MALAT1

Summary

MALAT1 (metastasis associated lung adenocarcinoma transcript 1, HGNC:29665) is a long non-coding RNA gene on chromosome 11q13.1.

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.

Source: NCBI Gene 378938 — RefSeq curated summary.

At a glance

• Gene type: non-coding (lncRNA) — no protein product; not a drug target. Variant/disease associations are omitted (they would be positional, from an overlapping protein-coding gene).

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29665
Approved symbol	MALAT1
Name	metastasis associated lung adenocarcinoma transcript 1
Location	11q13.1
Locus type	RNA, long non-coding
Status	Approved
Aliases	miPEP-52, PRO1073, MALAT-1, NCRNA00047, HCN, NEAT2, LINC00047, mascRNA
Ensembl gene	ENSG00000251562
Ensembl biotype	lncRNA
OMIM	607924
Entrez	378938
RNAcentral	URS0002A146E4 — lncRNA, 7472 nt, 1 organism(s)

Gene structure

Transcript identifiers

Ensembl transcripts: 73 — 73 lncRNA

ENST00000508832, ENST00000534336, ENST00000544868, ENST00000610481, ENST00000610851, ENST00000612781, ENST00000613376, ENST00000616527, ENST00000616691, ENST00000617489, ENST00000618132, ENST00000618227, ENST00000618925, ENST00000619449, ENST00000620465, ENST00000620902, ENST00000710847, ENST00000710848, ENST00000710849, ENST00000710852, ENST00000710855, ENST00000710856, ENST00000710857, ENST00000710858, ENST00000710859, ENST00000710860, ENST00000710861, ENST00000710862, ENST00000710863, ENST00000710864, ENST00000710865, ENST00000710866, ENST00000710867, ENST00000710868, ENST00000710869, ENST00000710870, ENST00000710871, ENST00000710874, ENST00000710875, ENST00000710876, ENST00000710877, ENST00000710878, ENST00000710879, ENST00000710880, ENST00000710925, ENST00000710926, ENST00000710927, ENST00000710933, ENST00000710934, ENST00000710935, ENST00000710936, ENST00000710937, ENST00000710938, ENST00000710939, ENST00000710940, ENST00000710941, ENST00000710942, ENST00000710943, ENST00000710944, ENST00000710945, ENST00000710946, ENST00000710947, ENST00000710948, ENST00000710949, ENST00000710950, ENST00000710951, ENST00000783044, ENST00000783046, ENST00000783047, ENST00000783048, ENST00000783049, ENST00000783050, ENST00000850956

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

ENST00000508832 — 2 exons

Exon	Start	End
ENSE00002080048	65502637	65505452
ENSE00002321105	65499042	65502393

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 99.99.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10233.6791 / max 555585.3478, expressed in 1828 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter ID	TPM avg	Samples expressed
115161	9853.5226	1828
115164	263.2706	1774
115163	94.4588	1717
115154	19.8940	1741
115165	1.2350	493
115157	1.0572	477
115160	0.4599	172
115152	0.3954	210
115155	0.2558	108
115158	0.1332	42

