- Review
- Open access
- Published:
Interaction between non-coding RNAs, mRNAs and G-quadruplexes
Cancer Cell International volume 22, Article number: 171 (2022)
Abstract
G-quadruplexes are secondary helical configurations established between guanine-rich nucleic acids. The structure is seen in the promoter regions of numerous genes under certain situations. Predicted G-quadruplex-forming sequences are distributed across the genome in a non-random way. These structures are formed in telomeric regions of the human genome and oncogenic promoter G-rich regions. Identification of mechanisms of regulation of stability of G-quadruplexes has practical significance for understanding the molecular basis of genetic diseases such as cancer. A number of non-coding RNAs such as H19, XIST, FLJ39051 (GSEC), BC200 (BCYRN1), TERRA, pre-miRNA-1229, pre-miRNA-149 and miR-1587 have been found to contain G-quadraplex-forming regions or affect configuration of these structures in target genes. In the current review, we outline the recent research on the interaction between G-quadruplexes and non-coding RNAs, other RNA transcripts and DNA molecules.
Introduction
G-quadruplexes are secondary helical structures formed as four-stranded nucleic acid structures between guanine (G)-rich nucleic acids. These structures have a helical shape and comprise guanine tetrads that can be made from one [1], two [2] or four molecules [3]. The unimolecular types are usually seen in the telomeric regions, as well as transcriptional regulatory regions [4]. G-quadruplex structures consist of a core G-rich section, including G-tetrads loaded on top of each other and zero or more connecting loops with diverse compositions [5]. The G-rich core classically contains at least two stacked G-tetrads that have a right-handed helical twist. These stacks are combined together by the normal sugar–phosphate backbone. Hydrogen bonds between the Gs in a plane, π–π interactions between the Gs in neighboring surfaces and charge–charge interaction between the partially negative O6 of the G bases and cations provide the binding energy in these structures. Monovalent cations, particularly K+ have the stabilizing role in these structures. Changes of the bases to non-G bases can destabilize these structures [6].
This structure is seen in the promoter regions of numerous genes under certain conditions. G-quadruplexes are involved in several cellular functions, including DNA replication, gene expression, protection of telomeres, and apoptosis [7,8,9].
These structures reside in important locations in genomic DNA within both coding and non-coding regions. Through residing in these strategic locations, they can participate in several crucial functions at cellular and organismal levels [10]. Formation of these structures between guanine-rich domains renders these regions thermodynamically stable [11]. These structures are formed by telomeric regions in the human genome and oncogenic promoter G-rich regions [12].
DNA G quadruplex-folded regions have been shown to be associated with alterations in transcriptional activity. A recent study has demonstrated that the presence of these structures in promoters is consistently linked with open chromatin configuration and increased transcription of genes. G quadruplex-folded has binding sites of transcription factors activator protein-1 (AP-1) and specificity protein-1 (Sp1), therefore being associated with determination of cell-specific transcriptional programs [13]. A recent study has suggested a model for understanding the mechanism by which G quadruplexes regulate transcription. This model suggests that G quadruplexes act as transcription suppressors through inhibiting polymerase processivity. A bulk of evidence has recently emerged to support this model. However, there is still a misrepresentation of G quadruplexes as transcriptional barriers. In fact, formation of G quadruplexes can potentially affect gene expression at several diverse levels through functioning as an important regulatory mechanism upsetting the landscape of epigenetic marks and chromatin structure [14]. The interaction between formation or disruption of G-quadruplexes and other epigenetic marks such as DNA and histone modifications, nucleosome positioning, and three-dimensional configuration of chromatin has essential role in regulation of gene expression [10].
Notably, wild-type Telomerase reverse transcriptase (hTERT) promoter sequences do not have the ability to make a hairpin structure in solution, yet they can fold into a compact arranged three-G-quadruplex configuration [15]. A number of cancer-related mutations have been shown to destabilize hTERT promoter G-quadruplexes and induce defects in telomere-repeat-binding-factor 2 (TRF2) binding. Notably, ligand-induced stabilization of G-quadruplexes could restore TRF2 binding and hTERT re-inhibition. Cumulatively, these structures are associated with regulation of hTERT activity [16]. Another study has shown that the basic N-terminal Gly/Arg-rich (GAR) domain of TRF2 can bind Telomere-repeat-encoding RNA (TERRA). In fact, disruption of the TERRA-TRF2 GAR complex by small molecules or defects in the GAR domain of TRF2 leads to defects in TERRA, and activation of γH2AX-related DNA damage in telomeres. This could result in reduced telomere length, and induction of telomere abnormalities such as fragility of telomeres. Cumulatively, G-quadruplex structure of TERRA can recognize element for TRF2 GAR domain. Interaction between TRF2 GAR and TERRA has a crucial role in the maintenance of telomere stability [17].
