Long non-coding RNA NEAT1-centric gene regulation

Abstract

Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA that is widely expressed in a variety of mammalian cell types. An increasing number of studies have demonstrated that NEAT1 plays key roles in various biological and pathological processes; therefore, it is important to understand how its expression is regulated and how it regulates the expression of its target genes. Recently, we found that NEAT1 expression could be regulated by signal transducer and activator of transcription 3 and that altered NEAT1 expression epigenetically regulates downstream gene transcription during herpes simplex virus-1 infection and Alzheimer’s disease, suggesting that NEAT1 acts as an important sensor and effector during stress and disease development. In this review, we summarize and discuss the molecules and regulatory patterns that control NEAT1 gene expression and the molecular mechanism via which NEAT1 regulates the expression of its target genes, providing novel insights into the central role of NEAT1 in gene regulation.

Introduction

Long non-coding RNAs (lncRNAs) are extremely diverse and have various significant physiological functions. The main cellular functions of lncRNAs are regulating gene expression, stabilizing protein complexes, and regulating subcellular architecture [1]. Among the characterized nuclear lncRNAs, nuclear paraspeckle assembly transcript 1 (NEAT1) has been reported to be involved in multiple physiological and pathological processes, such as the immune response [2, 3], viral infection [4–6], tumors [7, 8], and neurodegenerative diseases [9]. NEAT1 is composed of two isoform transcripts, NEAT1v1 (3.7 kb) and NEAT1v2 (23 kb), which are necessary components for nuclear paraspeckle formation that associate with other paraspeckle proteins, including paraspeckle component 1 (PSPC1), 54 KDa nuclear RNA- and DNA-binding protein (p54nrb), and splicing factor proline/glutamine rich (SFPQ) [10]. The long isoform NEAT1v2 first interacts with p54nrb/NONO and SFPQ/PSF to form an RNA–protein complex, following which the short isoform NEAT1v1 and PSPC1 are recruited to the complex [11].

The key role of NEAT1 is mediating gene expression. The first NEAT1-mediated regulatory pattern to be discovered was the nuclear retention of A-to-I hyper-edited RNAs catalyzed by dsRNA-dependent adenosine deaminases (ADARs) [12], which is a protective cellular mechanism that prevents the inappropriate translation of promiscuously edited RNAs. NEAT1 was then found to bind to genomic DNA [13], while we and other research groups have provided evidence that NEAT1 epigenetically regulates gene expression by recruiting transcription factors to and sequestering them from gene promoters and subsequently altering gene transcription [4, 5, 9]. NEAT1 can also regulate gene expression by associating with RNA-binding proteins (RBPs) to modulate RNA splicing and protein stabilization [14, 15], while NEAT1 was recently found to act as a competing endogenous RNA by sponging miRNAs to alter the expression of their target RNAs (Table 1).

Table 1.

MiRNAs sponged by NEAT1 and upregulated protein targets

MiRNA	Target	MiRNA	Target	MiRNA	Target
101	EZH2	106b-5p	ATAD2	204-5p	PI3K
107	CPT1A, CDK14, CDK6	124-3p	ATGL	214-3p	HMGA1
124	NF-κB/p65, STAT3	125a-5p	BCL2L12	23a-3p	SMC1A, KLF3
129	CTBP2	129-5p	KLK7	27b-3p	ZEB1
132	SOX2	133a	SOX4	29b-3p	BMP1
155	Tim-3	133b	TIMM17A	302a-3p	RELA
194	ZEB1	139-5p	CDK6, TGF-β1	335-5p	ROCK1, c-Met
204	ATG3, CXCR4, ZEB1	140-5p	HDAC4	339-5p	TGF-β1
211	HMGA2	146a-5p	ROCK1	34a-5p	BCL-2, c-Met, SIRT1, HOXA13
214	β-Catenin	146b-5p	LEF1	34c	BCL-2, CCND1
361	STAT3	181a-5p	HMGB2	361-5p	VEGFA
365	RGS20	181b	mLST8	377-3p	E2F3
377	E2F3	181c	OPN	382-3p	ROCK1
448	ZEB1	181d-5p	SOX5	449b-5p	c-Met
485	STAT3	186-5p	HIF-1α	495-3p	E2F3, CDK6
506	STAT3	193a	L17RD, MCL1	497-5p	PIK3R1
592	NOVA1	193a‐3p	KRAS	9-5p	SPAG9
1246	NF-κB	193b-3p	Cyclin D1	98-5p	HMGA2, MAPK6, CTR1
101-3p	WEE1, EMP2	196a-5p	GDNF	let-7a	IGF2

