Roles of Non-Coding RNAs in Normal Human Brain Development, Brain Tumor, and Neuropsychiatric Disorders
Abstract
:1. Introduction
2. Types and Functions of ncRNAs
2.1. miRNAs
2.2. lncRNAs
2.3. circRNAs
3. NcRNAs in Normal Brain Function
3.1. miRNAs in Brain Development and Function
3.2. lncRNAs in Brain Development and Function
3.3. circRNAs in Brain Development and Function
4. NcRNAs in the Brain Tumor
4.1. miRNAs in Glioma
4.2. lncRNAs in Glioma
4.3. Circular RNAs in Glioma
5. NcRNAs in Exosomes and Extracellular Vesicles in Glioma
6. NcRNAs in Neuropsychiatric Disorders
6.1. ncRNAs in Alzheimer’s Disease (AD)
6.2. ncRNAs in Parkinson’s Disease (PD)
6.3. ncRNAs in Autism
7. Publicly Available Tools and Platforms for ncRNA and Human Disease Study
7.1. DeepBase
7.2. StarBase
7.3. Circ2Traits
7.4. ExoRBase
8. Conclusions and Future Perspectives
Funding
Acknowledgments
Conflicts of Interest
References
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Non-Coding RNA Classes | Functions |
---|---|
Transfer RNAs (tRNAs) | Function at specific sites in the ribosome during translation, help translate mRNA into protein |
Ribosomal RNAs (rRNAs) | Act as the RNA component of the ribosome, help the mRNA translation |
MicroRNAs (miRNAs) | Function in RNA silencing, post-transcriptional regulation of gene expression |
Piwi-interacting RNAs (piRNAs) | Regulate DNA methylation, main function in germ line cells |
Small nucleolar RNAs (snoRNAs) | Guide modification of other RNAs (e.g., rRNA), rRNA processing |
Long non-coding RNAs (lncRNAs) | Non-protein coding transcripts longer than 200 nucleotides, heterogeneous class of RNAs, regulation of gene transcription |
Circular RNAs (circRNAs) | Covalently closed RNA rings, some have coding functions, potential gene regulators and miRNA sponges |
NcRNA | Action | Reference |
---|---|---|
MiRNA | ||
miR-21 | Acts as an oncogene in glioma by targeting IGFBP3, RECK, TIMP3, MMP, and PDCD4. | [46,47,49,50] |
miR-124 | Acts as a tumor suppressor in glioma via targeting CDK6, SOS1, CDK4, Capn4, and ROCK1. | [51,53,54,55] |
miR-137 | Acts as a tumor suppressor in glioma by targeting CDK6 and EGFR. | [51,52] |
LncRNA | ||
CRNDE | Acts as an oncogene in glioma via multi-faced way. | [56,57,58,59] |
H19 | Can be directly induced by c-Myc. Serves as precursor of miR-675. Knockdown of H19 suppresses tumorigenicity and stemness in U251 and U87MG glioma cells. | [60,61,62] |
XIST | An oncogenic lncRNA in glioma, which can promote glioma tumorigenicity and angiogenesis by acting as a molecular sponge of miR-429. Maintenance of GSCs via miR-152. | [63,64] |
GAS5 | Exerts tumor-suppressive roles in glioma cells by targeting miR-222. | [65] |
MALAT1 | Correlates with the malignant status and poor prognosis in glioma. Induces chemo-resistance by suppressing miR-203. | [66,67] |
Hotair | An oncogenic factor in glioma. Correlates with a poor prognosis. Critical regulator of the cell cycle. | [68,69] |
SOX2ot | Knockdown of SOX2OT inhibits the malignant biological behaviors of glioblastoma stem cells by up-regulating the expression of miR-194-5p and miR-122. | [70] |
CircRNA | ||
circBRAF | Negatively correlates with tumor malignancy grade; Protective effect for survival. | [71] |
circFBXW7 | Encodes a protein FBXW7-185aa; the upregulation of FBXW7-185aa inhibited proliferation and cell cycle acceleration of glioma cells. | [72,73] |
circSMARCA5 | Inhibits malignant glioma cell migration. | [74] |
circTTBK2 | Up regulated in glioma, and can act as an miR-217 sponge and promote cell proliferation, migration, and invasion. | [75] |
cZNF292 | Regulates glioma angiogenesis through a Wnt/β-catenin signaling pathway. | [76] |
circSHKBP1 | Regulates the angiogenesis of malignant glioma by interacting with miR-544a and miR-379. | [77] |
circNT5E | Acts as a sponge of miR-422a and controls multiple pathologic processes in glioblastoma tumorigenesis, including cell proliferation, migration, and invasion. | [78] |
circNFIX | Regulates the Notch signaling pathway to promote glioma progression by sponging miR-34a-5p. | [79] |
Exosome ncRNA | ||
miR-21 | The exosome levels of miR-21 from cerebrospinal fluids are associated with a poor prognosis and tumor recurrence of glioma patients. | [80] |
miR-148a | miR-148a delivered by exosomes may promote cancer cell proliferation and metastasis by targeting CADM1 to activate the STAT3 pathway. | [81] |
lncRNA PU03F3 | Exosomes from A172 glioma cell lines express a high level of PU03F3, which can lead to increased cell proliferation, migration, tube formation, and in vivo angiogenesis in glioma. | [82] |
