MALAT1 is a long non-coding RNA that is overexpressed in many cancers and associated with poor prognosis. It plays roles in alternative splicing, transcriptional regulation, acting as a ceRNA, and conferring drug resistance. Specifically, it localizes to nuclear speckles and regulates alternative splicing by interacting with splicing factors like SR proteins. It also interacts with PRC2 and recruits it to target genes to repress transcription. Additionally, MALAT1 can act as a ceRNA by sponging various miRNAs to regulate genes involved in processes like migration, invasion, and stemness.

1. MALAT1
Ahmed Adel Abdallah
MSc. Medical labs
Islamic University of Gaza
1/12/2021

2. Non coding RNAs
NcRNAs can be categorized into two groups according to their length: small
ncRNAs and long ncRNAs.
In addition, lncRNAs are subdivided by function, loci and post-transcriptional
modification.
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs. These are
transcribed by RNA polymerase II but not translated into proteins, and length
more than ≥200 nucleotides.
Transcriptome analyses have revealed that 70-90% of the mammalian genome
was transcribed, but only 1-2% may encode proteins.

3. Non coding RNAs
Additionally, lncRNAs that are localized to the nucleus possess stronger secondary
structures. Therefore, knockdown of lncRNAs may not be sufficiently effective at
evoking a phenotype and uncovering the physiological function of the lncRNA.
lncRNAs which were once considered transcriptional noise without any biological
function, have gained considerable interest as principal regulators of gene
expression.
The expression of lncRNAs is associated with numerous human diseases, including
cancer.
The present study focuses on the recent advances in the role of MALAT-1 in diverse
cancers, as MALAT-1 possesses a typical multifunctional lncRNA.

4. The roles of lncRNAs in
lung cancer growth,
metastasis, angiogenesis,
genomic instability,
drug resistance, energy
metabolism
reprogramming and
immune
microenvironment and
stem cell characteristics.

5. MALAT1
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), also termed
nuclear enriched abundant transcript 2 (NEAT2), is a long non-coding RNA with >8.5
kb, located on chromosome 11q13, and transcribed by RNA polymerase II.
Ji et al. (2003) found that MALAT1 was overexpressed in early-stage metastasizing
non-small cell lung cancer (NSCLC).
High expression levels of MALAT1 correlated with poor prognosis in NSCLC patients.
Therefore, MALAT1 has been proposed as a prognostic marker for metastasis and
NSCLC patient survival.

6. MALAT1
It was one of the first ncRNAs that was associated with lung cancer.
In addition, MALAT-1 is upregulated in a number of human carcinomas, highly
expressed in numerous cancer types, including bladder cancer, gallbladder
carcinoma, liver cancer, melanoma, colorectal cancer and gastric cancer, and
associated with metastasis.

7. MALAT1
MALAT-1 lacks a significant open reading frame; therefore, it may not translate
proteins in vitro.
Studies have indicated that MALAT-1 possesses a distinct sequence or secondary
structure that directs localization to nuclear speckles in human tumor cells.
• Notably, The quantitative loss of MALAT-1 did not affect proliferation, cell cycle
progression or nuclear architecture in human lung or liver cells.
• The MALAT-1 mouse model did not reveal any evident phenotype or
histological abnormalities compared with wild-type animals.
• In addition, the loss of abundant nuclear MALAT-1 is compatible with cell
viability and normal development.

8. MALAT1
• This previous studies have demonstrated that MALAT-1 which predominantly
retained in nuclear speckles, interacts with pre-mRNA splicing factors, including
the serine- and arginine-rich (SR) family of proteins, and acting by modulate the
distribution and levels of active pre-mRNA splicing factors (SR proteins).
• However, MALAT-1 function becomes apparent only in specific cell types, such
as metastatic cancer cells, and under particular conditions.