Zheng et al. have shown that an artificial protein can bind G-quadruplexes with high affinity and specificity. This protein has been used to capture G-quadruplexes in living cells from different species, providing the detailed landscape of these structures. This study has shown association between transcription and an extensive construction of G-quadruplexes in genes [18]. Another study has shown direct binding of Yin Yang-1 (YY1) to G-quadruplex structures. Moreover, YY1 binding sites have been shown to have extensive overlap with G-quadruplex structure loci in chromatin. In addition, YY1-mediated long-range DNA looping depends on its dimerization and takes place via its recognition of G-quadruplexes [19].
Predicted G-quadruplex-forming sequences are distributed across the genome in a non-random manner. Approximately half of the genes in the human genome are predicted to produce G-quadruplexes near their promoter regions. Many of these structures are present in the vicinity of oncogene promoters or regulatory genes [20]. The transcriptionally active single-stranded form, double-stranded form, and G-quadruplex structures of the promoter are in a delicate balance. Therefore, it is possible to inhibit expression of genes through stabilizing the G-quadruplex structure. Thus, a number of therapeutic strategies have been designed to stabilize secondary DNA structures that are present in the promoter regions of oncogenes. Since stabilization of G-quadruplexes is a possible modality for cancer therapy [21], identification of mechanisms of regulation of stability of G-quadruplexes has practical significance (Fig. 1). In the current review, we outline the recent insights about the presence of G-quadruplexes in non-coding RNAs, other transcripts and DNA molecules.
The G-quadruplex structure within pre-miRNA-149 has been demonstrated to suppress activity of Dicer, therefore decreasing maturation of miRNA-149 in neoplastic cells. Moreover, the inhibitory role of miR-149 on cell proliferation can be achieved through interfering with the G-quadruplex structures existing in the pre-miRNA-149. TmPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)porphine) is widely used as a photosensitizer and a modulator of nucleic acid secondary structur with an inhibitory effect on G-quadruplex formation could increase levels of miR-149 in breast cancer cells, leading to reduction of Zinc Finger And BTB Domain Containing 2 (ZBTB2) expression and attenuation of cell proliferation [22].
Detection of G-quadruplexes in cells and in vitro
Identification of G-quadruplex structures in cells can be accomplished using modified antibodies, G-quadruplex based aptamers as well as small molecules [32]. G-quadruplexes can be detected in chemically fixed human cells using specific antibodies. Previous studies have used immunostaining [33] or immunoprecipitation [34] techniques for this purpose. In these techniques, antibodies against G-quadruplexes bind with these structures in a non-native cellular setting following some treatments. However, these treatment steps might affect construction of G-quadruplex. It has been demonstrated that treatment with RNAse H can remove G-quadruplex in the non-transcribed strand of R-loop [35]. Therefore, identification of G-quadruplexes in living cells is a preferred method. Since antibodies cannot permeate into cells, it is not possible to use them for living cells. Moreover, cytoplasm has a reducing environment which interferes with construction of the disulfide bonds needed for preserving the tertiary structure of antibodies [36]. Zheng et al. have reported an artificial G-quadruplex probe protein which specifically binds G-quadruplex with high affinity. Application of this probe in living cells has led to identification of genome-wide landscape of G-quadruplexes [37].
Non-coding RNAs and G-quadruplexes
Both long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been found to contain G-rich regions predicted to form G-quadruplexes. For instance, NEAT1 contains such regions. NEAT1 functions as a platform for the assembly of paraspeckles, which are a type of organelle within the nucleus participating in the regulation of gene expression. Assembly of paraspeckles requires NEAT1-mediated recruitment of the RNA-binding protein NONO. NONO has been found to bind with the G-quadruplex structure of G-rich C9orf72 repeat RNA. NEAT1 contains several G-quadruplex motifs. Furthermore, NONO can bind with NEAT1 G-quadruplexes in a specific manner suggesting that G-quadruplex motifs may facilitate interaction between NONO and NEAT1. Notably, NONO binding sites on NEAT1 mainly correspond to G-quadruplex motifs. Consistent with this finding, disruption of G-quadruplexes with specific small molecules leads to separation of intuitive NONO-NEAT1 complexes. Therefore, G-quadruplexes have been suggested as principal candidates for the NONO-recruiting components of NEAT1 [38].