An increasing number of studies have demonstrated that NEAT1 is dysregulated during the progression of a variety of diseases. For instance, Fang et al. found that NEAT1 is significantly upregulated in digestive system tumors and respiratory carcinomas, while its expression is significantly associated with tumor size, TNM stage, distant metastasis, and overall patient survival [16]. NEAT1 dysregulation has also been identified in non-cancerous diseases, such as neurodegenerative diseases and viral infections. In mitochondrial permeability transition pore (MPTP)-induced Parkinson’s disease (PD) mice model and 1-methyl-4-phenylpyridinium (MPP+)-induced PD cell model, the NEAT1 expression was induced and upregulated NEAT1 promoted MPTP-induced autophagy, inhibited cell viability, and induced apoptosis [17–19]. However, Simchovitz et al. reported a protective role for NEAT1 upregulation in PD. They found that the depletion of NEAT1 exacerbated oxidative stress-induced neurons damage in a leucine-rich repeat kinase 2 (LRRK2)-mediated manner [20]. In addition, our recent study showed that NEAT1 expression was repressed during the early stages of Alzheimer's disease (AD), with NEAT1 downregulation reducing neuroglial cell mediating β-amyloid peptide (Aβ) clearance and thereby promoting the development of AD [9]. Another study investigating the roles of NEAT1 in herpes simplex virus-1 (HSV-1) infection demonstrated that HSV-1 infection significantly upregulates NEAT1 expression, which in turn facilitates the viral life cycle by promoting viral replication and gene expression [5]. Therefore, these studies indicate that NEAT1 could be a promising therapeutic target for treating various diseases.

In this review, we summarize and discuss the molecules and regulatory patterns that modulate NEAT1 expression. These molecules are mainly transcription factors and RBPs that can regulate NEAT1 expression at the transcriptional and post-transcriptional levels by altering gene transcriptional activity, RNA stabilization, and RNA splicing. We also summarize and discuss the molecular mechanisms via which NEAT1 regulates downstream gene expression, which are interestingly the same as those that regulate NEAT1 expression.

Factors and regulatory patterns that regulate NEAT1 expression

Since NEAT1 dysregulation has been reported in a variety of diseases, including cancers, neurodegenerative diseases, autoimmune diseases, and viral infections, numerous studies have investigated the molecular mechanisms regulating NEAT1 expression and have identified many factors involved in its expression. We have summarized these factors in Table 2, finding that they generally regulate NEAT1 gene transcription, NEAT1 stabilization, 3′-end processing. In this section, we discuss the regulatory patterns of these factors in NEAT1 gene expression.

Table 2.