lncRNA CCAT2 | Released by glioma cells, this exosome ncRNA can enhance angiogenesis and inhibit endothelial cell apoptosis. | [83] |
Name | Description | Link |
---|---|---|
miRNA | ||
DeepBase | A database for annotating and discovering small and long ncRNAs from high-throughput deep sequencing data. | https://www.webcitation.org/5tyh2Lsae?url=http://deepbase.sysu.edu.cn/ |
starBase | Decoding miRNA-ceRNA, miRNA-ncRNA, and protein-RNA interaction networks from large-scale CLIP-Seq data. | http://starbase.sysu.edu.cn/ |
microRNA.org | A database for experimentally observed miRNA expression patterns and predicts miRNA targets and target downregulation scores. | http://www.microrna.org/microrna/getExprForm.do |
miRTarBase | The experimentally validated miRNA-target interaction database. | http://mirtarbase.mbc.nctu.edu.tw/php/index.php |
MSDD | A manually curated database that provides comprehensive experimentally supported associations among miRNAs, SNPs, and human diseases. | http://www.bio-bigdata.com/msdd/ |
mirTrans | A repository that provides comprehensive information of miRNA transcription for different cell lines. | http://mcube.nju.edu.cn/jwang/lab/soft/mirtrans/ |
TransmiR | A database for transcription factor (TF)-miRNA regulations, through which one can find regulatory relations between TFs and miRNAs. | http://www.cuilab.cn/transmir |
Cupid | A method for simultaneous prediction of miRNA-target interactions and their mediated competing endogenous RNA (ceRNA) interactions. | http://cupidtool.sourceforge.net/ |
miRwalk | Aggregates and compares results from other miRNA-to-mRNA databases. | http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/ |
IMOTA | An interactive multi-omics-tissue atlas that helps you to find out more about relationships between miRNAs, proteins, and mRNAs by using charts as filters. | https://ccb-web.cs.uni-saarland.de/imota/. |
LncRNA | ||
DeepBase2.0 | A platform for annotating and discovering miRNAs, lncRNAs, and circRNAs from next generation sequencing data. | http://rna.sysu.edu.cn/deepBase/ |
lncRNdb | The reference database for functional lncRNAs. | http://lncrnadb.com/ |
LncRNAWiki | A wiki-based, publicly editable, and open-content platform for community curation of human lncRNAs. | http://lncrna.big.ac.cn |
NONCODE | An integrated knowledge database dedicated to ncRNAs, especially lncRNAs. | http://www.noncode.org |
lncRNome | A comprehensive searchable biologically oriented knowledgebase for lncRNAs in humans. | http://genome.igib.res.in/lncRNome/ |
NONCODE | A systematic database that is dedicated to present the most complete collection and annotation of ncRNAs, especially lncRNAs. | http://www.bioinfo.org/noncode/ |
RISE | A comprehensive repository of RNA-RNA interactions involving mRNA and lncRNAs. | http://rise.life.tsinghua.edu.cn/ |
Lnc2Meth | A comprehensive resource and web tool for clarifying the regulatory relationships between human lncRNAs and associated DNA methylation in diverse diseases. | http://bio-bigdata.hrbmu.edu.cn/Lnc2Meth/ |
circRNA | ||
circRNABase | Decodes miRNA-circRNA interaction network from CLIP-Seq data. | http://starbase.sysu.edu.cn/mirCircRNA.php |
circBase | Explores public circRNA datasets or discover circRNAs in your own RNA-Seq data. | http://www.circbase.org/ |
CircNet | A database of circRNAs derived from transcriptome sequencing data. | http://circnet.mbc.nctu.edu.tw/ |
Circ2Traits | A comprehensive collection for circRNAs is potentially associated with diseases and traits. | http://gyanxet-beta.com/circdb/ |
CSCD | A database for cancer-specific circRNAs. | http://gb.whu.edu.cn/CSCD/ |
Database for Circulating ncRNAs | ||
miRandola | A comprehensive manually curated classification of different extracellular circulating ncRNA types. | http://mirandola.iit.cnr.it/ |
ExoRBase | A repository of circRNA, lncRNA, and mRNA derived from RNA-Sequence data analyses of human blood exosomes. | http://wwww.exorbase.org |
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Nie, J.-H.; Li, T.-X.; Zhang, X.-Q.; Liu, J. Roles of Non-Coding RNAs in Normal Human Brain Development, Brain Tumor, and Neuropsychiatric Disorders. Non-Coding RNA 2019, 5, 36. https://doi.org/10.3390/ncrna5020036
Nie J-H, Li T-X, Zhang X-Q, Liu J. Roles of Non-Coding RNAs in Normal Human Brain Development, Brain Tumor, and Neuropsychiatric Disorders. Non-Coding RNA. 2019; 5(2):36. https://doi.org/10.3390/ncrna5020036
Chicago/Turabian StyleNie, Jun-Hua, Tian-Xiang Li, Xiao-Qin Zhang, and Jia Liu. 2019. "Roles of Non-Coding RNAs in Normal Human Brain Development, Brain Tumor, and Neuropsychiatric Disorders" Non-Coding RNA 5, no. 2: 36. https://doi.org/10.3390/ncrna5020036