Top tissues by expression

256 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
renal medulla	UBERON:0000362	99.99	gold quality
cardia of stomach	UBERON:0001162	99.99	gold quality
trigeminal ganglion	UBERON:0001675	99.99	gold quality
corpus callosum	UBERON:0002336	99.99	gold quality
dorsal root ganglion	UBERON:0000044	99.98	gold quality
seminal vesicle	UBERON:0000998	99.98	gold quality
pylorus	UBERON:0001166	99.98	gold quality
lateral globus pallidus	UBERON:0002476	99.98	gold quality
calcaneal tendon	UBERON:0003701	99.98	gold quality
tendon	UBERON:0000043	99.97	gold quality
urethra	UBERON:0000057	99.97	gold quality
substantia nigra pars compacta	UBERON:0001965	99.97	gold quality
substantia nigra pars reticulata	UBERON:0001966	99.97	gold quality
tendon of biceps brachii	UBERON:0008188	99.97	gold quality
bone marrow cell	CL:0002092	99.96	gold quality
colonic epithelium	UBERON:0000397	99.96	gold quality
medulla oblongata	UBERON:0001896	99.96	gold quality
pericardium	UBERON:0002407	99.96	gold quality
ventral tegmental area	UBERON:0002691	99.96	gold quality
lateral nuclear group of thalamus	UBERON:0002736	99.96	gold quality
kidney epithelium	UBERON:0004819	99.96	gold quality
inferior vagus X ganglion	UBERON:0005363	99.96	gold quality
superior vestibular nucleus	UBERON:0007227	99.96	gold quality
superior surface of tongue	UBERON:0007371	99.96	gold quality
superficial temporal artery	UBERON:0001614	99.95	gold quality
dorsal plus ventral thalamus	UBERON:0001897	99.95	gold quality
trachea	UBERON:0003126	99.95	gold quality
subthalamic nucleus	UBERON:0001906	99.94	gold quality
occipital lobe	UBERON:0002021	99.94	gold quality
synovial joint	UBERON:0002217	99.94	gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-10662	yes	144066.73
E-GEOD-180759	yes	131155.66
E-MTAB-9543	yes	35273.99
E-MTAB-10287	no	157457.20
E-CURD-126	no	131275.09
E-HCAD-35	no	87712.77
E-MTAB-10596	no	59675.39
E-ANND-5	no	1050.73
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CREB1, DNMT1, POU5F1, SOX17, SRY

Literature-anchored findings (GeneRIF, showing 40)