The regulatory factors for NEAT1 expression

Cell type	Factor	Expression	Regulatory pattern	References
MCF-7 cells	P53	Upregulated	Transcription	[24]
Burkitt’s lymphoma cells	P53	Upregulated		[25]
H1299 and SaOS2 cells	P53	Upregulated		[26]
MCF-7 cells	HIF2α	Upregulated		[89]
NSC-34 cells	TDP-43	Upregulated		[38]
Primary microglial cells	YY1	Upregulated		[86]
HEK293 cells	P-TEFb	Upregulated		[90]
LnCaP and PC3 cells	ERα	Upregulated		[84]
QGY-7703 cells	STAT3	Upregulated		[22]
HeLa cells	STAT3	Upregulated		[5]
N5 and N9 cells	STAT3	Upregulated		[23]
MCF-7 cells	HSF1	Upregulated		[87]
HEK293 cells	P65	Upregulated		[85]
N5 and N9 cells	P65	Upregulated		[23]
NB4 cells	C/EBPβ	Upregulated		[88]
A549 and CL1–0 cells	OCT4	Upregulated		[83]
MCF-7 cells	RUNX1	Upregulated		[82]
MCF10A cells	BRCA1	Downregulated		[29]
Dendritic cells	E2F1	Downregulated		[33]
HeLa cells	CARM1	Downregulated		[36]
K562 cells	c-Myc	Downregulated		[31]
mESCs	TDP-43	Upregulated (NEAT1v1), Downregulated (NEAT1v2)	3′-End processing	[58]
HeLa cells	CPSF6	Upregulated (NEAT1v1), Downregulated (NEAT1v2)		[53]
HeLa cells	NUDT21	Upregulated (NEAT1v1), Downregulated (NEAT1v2)		[53]
HeLa cells	HNRNPK	Upregulated (NEAT1v2), Downregulated (NEAT1v1)		[53]
HCC cells	PTBP3	Upregulated		[60]
OVCAR‐3 cells	HuR	Upregulated	RNA stability	[43]
NSC-34 cells	hnRNPM	Upregulated (NEAT1v2)		[38]
Glioma cells	SRSF1	Upregulated		[45]
EOC cells	LIN28B	Upregulated		[47]
HEK293 and HeLa cells	AUF1	Downregulated		[42]
HEK293 cells	miR-140	Upregulated		[50]

Transcription

In our previous study, we investigated the roles of NEAT1 in HSV-1 infection and identified for the first time the relationship between NEAT1 transcription and signal transducer and activator of transcription 3 (STAT3), which acts as an important transcription factor for gene transcription by associating with chromatin [21]. Moreover, we identified a STAT3-binding site 1411–1402 bp upstream of the human NEAT1 transcriptional start site (TSS) and found that HSV-1 infection promotes the binding of STAT3 to this motif to enhance gene transcription [5]. It has also been reported that STAT3 is responsible for NEAT1 upregulation in tumorigenesis. In human hepatocellular carcinoma (HCC), IL-6 signaling increases NEAT1 expression by altering histone modification at the NEAT1 promoter and enhancing gene transcription, with STAT3 involved in this process by binding to the NEAT1 promoter [22]. In glioblastoma, NEAT1 expression is significantly elevated by the EGFR pathway, which promotes STAT3 phosphorylation at Tyr705 (pSTAT3 Y705) and increases its recruitment to the NEAT1 promoter [23]. p53 is another transcriptional regulator of NEAT1. As an important tumor suppressor gene, p53 directly targeted promoter region of NEAT1 to enhance its transcription which contributed to tumor suppression in response to DNA damage in cancers [24–26]. Other transcription factors and regulators like STAT3 and p53 can bind directly to different NEAT1 promoter sites to influence its transcription (Fig. 1). Most promote NEAT1 transcription, with only breast cancer susceptibility gene 1 (BRCA1), E2F1, coactivator-associated arginine methyltransferase 1 (CARM1), and c-Myc inhibiting NEAT1 transcription (Table 2); however, numerous studies have demonstrated that BRCA1, E2F1, CARM1, and c-Myc have dual roles in gene transcription, acting as an activator or a repressor depending on their interacting partners. Herein, we describe the regulatory roles of these factors in NEAT1 transcription.

Fig. 1.

Schematic representation of the binding site of transcriptional factors in the NEAT1 gene. The black box shows the potential binding site

BRCA1 was the first identified breast and ovarian cancer susceptibility gene [27] and increasing evidence has demonstrated that BRCA1 acts as a powerful transcriptional regulator by associating with different transcription factors, including STAT1, p53, ZBRK1, CtIP, c-Myc, and estrogen receptor-α (ER-α). Associations between BRCA1 and c-Myc or ER-α repress the transcription of target genes [28], while a study investigating the upregulation of NEAT1 expression in breast cancer found that BRCA1 negatively regulates NEAT1 expression. Moreover, the study identified and verified a BRCA1-binding site ~ 1.4 kb upstream of the NEAT1 TSS, suggesting that BRCA1 may downregulate NEAT1 expression by directly binding the NEAT1 promoter and then recruiting other transcriptional factor(s) to inhibit NEAT1 transcription [29].

c-Myc is also a bi-functional transcriptional regulator that can downregulate the transcriptional activity of numerous target genes by associating with BRCA1 [30]. Zeng et al. found that NEAT1 expression and transcription are significantly repressed by BCR–ABL-mediated pathways in chronic myelogenous leukemia. As a downstream effector of BCR–ABL-mediated pathways, c-Myc was found to be involved in BCR–ABL-mediated NEAT1 transcription and bind directly to the 500 bp region upstream of the NEAT1 TSS [31].

