK8 and PPM1K were downregulated in stably transfected psi PPM1K-overexpressing cells, but not in cells transfected with an esiRNA1-deletion mutant of psi PPM1K. Furthermore, expression of NEK8 in psi PPM1K-transfected cells demonstrated that NEK8 can counteract the growth inhibitory effects of psi PPM1K. These findings indicate that a transcribed pseudogene can exert tumour-suppressor activity independent of its parental gene by generation of esiRNAs that regulate human cell growth.