Search Results for: functions of lncrna
Unexpected functions of lncRNAs in gene regulation
Long non-coding RNAs (lncRNAs) are a group of molecules that function in gene regulation in yeast, plants and mammals. The precise mechanisms of action for lncRNAs, however, remain largely unclear. The GAL gene cluster has been used as a model system to study the function of these molecules in Saccharomyces cerevisiae, with a historical focus on lncRNA-dependent repression. Strikingly, in characterizing the role of the RNA helicase Dbp2, we discovered that the GAL lncRNAs could also promote transcriptional activation of the targeted GAL protein-coding genes. Interestingly, these lncRNAs help determine how quickly the GAL genes can be induced in response to galactose, without altering final steady-state transcript levels. This unexpected finding suggests that one role for lncRNAs is to promote the timing of gene expression. Herein, the authors discuss their discoveries in the context of current models of lncRNA functions in eukaryotes, with a key emphasis on future challenges for genomic research.
- Wang S, Tran EJ. (2013) Unexpected functions of lncRNAs in gene regulation. Commun Integr Biol 6(6), e27610. [article]
lncRNASNP - a database of SNPs in lncRNAs and their potential functions
Long non-coding RNAs (lncRNAs) play key roles in various cellular contexts and diseases by diverse mechanisms. With the rapid growth of identified lncRNAs and disease-associated single nucleotide polymorphisms (SNPs), there is a great demand to study SNPs in lncRNAs. Aiming to provide a useful resource about lncRNA SNPs, researchers from the Huazhong University of Science and Technology systematically identified SNPs in lncRNAs and analyzed their potential impacts on lncRNA structure and function. In total, they identified 495,729 and 777,095 SNPs in more than 30,000 lncRNA transcripts in human and mouse, respectively. A large number of SNPs were predicted with the potential to impact on the miRNA-lncRNA interaction. The experimental evidence and conservation of miRNA-lncRNA interaction, as well as miRNA expressions from TCGA were also integrated to prioritize the miRNA-lncRNA interactions and SNPs on the binding sites. Furthermore, by mapping SNPs to GWAS results, they found that 142 human lncRNA SNPs are GWAS tagSNPs and 197,827 lncRNA SNPs are in the GWAS linkage disequilibrium regions. All these data for human and mouse lncRNAs were imported into lncRNASNP database, which includes two sub-databases lncRNASNP-human and lncRNASNP-mouse. The lncRNASNP database has a user-friendly interface for searching and browsing through the SNP, lncRNA and miRNA sections.
Availability – the lncRNASNP database is available at: http://bioinfo.life.hust.edu.cn/lncRNASNP/
- Gong J, Liu W, Zhang J, Miao X, Guo AY. (2015) lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res 43(Database issue):D181-6. [article]
Non-coding RNA - Zooming in on lncRNA functions
Long non-coding RNAs (lncRNAs) are emerging as important regulators of gene expression; however, in contrast to transcription factors, their functional domain architecture remains poorly understood. Now, a new method has been developed to simultaneously map RNA–RNA, RNA–DNA and RNA–protein interactions at the level of individual RNA domains with increased sensitivity.
Quinn et al. developed a method called domain-specific chromatin isolation by RNA purification (dChIRP), in which several antisense oligonucleotide pools are used to target specific domains of lncRNAs. In this method, cells are subjected to fixation, crosslinking and sonication, and the resultant sheared chromatin is hybridized to the biotinylated oligonucleotide pools to recover chromatin fragments containing specific lncRNA domains of interest. The RNA, DNA and protein components associated with the lncRNA domains can then be analysed separately.
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lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome
lncRNAMap is an integrated and comprehensive database relating to exploration of the putative regulatory functions of human lncRNAs with two mechanisms of regulation, by encoding siRNAs and by acting as miRNA decoys. To investigate lncRNAs producing siRNAs that regulate protein-coding genes, lncRNAMap integrated small RNAs (sRNAs) that were supported by publicly available deep sequencing data from various sRNA libraries and constructed lncRNA-derived siRNA-target interactions. In addition, lncRNAMap demonstrated that lncRNAs can act as targets for miRNAs that would otherwise regulate protein-coding genes. Previously studies indicated that intergenic lncRNAs (lincRNAs) either positive or negative regulated neighboring genes, therefore, lncRNAMap surveyed neighboring genes within a 1Mb distance from the genomic location of specific lncRNAs and provided the expression profiles of lncRNA and its neighboring genes. The gene expression profiles may supply the relationship between lncRNA and its neighboring genes.
lncRNAMap is a powerful user-friendly platform for the investigation of putative regulatory functions of human lncRNAs with producing siRNAs and acting as miRNA decoy.
Availability - lncRNAMap is freely available on the web at http://lncRNAMap.mbc.nctu.edu.tw/
- Chan WL, Huang HD, Chang JG. (2014) lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome. Comput Biol Chem [Epub ahead of print]. [abstract]
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Wild West landscape of lncRNA functions and mechanisms
Recent studies show that transcription of the mammalian genome is not only pervasive but also enormously complex. It is estimated that an average of 10 transcription units, the vast majority of which make long noncoding RNAs (lncRNAs), may overlap each traditional coding gene. These lncRNAs include not only antisense, intronic, and intergenic transcripts but also pseudogenes and retrotransposons. Do they universally have function, or are they merely transcriptional by-products of conventional coding genes? A glimpse into the molecular biology of multiple emerging lncRNA systems reveals the “Wild West” landscape of their functions and mechanisms and the key problems to solve in the years ahead toward understanding these intriguing macromolecules.
- Lee JT. (2012) Epigenetic regulation by long noncoding RNAs. Science 338(6113), 1435-9. [abstract]