The transcription factor E2F1 was found to act as a transcriptional repressor by interacting with the retinoblastoma protein (pRB) and inhibiting the recruitment of other transcriptional co-activators to the promoters of target genes by blocking the transcriptional activation domain of the E2F1–DP complex [32]. Moreover, a study examining the roles and underlying mechanisms of NEAT1 in immune tolerance found that E2F1 inhibits NEAT1 transcription by reducing acetylated histone H3 at lysine 27 (H3K27Ac) enrichment, a hallmark of gene transcriptional activation, at the NEAT1 promoter [33].

CARM1, also known as protein arginine methyltransferase 4 (PRMT4), is a member of the PRMT family that can specifically methylate histones and other chromatin-associated proteins to regulate gene transcription [34]. Indeed, its methylation of the CREB-binding protein (CBP)/p300 reduces the transcriptional activity of target genes by blocking the recruitment of CREB to the CBP/P300 complex [35]. A study investigating the roles of CARM1 in the nuclear retention of mRNAs containing IRAlus found that CARM1 is negatively associated with NEAT1 gene transcription and is enriched at the promoter near the NEAT1 gene TSS, suggesting that CARM1 may act as a corepressor of NEAT1 gene transcription by mediating the methylation of its cofactor [36].

RNA stability

To date, a number of RBPs have been found to be involved in regulating the stability of NEAT1 transcripts, including Heterogeneous nuclear ribonucleoprotein M (hnRNPM), AU-binding factor 1 (AUF1), HuR, SRSF1, and LIN28B. Of these, hnRNPM, serine and arginine-rich splicing factor 1 (SRSF1), and Lin-28 Homolog B (LIN28B) have been reported to act as splicing factors during pre-mRNA or pre-miRNA processing, while miR-140 has been shown to stabilize NEAT1. In this section, we will discuss the newly identified roles of these molecules in gene expression.

hnRNPMm, a member of the hnRNP subfamily, mainly influences pre-mRNA splicing by associating with pre-mRNAs in the nucleus by binding to poly(G)- and poly(U)-RNA homopolymers [37]; however, a recent study showed that hnRNPM also affects RNA stability. The study found that the upregulation of NEAT1 expression by hnRNPM was involved in poly-PR-induced neurotoxicity, with hnRNPM post-transcriptionally increasing NEAT1v2 expression by stabilizing NEAT1 [38].

Increasing evidence has shown that another hnRNP AUF1, also known as hnRNPD, influences various steps of RNA processing, including transcription, pre-mRNA splicing, mRNA export from the nucleus to the cytoplasm, and translation. In particular, AUF1 has been found to promote the decay of many target mRNAs by binding to AU-rich elements (AREs) at their 3′-untranslated region (UTR) [39]; however, a study investigating the roles of AUF1 in RNA fate and genome integrity discovered that AUF1 preferentially recognizes U-/GU-rich sequences in mRNA and non-coding RNAs to influence RNA stability. The study also found that AUF1 can directly bind to NEAT1, thereby decreasing NEAT1 stability, the number of paraspeckles, and the nuclear accumulation of NEAT1-exported mRNAs. HuR, which stabilizes mRNAs by binding to their AREs [40, 41], was found to cooperate with AUF1 to decrease NEAT1 stability in HeLa cells [42]; however, a study investigating the molecular mechanism via which NEAT1 expression is upregulated in ovarian cancer (OC) found that HuR positively regulates NEAT1 expression by binding to NEAT1 and increasing its stability in OVCAR‐3 cells [43].

