Background/Aim: Two-thirds of head and neck squamous cell carcinoma (HNSCC) patients present with locally advanced (LA) stages and have a poor survival rate. The aim of this study was to investigate the roles of the long non-coding RNAs MALAT1 on radiation and cisplatin sensitivity of HNSCC cells. Materials and Methods: Clonogenic, cell viability, and apoptosis assays were performed in cells following MALAT1 knockdown using CRISPR/Cas9 system. Results: MALAT1 was overexpressed in HNSCC cell lines as compared to a non-tumorigenic cell line. The number of colonies formed after radiation was significantly reduced in MALAT1 knockdown cells. The IC50 value of cisplatin in MALAT1 knockdown cells was lower than that of the control cells. MALAT1 knockdown resulted in cell cycle arrest at G2/M phase, DNA damage and apoptotic cell death. Conclusion: MALAT1 knockdown enhanced the sensitivity of HNSCC cells to radiation and cisplatin partly through the induction of G2/M cell cycle arrest resulting in DNA damage and apoptosis.
MALAT1 metastasis associated lung adenocarcinoma transcript 1 [ Homo sapiens (human) ]
Gene ID: 378938, updated on 3-May-2020Summary
- Official Symbol
- MALAT1provided by HGNC
- Official Full Name
- metastasis associated lung adenocarcinoma transcript 1provided by HGNC
- Primary source
- HGNC:HGNC:29665
- See related
- Ensembl:ENSG00000251562 MIM:607924
- Gene type
- ncRNA
- RefSeq status
- REVIEWED
- Organism
- Homo sapiens
- Lineage
- Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
- Also known as
- HCN; NEAT2; PRO2853; LINC00047; NCRNA00047
- Summary
- This gene produces a precursor transcript from which a long non-coding RNA is derived by RNase P cleavage of a tRNA-like small ncRNA (known as mascRNA) from its 3' end. The resultant mature transcript lacks a canonical poly(A) tail but is instead stabilized by a 3' triple helical structure. This transcript is retained in the nucleus where it is thought to form molecular scaffolds for ribonucleoprotein complexes. It may act as a transcriptional regulator for numerous genes, including some genes involved in cancer metastasis and cell migration, and it is involved in cell cycle regulation. Its upregulation in multiple cancerous tissues has been associated with the proliferation and metastasis of tumor cells. [provided by RefSeq, Mar 2015]
- Expression
- Ubiquitous expression in bone marrow (RPKM 137.2), thyroid (RPKM 115.3) and 24 other tissues See more
- Orthologs
- mouse all
Genomic context
See MALAT1 in Genome Data Viewer
- Location:
- 11q13.1
- Exon count:
- 2
| Annotation release | Status | Assembly | Chr | Location |
|---|---|---|---|---|
| 109.20200228 | current | GRCh38.p13 (GCF_000001405.39) | 11 | NC_000011.10 (65497738..65506516) |
| 105 | previous assembly | GRCh37.p13 (GCF_000001405.25) | 11 | NC_000011.9 (65265224..65273940) |
Chromosome 11 - NC_000011.10
Genomic regions, transcripts, and products
Genes, Ensembl release 99
Biological regions, aggregate, NCBI Homo sapiens Annotation Release 109.20200228
Clinical, dbSNP b153 v2
Cited Variations, dbSNP b153 v2
RNA-seq intron-spanning reads, aggregate (filtered), NCBI Homo sapiens Annotation Release 109 - log base 2 scaled
Genes, NCBI Homo sapiens Annotation Release 109.20200228
RNA-seq intron features, aggregate (filtered), NCBI Homo sapiens Annotation Release 109
RNA-seq exon coverage, aggregate (filtered), NCBI Homo sapiens Annotation Release 109 - log base 2 scaled
Live RefSNPs, dbSNP b153 v2
Expression
- Project title: HPA RNA-seq normal tissues
- Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
- BioProject: PRJEB4337
- Publication: PMID 24309898
- Analysis date: Wed Apr 4 07:08:55 2018
Bibliography
Related articles in PubMed
- The long-noncoding RNA MALAT1 regulates TGF-β/Smad signaling through formation of a lncRNA-protein complex with Smads, SETD2 and PPM1A in hepatic cells.Zhang J, et al. PLoS One, 2020. PMID 31995604, Free PMC Article
- Long non-coding RNA MALAT1 facilitates the tumorigenesis, invasion and glycolysis of multiple myeloma via miR-1271-5p/SOX13 axis.Liu N, et al. J Cancer Res Clin Oncol, 2020 Feb. PMID 31953613, Free PMC Article
- Secondary Structural Model of Human MALAT1 Reveals Multiple Structure-Function Relationships.McCown PJ, et al. Int J Mol Sci, 2019 Nov 9. PMID 31717552, Free PMC Article
- LncRNA-MALAT1 mediates cisplatin resistance via miR-101-3p/VEGF-C pathway in bladder cancer.Liu P, et al. Acta Biochim Biophys Sin (Shanghai), 2019 Nov 18. PMID 31650173
- Silencing of MALAT1 inhibits migration and invasion by sponging miR‑1‑3p in prostate cancer cells.Dai X, et al. Mol Med Rep, 2019 Oct. PMID 31485645, Free PMC Article
GeneRIFs: Gene References Into Functions
What's a GeneRIF?