Another study has reported the presence of an evolutionarily conserved G-rich region at the 5′ end of the H19 coding gene which is predicted to form a G-quadruplex structure. Further assays with G-quadruplex-specific ligands have shown the ability of the G-rich motif adjacent to the transcription start site in constructing a G-quadruplex. Most notably, this G-quadruplex has been found to regulate expression of the H19 gene. Sp1 and E2F1 are two transcription factors that interact with this G-quadruplex to either inhibit or enhance transcription of H19, respectively. In addition, expression of H19 in the course of differentiation of mice embryonic stem cells seems to be controlled by a G-quadruplex structure in this lncRNA [39].
Telomeric Repeat-containing RNA (TERRA), which is transcribed from telomeres, has been shown to contain G-quadruplex structures. Notably, unstructured hinge domains that participate in the targeting of HP1α to constitutive heterochromatin regions recognize these structures of TERRA. Through this mechanism, TERRA contributes to the enrichment of HP1α at telomeric regions to preserve the heterochromatin structure. Additionally, HP1α has been shown to bind more quickly to G-quadruplex structures having parallel topology versus those with antiparallel topology. These G-quadruplex structures have been seen in the regulatory portions of numerous oncogenes. Therefore, such non-canonical configurations have been determined as regulators of HP1α function and chromatin domain structure participating in the epigenetic regulation of gene expression [40].
In an attempt to assess the expression profile of colon cancer samples, Matsumura et al. have identified a novel up-regulated lncRNA in colon cancer tissues, namely FLJ39051 or GSEC (G-quadruplex-forming sequence containing lncRNA). Inhibition of GSEC lncRNA transcription resulted in a significant decrease in the motility of cancer cells. This lncRNA was shown to bind to the DHX36 RNA helicase through its G-quadruplex-forming sequence and suppress the DHX36 G-quadruplex unwinding function. Thus, GSEC is thought to participate in the migration of colon cancer cells through suppression of activity of DHX36 through its G-quadruplex configuration [41]. Interestingly, G-quadruplex structures are conserved in L1 sub-families and may therefore result in an increased level of retro-transposition activity [42].
In addition to these G-quadruplex-containing lncRNAs, some lncRNAs have been found to alter expression of genes by affecting G-quadruplex structures in target genes. LncRNA XIST has been found to be processed into a small transcript called XPi2. This small transcript has a gender-independent expression pattern, implying that it has a role outside of X-chromosome inactivation. Nucleolin and hnRNP A1 are two XPi2-related proteins that are functionally associated with G-quadruplex structures. XPi2 silencing has decreased the activity of the KRAS pathway. Further studies have supported the interaction between XPi2 and the polypurine–polypyrimidine regions of KRAS. Therefore, XPi2 might induce expression of KRAS by decreasing G-quadruplex formation. Thus, it suggests that XPi2 has a role in KRAS- associated tumorigenesis through regulation of G-quadruplex structures [43].
A further group of lncRNAs has neither G-quadraplex structures nor directly regulate expression of target genes through affecting stability of these structures, but instead have interactions with ATP-dependent RNA helicases such as RHAU that exhibit high affinity for G-quadruplex structures. An example of these lncRNAs is BC200. This lncRNA does neither form G-quadruplex structures nor interact with the quadruplex-interacting region of RHAU, but it directly binds to RHAU. BC200 acts as an acceptor of unwound quadruplexes through a cytosine-rich area in the vicinity of the 3′-end of this transcript. BC200 has an interaction with the G-quadruplex-containing telomerase RNA. Therefore, RHAU might facilitate BC200 binding and consequent regulatory effects with G-quadruplex-harboring nucleic acid regions [44].
Importantly, G-quadruplexes within premature microRNA precursors (pre-miRNAs) might also affect risk of human disorders. For instance, pre-miRNA-1229 has been shown to contain a variant that is associated with risk of Alzheimer’s disease. The mature form of this miRNA modulates translation of SORL1. Pre-miRNA-1229 forms a G-quadruplex configuration that co-occurs in a balanced state with the canonical hairpin structures, possibly regulating levels of miR-1229-3p. Most notably, the Alzheimer’s disease-associated variant of pre-miR-1229 appears to alter the balance between these structures. Consequently, this G-quadruplex structure has been suggested as a putative therapeutic target for Alzheimer’s disease [45] (Fig. 2).
The G-quadruplex structure within pre-miRNA-149 has been demonstrated to suppress activity of Dicer, therefore decreasing maturation of miRNA-149 in neoplastic cells. Moreover, the inhibitory role of miR-149 on cell proliferation can be achieved through interfering with the G-quadruplex structures existing in the pre-miRNA-149. TmPyP4 with an inhibitory effect on G-quadruplex formation could increase levels of miR-149 in breast cancer cells, leading to reduction of ZBTB2 expression and attenuation of cell proliferation [22].