Like hnRNPM and AUF1, SRSF1, a member of the SRSF protein family, has been reported to be involved in pre-mRNA splicing. In particular, SRSF1 is responsible for preventing exon skipping, regulating alternative splicing, and ensuring the accuracy of splicing by associating with the exonic splicing enhancers of pre-mRNAs and other spliceosome components [44]. A study investigating the roles of NEAT1 in glioma demonstrated that NEAT1 promotes cell proliferation by regulating the cell cycle, while SRSF1 affects NEAT1-mediated cyclin and CDK expression by directly binding NEAT1 and increasing its stability in a splicing-independent manner [45].

LIN28B, which belongs to the lin-28 family, was previously thought to suppress microRNA processing by binding and sequestering pre-miRNAs from the microprocessor complex [46]; however, recent studies have found that LIN28B could also regulate RNA stability. Wu et al. investigated the mechanism of NEAT1 upregulation in high-grade serous ovarian cancer (HGSOC), finding that LIN28B positively regulates NEAT1 expressional level in HGSOC by directly interacting with NEAT1 and increasing its half-life, suggesting that LIN28B enhances NEAT1 stability [47].

Previous studies have demonstrated that miRNAs mainly repress mRNA stability and translation by associating with the RNA-induced silencing complex (RISC) and 3′ UTR of target mRNAs. However, we and other researchers have found that some mature miRNAs can translocate back into the nucleus and act as transcriptional regulators that facilitate gene expression by binding to chromatin and altering histone modification at gene promoters [48, 49]. In addition to its role in gene expression, miR-140 was found to positively regulate and stabilize NEAT1 by binding to NEAT1 at 974–998 bp in the nucleus [50].

3′-End processing

The two isoforms of NEAT1, NEAT1v1 and NEAT1v2, are transcribed by a single RNA polymerase II promoter but undergo different 3′-end processing; NEAT1v1 contains a canonically polyadenylated tail, whereas NEAT1v2 has a non-polyadenylated 3′-end with a characteristic triple-helix structure that is critical for RNA stabilization [51, 52]. An increasing number of studies have shown that NEAT1v2 forms a core structure for paraspeckle formation whereas NEAT1v1 overexpression decreases the number of paraspeckles [53, 54], suggesting that their 3′-end processing plays a vital role in paraspeckle formation. Nuclear-enriched RNA-binding protein TAR DNA-binding protein 43 (TDP-43), cleavage and polyadenylation-specific factor 6 (CPSF6), nudix hydrolase 21 (NUDT21), heterogeneous nuclear ribonucleoprotein K (hNRNPK), and polypyrimidine tract-binding protein 3 (PTBP3) have been found to be involved in the 3′-end processing of NEAT1, of which TDP-43, CPSF6, NUDT21, and HNRNPK are paraspeckle protein components.

TDP-43 is a known paraspeckle RBP [55] and previous studies have demonstrated that TDP-43 is an RNA/DNA-binding protein that regulates transcription, alternative splicing, and RNA stability [56, 57]. A recent study investigating the roles of TDP-43 in pluripotency and differentiation found that TDP-43 maintains pluripotency by repressing paraspeckle formation in pluripotent cells. TDP-43 was shown to regulate the alternative polyadenylation (PA) of NEAT1 and enhance the splicing of the NEAT1 transcript by binding to conserved clusters of GU-rich motifs upstream of the NEATv1 PA site, inducing the production of polyadenylated NEAT1v1, reducing the production of NEAT1v2, and thus reducing paraspeckle formation [58]. Other paraspeckle RBPs, including CPSF6, NUDT21, and HNRNPK, have been reported to regulate the 3′ RNA cleavage and polyadenylation processing of NEATv1. CPSF6 and NUDT21 form a heterodimer complex that promotes the 3′-end processing of NEAT1v1 by binding to UGUA sequences, whereas HNRNPK disrupts the 3′-end processing of NEAT1v1 by binding to CU-rich sequences and sequestering NUDT21 from the CPSF6/NUDT21 complex [53].

