The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer
Abstract
:Simple Summary
Abstract
1. Introduction
2. LncRNA Genes and Their Expression Patterns
3. LncRNAs and Their Association with Ovarian Cancer
4. LncRNAs Involved in Epigenetic Mechanisms in Ovarian Cancer
LncRNA | Regulatory Mechanism | Target | Source | Refs. |
---|---|---|---|---|
FAL1 (FALEC) | Stabilization of BMI1 protein and PRC1-mediated deposition of repressive histone marks | CDKN1A | LncTarD and EVLncRNAs databases | [84,85] |
PVT1 | EZH2 recruitment | miR-214 | LncTarD database | [86] |
TARID | Recruitment of GADD45A and TET-dependent DNA demethylation | TCF21 | LncTarD database | [87,88] |
LINC01210 | EZH2 recruitment and PRC2-mediated deposition of repressive histone marks | KLF4 | Literature mining | [89] |
TP73-AS1 | EZH2 recruitment and PRC2-mediated deposition of repressive histone marks | CDKN1A | Literature mining | [90] |
UNC5B-AS1 | EZH2 recruitment and PRC2-mediated deposition of repressive histone marks | NDRG2 | Literature mining | [91] |
ABHD11-AS1 | EZH2 recruitment and PRC2-mediated deposition of repressive histone marks | TIMP2 | Literature mining | [92] |
5. A Concise Guide to Exploring lncRNA Databases
6. Conclusions and Perspectives
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Database | Aim | Website | Refs. |
---|---|---|---|
lncRNA annotation | |||
NONCODE v5.0 | Collects and annotates a comprehensive set of ncRNAs, especially lncRNAs. | http://www.noncode.org/ | [105] |
LNCipedia 5.2 | Collects sequences and annotation data for a comprehensive set of lncRNA transcripts. | https://lncipedia.org | [107,111] |
LncRNAWiki | Collects and integrates comprehensive information on human lncRNAs relying on collaborative curation. | http://lncrna.big.ac.cn | [110,112] |
EVLncRNAs | Collects lncRNAs that were validated by low-throughput experiments. | http://biophy.dzu.edu.cn/EVLncRNAs | [109] |
LncRBase | Provides information on a comprehensive set of lncRNAs, ranging from basic transcript features to additional details on their genomic context. | http://bicresources.jcbose.ac.in/zhumur/lncrbase | [106] |
LncBook | Collects a comprehensive set of human lncRNAs and provides multi-omics data integration, functional annotation, and disease association for these transcripts. | http://bigd.big.ac.cn/lncbook | [108,113] |
lncRNA regulatory functions (interactions, mechanisms, and effects) | |||
ENCORI | Integrates multi-dimensional sequencing data to provide a comprehensive collection of RNA–RNA and protein–RNA interaction networks. | http://starbase.sysu.edu.cn/ | [114,115] |
LncRNA2Target v2.0 | Collects lncRNA–target associations supported by high- and low-throughput methods. | http://123.59.132.21/lncrna2target/ | [116] |
LncTarD | Collects and illustrates experimentally supported lncRNA–target regulations in human diseases. | http://bio-bigdata.hrbmu.edu.cn/LncTarD | [117] |
NPInter v4.0 | Integrates literature reported evidence and high-throughput data processing to collect and illustrate functional interactions between ncRNAs and biomolecules. | http://bigdata.ibp.ac.cn/npinter | [118] |
LncACTdb 2.0 | Collects and illustrates information on ceRNA relationships between different types of RNAs in diverse diseases. | http://www.bio-bigdata.net/LncACTdb/ | [119] |
miRSponge | Collects experimentally validated miRNA sponges and ceRNA interactions. | http://bio-bigdata.hrbmu.edu.cn/miRSponge/ | [120] |
Co-LncRNA | Allows the identification of lncRNA coexpressed protein-coding genes and the assessment of the effects of individual or multiple lncRNAs in GO annotations and KEGG pathways. | http://bio-bigdata.hrbmu.edu.cn/Co-LncRNA/ | [121] |
Lnc2Meth | Integrates experimental and computational evidence to provide information on regulatory relationships between lncRNAs and DNA methylation in diverse human diseases. | http://bio-bigdata.hrbmu.edu.cn/Lnc2Meth/ | [122] |
lncRNA–disease associations | |||
LncRNADisease 2.0 | Integrates experimental and computational evidence to provide information on lncRNA/circRNA–disease associations, including causal relationships. | http://www.rnanut.net/lncrnadisease/ | [123,124] |
Lnc2Cancer v3.0 | Collects and integrates experimentally supported associations between lncRNAs and cancer subtypes. | http://www.bio-bigdata.net/lnc2cancer/ | [125,126] |
MNDR v2.0 | Collects and integrates experimentally supported and predicted ncRNA–disease associations in mammals. | http://www.rna-society.org/mndr/ | [127] |
ncRPheno | Collects comprehensive ncRNA–disease association data and offers web applications to facilitate analysis and visualization of this data. | http://lilab2.sysu.edu.cn/ncrpheno | [128] |
Lnc2Catlas | Integrates multiple methods and data sources to collect quantitative associations between lncRNAs and cancer. | http://lnc2catlas.bioinfotech.org/ | [129] |
CSCD | Collects and integrates information on cancer-specific circRNAs. | http://gb.whu.edu.cn/CSCD | [130] |
Circ2Disease | Collects information on experimentally supported circRNAs in human diseases. | http://bioinformatics.zju.edu.cn/Circ2Disease/index.html | [131] |
CircR2Disease | Collects information on experimentally validated associations between circRNAs and diseases. | http://bioinfo.snnu.edu.cn/CircR2Disease/ | [132,133] |
MiOncoCirc | Collects data on circRNA formation and abundance in cancer. | https://mioncocirc.github.io/ | [134] |
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Calanca, N.; Abildgaard, C.; Rainho, C.A.; Rogatto, S.R. The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer. Cancers 2020, 12, 2701. https://doi.org/10.3390/cancers12092701
Calanca N, Abildgaard C, Rainho CA, Rogatto SR. The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer. Cancers. 2020; 12(9):2701. https://doi.org/10.3390/cancers12092701
Chicago/Turabian StyleCalanca, Naiade, Cecilie Abildgaard, Cláudia Aparecida Rainho, and Silvia Regina Rogatto. 2020. "The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer" Cancers 12, no. 9: 2701. https://doi.org/10.3390/cancers12092701