9. MALAT1 biogenesis
• At the posttranscriptional level, a processing mechanism can modify the 3′-end
of MALAT1.
• The processing at the 3′-end is executed by two endogenous RNases—RNase P
and RNase Z.
• RNases act on MALAT1 to generate a larger fragment of ~ 6.7kb and a smaller
fragment of 61 nucleotides known as MALAT1-associated small cytoplasmic RNA
(mascRNA).
• The larger fragment or mature transcript of MALAT1 is very stable owing to a
unique triple-helix structure on the 3’ end that protects it from exonucleases.

10. MALAT1 biogenesis
The larger fragment or mature MALAT1 transcript stays in the nucleus and
localizes on nuclear speckles (NSs).
However, the smaller fragment mascRNA with structural similarity to tRNA
moves to cytoplasm and has no known function.
MALAT1 half-life (9–12 h) is longer than other lncRNAs, probably for the
presence of a triple helix structure at its 3′ end that confers stability by engaging
a downstream A-rich tract.

11. MALAT1 biogenesis

12. MALAT1 molecular functions
Alternative splicing:
- Regulation of alternative splicing is the first identified function for MALAT1.
- The nuclear MALAT1 can be recruited to nuclear speckles, a site for pre-mRNA
splicing factor storage and modification.
- By binding pre-mRNA splicing factors, MALAT1 regulates their distribution in
nuclear speckle domains and thereby modulates pre-mRNA splicing, mRNA
expression, and cellular function.
- It has been well studied that Alternative Splicing is regulated by trans-acting
protein factors which include the small nuclear ribonucleoproteins (snRNPs),
the serine/arginine-rich (SR) family of nuclear phosphoproteins, and the
heterogeneous nuclear ribonucleoproteins (hnRNPs).

14. Alternative splicing
Malat1 localizes to the nuclear speckles that are enriched with pre-mRNA splicing
factors.
Formaldehyde-cross-linked immunoprecipitation analyses demonstrated that Malat1
associates with a set of SR proteins, including SRSF1, SRSF2, and SRSF3.
MALAT1 is able to control SRSF phosphorylation, which enhances SRSF activity to
promote AS.
Tripathi et al. showed that deletion of Malat1 led to mislocalization of splicing factors,
such as SF1, U2AF65, SF3a60, and U2B, in the nuclear speckles.
Malat1 deletion also impair the phosphorylation and the expression pattern of SR
proteins, ultimately affecting pre-mRNAs alternative splicing.
In addition, antisense oligonucleotide mediated repression of Malat1 in HeLa cells alters
the pattern of Alternative splicing of particular pre-mRNAs.

15. Alternative splicing
This findings together, suggest that Malat1 indirectly controls alternative splicing
by changing the distribution of splicing regulators in the nuclear speckles in
certain cell lines.
However, it seems that the effects of Malat1 on AS can hardly be observed in in
vivo models.
Zhang et al. generated Malat1 knockout mouse which lacks genomic region
containing the end of Malat1 gene and its promoter, The Malat1 knockout mice
were viable and fertile.
Next, they isolated mouse embryo fibroblasts (MEFs) and found that Malat1
deletion has no significant effects on neither the formation/structure of nuclear
speckles nor the level/phosphorylation status of SR proteins.

16. Alternative splicing
Similar observations were reported by Nakagawa et al. They generated Malat1
knockout mice by homologous recombination and found no apparent
abnormalities in these animals.
They also showed that nuclear speckle components are correctly localized in
Malat1 knockout mice.
However, loss of MALAT1 in the mouse mammary tumor virus (MMTV)-PyMT
mammary carcinoma mice results in alterations in the expression and splicing of
genes important for cell differentiation and tumorigenesis.

17. Alternative splicing
One explanation for the discrepancy between Malat1 function in vitro and in
vivo could be Malat1 only plays certain function under specific stress conditions
and Malat1 is not effective in regulation of AS under normal physiologic
conditions.
It can therefore be proposed that MALAT1 regulates premRNA splicing in specific
cells and tissues under particular conditions.