PTBP3, which acts as an alternative splicing factor for pre-mRNA splicing by binding to their poly(G)- and poly(U)-sequences [59], has also been found to participate in the 3′-end processing of NEAT1v2. A recent study investigating the roles and molecular mechanism of PTBP3 in HCC discovered that PTBP3 positively regulates NEAT1v1 and NEAT1v2 expression, but negatively regulates the expression of miR-612, which is transcribed from part of the NEAT1v2 DNA sequence. When investigating the underlying mechanism, PTBP3 was found to act as a splicing factor in pre-miR-612 processing by binding to the 3′-end of NEAT1v2 [60].

Regulatory patterns via which NEAT1 regulates gene expression

Early study showed that NEAT1 regulates the nuclear retention of some A-to-I hyper-edited transcripts to avoid inappropriate translation [12]. Here, we will summarize and discuss recent discoveries regarding the regulatory pattern of NEAT1 in gene regulation, including its regulation of gene transcription by recruiting transcriptional factors to and sequestering them from gene promoters, mediating pri-miRNA or pre-mRNA splicing by associating with splicing factors, inhibiting c-Myc mRNA translation by sequestering p54nrb/SFPQ to paraspeckles, and enhancing protein stability by directly or indirectly interacting with target proteins (Table 3).

Table 3.

NEAT1 regulatory roles in gene expression

Cell type	Associated factor	Target	Expression	Regulatory pattern	References
HeLa TO cells	SFPQ	IL-8	Upregulated	Transcription	[4]
HeLa cells	SFPQ	ADARB2	Downregulated		[71]
HUVECs and HeLa cells	SFPQ	RIG-I and DDX60	Upregulated		[6]
HepG2	ERα	AQP7	Upregulated		[62]
HeLa and MEF cells	STAT3	ICP0 and TK	Upregulated		[5]
U251 cells	P300/CBP	CAV2, TGFB2 and TGFBR1	Upregulated		[9]
PC3 and DU145 cells	CDC5L	AGRN	Upregulated		[63]
HCASMCs	WDR5	Calponin and SM22α	Downregulated		[70]
MG63 and U2OS cells	Snail/G9a/DNMT1 complex	CDH1	Downregulated		[7]
MCF-7 cells	FOXN3/SIN3A	GATA3, TJP1	Downregulated		[8]
MCF10A and MCF10DCIS cells	–	miR-129	Downregulated		[29]
CD4+ T cells	Ezh2	ITCH	Downregulated		[3]
QBC939 and RBE cells	EZH2	E-cadherin	Downregulated		[65]
N5, N9, and N33 cells	EZH2	ICAT, GSK3B and Axin2	Downregulated		[23]
C2C12 cells	Ezh2	P21, Myog, Myh4 andTnni2	Downregulated		[66]
HeLa and C2C12 cells	P54nrb, SFPQ	Pri-miRNAs	Upregulated	Splicing	[76]
3T3-L1 cells	SRp40	PPARγ	Upregulated		[14]
CD4+ T cells	–	STAT3	Upregulated	Protein stability	[80]
CD4+ T cells	Ezh2	STAT3	Upregulated		[3]
IBMDM and HEK293T cells	–	Caspase-1	Upregulated		[2]
HCT116, HT29 and SW1116 cells	–	DDX5	Upregulated		[81]
HeLa and MCF-7 cells	P54nrb and PSF	c-Myc	Downregulated	Translation	[79]

Transcription

Our previous study investigating the role of NEAT1 in HSV-1 infection found that NEAT1 upregulation by HSV-1 infection facilitated viral replication and gene expression by recruiting STAT3 to viral gene promoters to promote gene expression [5]. In another study investigating the role of NEAT1 in the development of AD, we found that NEAT1 expression was repressed during the early stages of AD and inhibited Aβ clearance by reducing the expression of endocytosis-related genes, which are an important method of Aβ uptake [61], through associating with the acetyltransferase CBP/P300 complex, recruiting the complex to the promoter of endocytosis-related genes, and thereby altering nearby histone modifications [9].