• Upregulation of MALAT-1 is associated with endometrial stromal sarcoma of the uterus (PMID:16441420)
• Study identified a highly conserved small RNA of 61 nucleotides originating from the MALAT1 locus that is broadly expressed in human tissues; although the long MALAT1 transcript localizes to nuclear speckles, the small RNA is found only in the cytoplasm. (PMID:19041754)
• Results suggest that MALAT-1 in placenta previa I/P is increased and its down-regulation inhibits trophoblast-like cell invasion. MALAT-1 might be involved in regulating trophoblast invasion during the development of advanced invasive placentation. (PMID:19690017)
• expression of the tumor marker MALAT1 noncoding RNA is sensitive to cell surface receptor activation by oxytocin in a neuroblastoma cell line (PMID:20149803)
• Our data demonstrated that MALAT1 was involved in cervical cancer cell growth, cell cycle progression, and invasion through the regulation of gene expression. (PMID:20213048)
• The expression of the long ncRNA MALAT1 correlates with tumor development, progression or survival in lung, liver and breast cancer. (PMID:20711585)
• MALAT1 regulates alternative splicing by modulating the levels of active serine/arginine (SR) splicing factors. (PMID:20797886)
• mutations were found on the long non-coding RNA MALAT-1 in CRC colorectal cancer (PMID:21503572)
• Our data suggest that MALAT1 plays an important role in tumor progression and could be a novel biomarker for predicting tumor recurrence after liver transplantation (PMID:21678027)
• Studies indicate the correlation of differential expression of metastasis-associated lung adenocarcinoma transcript1 (MALAT1) with tumor development, progression or survival in several cancerous conditions. (PMID:21941126)
• Pc2, methylation controls the protein’s interaction with two distinct ncRNAs, TUG1 and NEAT2, which results in the exclusive subnuclear localization of methylated and unmethylated Pc2 in Polycomb bodies and interchromatin granules, respectively. (PMID:22078878)
• Our results suggest that MALAT-1 transcript induces migration in Non-small cell lung cancers and stimulates tumor growth and invasion in vivo. (PMID:22088988)
• MALAT-1 is upregulated in specific regions of the human alcoholic brain. (PMID:22560368)
• Study verified that MALAT-1 levels were upregulated in bladder cancer tissues compared with adjacent normal tissues, and MALAT-1 expression was remarkably increased in primary tumors that subsequently metastasized (PMID:22722759)
• The quantitative loss of MALAT1 did neither affect proliferation nor cell cycle progression nor nuclear architecture in human lung or liver cancer cells. (PMID:22858678)
• Formation of triple-helical structures by the 3’-end sequences of MALAT1 and MENbeta noncoding RNAs, is reported. (PMID:23129630)
• MALAT1 is upregulated in urothelial carcinoma of the bladder, and high MALAT1 expression levels were associated with high-grade and high-stage carcinoma. (PMID:23153939)
• The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. (PMID:23243023)
• These findings provide mechanistic insights on the role of MALAT1 in regulating cellular proliferation (PMID:23555285)
• MALAT-1 miniRNA can be used as a novel plasma-based biomarker for prostate cancer detection and can improve diagnostic accuracy by predicting prostate biopsy outcomes. (PMID:23726266)
• The levels of plasma lncRNAs, H19, HOX antisense intergenic RNA (HOTAIR), and metastasis associated lung adenocarcinoma transcript-1 (MALAT1), were analyzed in patients with gastric cancer (GC) and healthy controls. (PMID:23898077)
• down-regulation of MALAT-1 expression compromised the cytoplasmic translocation of hnRNP C in the G2/M phase and resulted in G2/M arrest (PMID:23973260)
• microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus. (PMID:23985560)
• Genetic translocations involving MALAT1 gene is associated with mesenchymal hamartoma of the liver. (PMID:24120702)
• malat1 promotes bladder cancer metastasis by associating with suz12. (PMID:24449823)
• Malat1 is a critical regulator of maintaining the transformative phenotype in liver cancer. (PMID:24468535)
• MALAT1 regulates endothelial cell proliferation/migration and vessel growth. (PMID:24602777)
• MALAT1 might serve as an oncogenic lncRNA that promotes proliferation and metastasis of gallbladder cancer and activates the ERK/MAPK pathway. (PMID:24658096)
• MALAT1 might be considered as a potential prognostic indicator and may be a target for diagnosis and gene therapy for pancreatic duct adenocarcinoma. (PMID:24815433)
• These results suggest that MALAT1 may function as a promoter of gastric cancer cell proliferation partly by regulating SF2/ASF. (PMID:24857172)
• Knockdown of UCA1 or Malat-1 lncRNA could attenuate the migrational ability of melanoma cells in in-vitro studies. Increased expression of UCA1 and Malat-1 lncRNAs might have a correlation with melanoma metastasis. (PMID:24892958)
• MALAT1 binds to SFPQ releasing PTBP2 from the SFPQ/PTBP2 complex, the increased SFPQ-detached PTBP2 promotes cell proliferation and migration in colorectal cancer. (PMID:25025966)
• The expression of MALAT1 is upregulated in colorectal cancer (PMID:25031737)
• An interaction of Bcl-2 with MALAT-1 lncRNA expression was revealed, which merits further investigation for risk prediction in resectable NSCLC patients. (PMID:25036876)
• Findings establish a novel PCDH10-Wnt/beta-catenin-MALAT1 regulatory axis that contributes to EEC development. (PMID:25085246)
• the mechanism of transcriptional activation of LTBP3 promoter depends on MALAT1 initiated from neighboring gene LTBP3 and involves both the direct interaction of the Sp1 and promoter-specific activation (PMID:25187517)
• Results showed that the high level of MALAT1 is associated with lung cancer brain metastasis and survival and demonstrated the potential role of MALAT1 in identification of non-small cell lung cancer patients at high risk of brain metastasis (PMID:25217850)
• MALAT-1 may serve as an oncogenic lncRNA that is involved in malignancy phenotypes of pancreatic cancer. (PMID:25269958)
• High MALAT1 expression drives gastric cancer development and promotes peritoneal metastasis. (PMID:25280565)
• MALAT1 was overexpressed in patients with myeloma and may play a role in its pathogenesis. In addition, MALAT1 may serve as a molecular predictor of early progression. (PMID:25369863)

Cross-species orthologs

0 orthologs

Protein

Non-coding RNA — no protein product; not a drug target.

Function

No curated pathway, Gene-Ontology, or interaction data.

Disease & clinical

No curated disease, variant, or cancer-driver associations.

Drugs & pharmacology

No drug or pharmacology data — not an established drug target.