18. Transcriptional regulation
Transcriptional regulation; MALAT1 in Cancer and Metastasis
Previous studies have revealed that several lncRNAs, such as HOTAIR and Xist, bind
to Polycomb repressor complex 2 (PRC2) enhancing tri-methylation of histone H3
on lysine 27 (H3K27me3), that results in epigenetic silencing of target gene.
It was reported that MALAT1 also affect gene expression by interacting with
PRC2 through different subunits (EZH2, SUZ12).
- Polycomb repressive complex 2 (PRC2) induces histone H3 lysine 27 (H3K27)
tri-methylation and transcriptional repression of tumor suppressor genes.

19. Transcriptional regulation
- It has been shown that MALAT1 is required for PRC2 complex binding to gene
promoters and consequent regulation of gene transcription.
- MALAT1 forms RNA protein complex with EZH2 and SUZ12, two components of
the PRC2 complex.
- MALAT1 bind to EZH2 and then recruits PRC2 to target genes.
- Then, p21 and p27 expression is epigenetically repressed by H3K27me3.
- Then, activated CDK1 and CDK2 promotes phosphorylation of EZH2 at T350,
resulting in increase binding to MALAT1.

20. Transcriptional regulation
Low expression or knockdown of MALAT1 decrease the recruitment of PRC2 to
targeted genes p21 and p27, which inhibit CDKs activities, causing cell cycle
arrest and decreased phosphorylation of EZH2 at T350.
In addition, MALAT1 increases histone H3K27 trimethylation at the promoters of
tumor suppressor genes such as E-cadherin and N-Myc downregulated gene-1
(NDRG1) and suppresses their gene expression.
◦ - The loss of E-cadherin expression has been thought to allow malignant
tumor cells to dissociate from the primary tumor mass and invade the
extracellular matrix and surrounding stroma.
◦ - NDRG1: is a metastasis suppressor gene.

23. ceRNA
MALAT1 as Competitive Endogenous RNA (ceRNA);
-- MALAT1 is a long and highly abundant lncRNA that contains many putative
binding sites of miRNAs. A number of studies reported that MALAT1 functions
through sponging miRNAs, including miR-145, miR-1, miR-202, miR-200c, miR-
206, miR-204, and so on.
-- In these studies, the authors typically showed that siRNA-mediated knockdown
of MALAT1 in cancer cell lines resulted in a certain phenotype, such as
proliferation, migration, invasion, chemosensitivity, or radiosensitivity.

24. ceRNA
◦ miR-1, miR- 124, and miR-448: up-regulates CDK4 expression, and induces
breast cancer cell
cycle progression, cell migration, and invasion
◦ miR145-5p: Decreases miR145-5p, increases NEDD9 protein, and induces non-
small cell lung
cancer cell migration and invasion
◦ EZH2: Decreases p21 and p27 expression, leading to mantle cell lymphoma
cell survival, and proliferation.
◦ miR-211: induces ovarian cancer cell proliferation, invasion.
..

25. Drug resistance
MALAT1 has been implicated in promoting resistance to various
chemotherapeutic agents like cisplatin, oxaliplatin, temozolomide, etc by
modulating cancer stem cells through pathways like hippo-YAP1, Wnt/β-catenin,
and Notch1.
The attenuation of MALAT1 expression may increase the sensitivity of cancer
cells to chemotherapeutic agents.
MALAT1 further stabilized YAP1 mRNA and resulted in the sponging of miR-
1914-3p, This leads to resistance to cisplatin.

26. Drug resistance
Knockdown of m6A modifications of YAP1 by METTLE3 resulted in the enhanced
cisplatin sensitivity.
Similar to YAP1 signaling, Wnt/β-catenin also mediates drug resistance to
cisplatin.
In lung cancer via ceRNA action of MALAT1 which sponges on miR-101.
MALAT1 also promoted resistance to oxaliplatin by downregulating miR-218