Recent studies have also revealed that NEAT1 acts as a transcriptional regulator during the development of diverse diseases and in multiple biological processes. During hepatic steatosis, NEAT1 is involved in the ER-α-mediated transcription of AQP7 and suppresses steatosis by associating with ER-α [62]. In prostate cancer, NEAT1 promotes cancer cell proliferation by interacting with the transcription factor cell division cycle 5-like protein (CDC5L) and recruiting it to the promoter of ARGN, an essential cell cycle and proliferation regulator, to initiate gene transcription [63]. In osteosarcoma, NEAT1 facilitates osteosarcoma cell migration, invasion, metastasis, and epithelial–mesenchymal transition (EMT) by significantly inhibiting the expression of E-cadherin, an EMT marker, via its interaction with the transcriptional repressive complex G9a/DNMT1/Snail and by regulating H3K9me2 and DNA methylation levels on the CDH1 promoter that encodes the E-cadherin protein [7]. In cholangiocarcinoma, NEAT1 upregulation significantly represses E-cadherin expression by recruiting enhancer of zeste homolog 2 (EZH2), which transcriptionally represses target genes by methylating lysine (K) residues 9 and 27 of histone H3 and K26 of histone H1 [64], to the gene promoter and enriching H3K27me3 at the promoter, thus promoting cancer cell proliferation, metastasis, and invasion [65]. NEAT1 may also interact with EZH2 to downregulate the expression of other genes, such as ITCH in Th2 cell differentiation [3], ICAT, GSK3B, and Axin2 in glioblastoma [23], and P21, Myog, Myh4, and Tnni2 during myogenesis [66].

A study investigating the roles of NEAT1 in breast cancer found that NEAT1 epigenetically silences the expression of GATA3 and TJP1, two important regulators of EMT in breast cancer development [67, 68], by associating with the FOXN3/SIN3A complex and downregulating histone H3 acetylation at the GATA3 and TJP1 promoters [8]. Another study investigating how NEAT1 upregulation contributes to breast tumorigenesis found that NEAT1 enhances the malignancy and stemness of breast tumor cells by increasing the expression of WNT4, an activator of the Wnt signaling pathway. Furthermore, NEAT1 has been shown to epigenetically silence the expression of miR-129-5p, which can target the 3′-UTR of WNT4 and repress its expression by increasing CpG island DNA methylation in miR-129 gene. However, the mechanism via which NEAT1 alters DNA methylation has not yet been elucidated [29].

When investigating the role of NEAT1 in the phenotypic switching of vascular smooth muscle cells (VSMCs) following vascular injury, NEAT1 expression was found to be induced in VSMCs during phenotypic switching. Moreover, NEAT1 upregulation promotes VSMC proliferation and migration by inhibiting the expression of SM-specific genes. In addition, mechanistic studies have demonstrated that WDR5, a critical adaptor protein in mixed lineage leukemia H3K4 methylase complexes that activates gene expression, is sequestered from SM-specific gene loci by NEAT1. This decreases the enrichment of active histone modifications (H3K4me3 and H3K9ac) and increases the enrichment of inactive modifications (H3K27me3) in the CArG box regions of SM-specific genes, thus increasing the binding of serum response factor (SRF), a critical transcription factor for many SM-specific genes [69], to the CArG box regions to initiate the transcription of these genes [70].

Like WDR5, the paraspeckle protein component SFPQ was verified as a transcriptional regulator that can be sequestered by NEAT1 from the promoters of target genes. A study investigating the relationship between paraspeckle enlargement and upregulated NEAT1 transcription found that NEAT1 upregulation could result in its sequestration of SFPQ into paraspeckles from the adenosine deaminase RNA-specific B2 (ADARB2) gene promoter to repress ADARB2 transcription [71]. In another study, NEAT1 was found to participate in the innate immune response by increasing interleukin-8 (IL8) expression, while a mechanical study demonstrated that NEAT1 could sequester SFPQ, which transcriptionally activates the IL-8 gene, from the IL-8 promoter to enhance ADARB2 transcription [4]. In addition, NEAT1 upregulation by Hantaan virus (HTNV) infection was found to promote the transcription of RIG-I and DDX60, two genes that are important for interferon γ (IFN- γ) production [72, 73] and control viral replication, by relocating SFPQ from the promoters of these two genes to paraspeckles [6].