- Our research proposes a novel mechanism where the role of MALAT1 is dependent on the MALAT1/miR-181a-5p/AKT3 axis. MALAT1 competes with AKT3 for miR-181a-5p binding, thereby upregulating the AKT3 protein level and ultimately promoting the growth of gastric adenocarcinoma.
- LncRNA MALAT1 induced the upregulation of CRP expression through inhibiting the expression of hsa-miR-145-5p, hsa-miR-140-5p, hsa-miR-483-3p, and hsa-miR-338-3p.
- regulates TGF-beta/Smad signaling through formation of a lncRNA-protein complex with Smads, SETD2 and PPM1A in hepatic cells
- lncRNA-MALAT1 mediates hypoxia-induced pro-survival autophagy of endometrial stromal cells in endometriosis.
- High MALAT1 expression is associated with diabetic nephropathy.
- Long non-coding RNA Malat1 activated autophagy and promoted cell proliferation, yet inhibited apoptosis by sponging miR-101 in colorectal cancer cells.
- The authors show that MALAT1-induced epithelial-to-mesenchymal transition in high glucose -treated HK-2 cells through activating the Wnt/beta-catenin pathway.
- microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus.
- demonstrates that cancer cell-specific chromatin-chromatin interactions are formed at the MALAT1 locus under hypoxia, implicating a novel mechanism of MALAT1 regulation in cancer
- The model indicates that approximately half of human MALAT1 is structured, forming 194 helices, 13 pseudoknots, five structured tetraloops, nine structured internal loops, and 13 intramolecular long-range interactions that give rise to several multiway junctions.
Phenotypes
NHGRI GWAS Catalog
| Description |
|---|
| Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. NHGRI GWA Catalog |
Interactions
| Products | Interactant | Other Gene | Complex | Source | Pubs | Description |
|---|---|---|---|---|---|---|
| BioGRID:132077 | BioGRID:118041 | AGO2 | BioGRID | PubMed | Affinity Capture-RNA | |
| BioGRID:132077 | BioGRID:109822 | ILF3 | BioGRID | PubMed | Affinity Capture-RNA | |
| BioGRID:132077 | BioGRID:107312 | RUNX3 | BioGRID | PubMed | Affinity Capture-RNA | |
| BioGRID:132077 | BioGRID:113500 | TRIM25 | BioGRID | PubMed | Affinity Capture-RNA |
General gene information
Homology
- Orthologs from Annotation Pipeline: 1 organisms have orthologs with human gene MALAT1
Other Names
- hepcarcin
- long intergenic non-protein coding RNA 47
- metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)
- nuclear enriched abundant transcript 2
- nuclear paraspeckle assembly transcript 2 (non-protein coding)
NCBI Reference Sequences (RefSeq)
RefSeqs maintained independently of Annotated Genomes
These reference sequences exist independently of genome builds. Explain
RNA
- NR_002819.4 RNA SequenceStatus: REVIEWED
- Description
- Transcript Variant: This variant (1) represents the unspliced, longest transcript.
- Source sequence(s)
- AI805768, CA394984, EF177381
- Related
- ENST00000534336.1
- NR_144567.1 RNA SequenceStatus: REVIEWED
- Description
- Transcript Variant: This variant (2, also known as long) lacks an alternate segment in the 5' region compared to variant 1.
- Source sequence(s)
- AI805768, BK001418, CA394984, EF177381
- NR_144568.1 RNA SequenceStatus: REVIEWED
- Description
- Transcript Variant: This variant (3, also known as short) lacks two alternate segments compared to variant 1.
- Source sequence(s)
- AI805768, BK001411, CA394984, EF177381
RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.
The following sections contain reference sequences that belong to a specific genome build. Explain
Reference GRCh38.p13 Primary Assembly
Genomic
- NC_000011.10 Reference GRCh38.p13 Primary Assembly
- Range
- 65497738..65506516
- Download
- GenBank, FASTA, Sequence Viewer (Graphics)
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