Splicing

During miRNA maturation, pri-miRNAs transcribed by RNA polymerase II (RNAP II) are spliced by microprocessor into pre-miRNAs that are further cleaved into mature miRNAs by Dicer [74]. Numerous RBPs have been found to transcriptionally and post-transcriptionally mediate miRNA biogenesis via various processing steps [75]; however, these RBPs usually regulate a single miRNA or a specific cluster of miRNAs by associating with pri-miRNA or pre-miRNA. Interestingly, a study investigating the role of paraspeckles in miRNA maturation revealed that NEAT1 is involved in miRNA biogenesis at a global level and that NEAT1 globally enhances pri-miRNA processing by associating with P54nrb/SFPQ, pri-miRNAs, and the microprocessor component DGCR8 and acting as a scaffolding structure to facilitate the interaction between microprocessor and pri-miRNAs [76].

NEAT1 has also been reported to mediate the alternative splicing of pre-mRNA. During adipogenesis, NEAT1 regulates the alternative splicing of peroxisome proliferator activated receptor γ (PPARγ), an important driver of adipogenesis, by interacting with pre-mRNA splicing factor SRP40, also known as SRSF5, and promoting SRP40 phosphorylation to enhance SRP40 splicing activity [14].

Translation

A study investigating the role of NEAT1 in nucleolar stress found that NEAT1 is involved in the RNAP I inhibitor (CX-5461)-mediated inhibition of rRNA transcription, with NEAT1 depletion alleviating CX-5461-induced 47S rRNA precursor reduction and nucleolar disruption. Mechanistically, NEAT1 and the paraspeckle proteins P54nrb and SFPQ have been found to regulate the translation of c-Myc, which may inhibit the effects of CX-5461 on rRNA synthesis by competitively binding to the RNAP I subunit SL1 [77, 78]. P54nrb and SFPQ interact directly with the internal ribosome entry segment (IRES) of c-Myc and NEAT1 depletion enhances this interaction, suggesting that NEAT1 attenuates c-Myc translation by sequestering p54nrb/SFPQ from the IRES of c-Myc mRNA [79].

Protein stability

During the development of rheumatoid arthritis, NEAT1 promotes the differentiation of CD4+ T cells into Th17 cells by increasing the expression of STAT3, a critical factor for Th17 cell differentiation. Mechanistic studies have revealed that NEAT1 physically interacts with STAT3 and protects it from degradation by reducing its ubiquitination [80]. Likewise, during Th2 cell differentiation, NEAT1 inhibits STAT6 ubiquitination to upregulate its protein levels by epigenetically regulating the expression of ITCH, an E3 ubiquitin-protein ligase that accelerates the ubiquitination and degradation of target proteins [3, 15].

In addition, NEAT1 can stabilize proteins by directly interacting with them. During the activation of the NLRP3, NLRC4, and AIM2 inflammasomes, NEAT1 interacts directly with pro-caspase-1, an important component of these inflammasomes, to stabilize the caspase-1 hetero-tetramers and thus enhance their protease activity [2]. Moreover, NEAT1 was found to promote colorectal cancer progression by interacting directly with and enhancing the stability of DDX5, an activator of the Wnt signaling pathway [81].

Conclusion

Altered NEAT1 expression and regulation have been implicated in multiple biological processes and the development of various diseases. In this review, we focused on how these physiological and pathological processes regulate NEAT1 expression and, in turn, how NEAT1 regulates these processes. In particular, we summarized and discussed the molecules and regulatory patterns that influence NEAT1 expression, finding that most of these molecules are transcription factors and RBPs that play important roles in the transcription, 3′ end processing, and RNA stability of NEAT1. In addition, NEAT1 dysregulation was found to be involved in these processes by regulating the expression of these genes. The general regulatory pattern currently seems to be that NEAT1 recruits or sequesters RNA-/DNA-binding proteins to or from promoters or target gene transcripts to influence their gene transcription, splicing, RNA stability, or translation. Interestingly, some RNA-/DNA-binding proteins not only regulate NEAT1 expression, but also associate with NEAT1 to regulate the expression of other genes, such as STAT3 and TDP-43. Overall, this review discusses NEAT1-centric gene regulation and highlights its potential clinical utilities.

Compliance with ethical standards

Conflict of interest

The authors have declared that no conflict of interest exists.