In a separate example involving G-quadruplexes and miRNAs, miR-1587 has been shown to contain a G-rich region forming stable G-quadruplex structure in certain conditions described by the presence of potassium and sodium ions and low levels of ammonium cation. High levels of ammonium cation or molecular crowding milieus have been shown to induce a dimeric G-quadruplex in miR-1587 via 3′-to-3′ assembling of two monomeric G-quadruplex units with one ammonium ion confined between the edges. Notably, two manufactured jatrorrhizine products have been shown to trigger the dimerization of miR-1587 G-quadruplexes. On the other hand, jatrorrhizine could not induce this structure in spite of its ability to bind with the dimeric miR-1587 G-quadruplexes [47].
Table 1 shows the list of noncoding RNAs which have G-quadruplexes or regulate expression of genes through modulation of these structures.
Protein coding transcripts and G-quadruplexes
G-quadruplexes structures are enriched in 3′ UTRs of mRNAs, where miRNAs could also bind. G-quadruplex structures have been shown to affect miRNA binding to target mRNAs, providing a new mechanism for G-quadruplex-dependent modulation of miRNA-mRNA interactions that have fundamental roles in the maintenance of gene expression [51]. FMRP binding with the G-rich region of the PSD-95 transcript provides an important example of the interference of G-quadruplexes with miRNA-mRNA interactions. Notably, 3′ UTR of PSD-95 transcript has a miR-125a binding site which is located in a G-rich region bound by FMRP. FMRP regulates expression of PSD-95 through phosphorylation-related mechanisms. Both unphosphorylated FMRP and its phosphomimic FMRP S500D have a high affinity for binding with G-quadruplexes within PSD-95 transcript. However, only FMRP S500D can bind with to miR-125a. Therefore, FMRP functions as a molecular switch to regulate stability of the complex constructed between the miR-125a-RISC and PSD-95 transcript in a phosphorylation-dependent manner [52].
G-quadruplexes have also been found to form within other regions of mRNAs. For instance, a G-quadruplex structure has been found within the 5′ UTR of the potassium 2-pore domain leak channel Task3 transcript. The stability of this structure has been preserved under physiological ionic concentrations. Such structures can inhibit translation of Task3. A G-quadruplex-specific helicase, namely DHX36 can intervene with this structure resulting in as increase in K+ leak flow and induction of membranes hyperpolarization. The G-quadruplex structure has an essential role in transport of Task3 transcripts to distal primary cortical neurites. Since abnormal Task3 levels have been correlated with abnormal function of neurons, the role of this G-quadruplex in the regulation of K+ leak within neurons shows the importance of this route in the pathogenesis of neurological disorders [53].
BAG-1 is another gene that contains a G-rich region in its 5′UTR capable of forming a G-quadruplex structure. This structure has been found to regulate cap-dependent as well as cap-independent expression of BAG-1. SNRPA has been demonstrated to bind directly to the BAG-1 transcript via these G-quadruplexes modulating expression of the BAG-1 gene [54].
Another study has shown that translation of NRXN2α is regulated by a G-quadruplex structure in its 5′ UTR. The 5′ UTR of this gene has an inhibitory effect on its expression. Notably, there is a crucial subregion in this area that accounts for the main inhibitory effect through formation of a certain secondary G-quadruplex configuration. In addition, the upstream AUGs work in a synergistic mode with G-quadruplex to inhibit NRXN2α-expression. Therefore, the 5′ UTR of NRXN2α suppresses its translation through different mechanisms [55].
In spite of the observed inhibitory effect of G-quadruplexes in the 5′ UTR of genes on their expression [55], two G-quadruplex structures in the 5′ UTR of TGFβ2 mRNA have been shown to increase its expression. These structures are thought to work additively to noticeably upregulate TGFβ2 expression [56]. Consistent with this study, is the enhanced expression of an isoform of ARC2 through the presence of a G-quadruplex structure in the longer variant of the 5′ UTR of the ARPC2 transcript. This variant of the 5′ UTR also has an internal ribosome entry site (IRES). This variant of 5′ UTR has been shown to promote cap-independent translation of ARPC2. The G-quadruplex also contributes to the activity of IRES. Consistent with the supposed role of IRES in induction of expression of genes under cellular stress through cap-dependent translation, expression of ARPC2 has been shown to be increased at high cell density. Therefore, it is proposed that a mechanistic model of IRES upregulation is underpinned by the G-quadruplex motif exposed from the chief stem-loop component [57]. Figure 3 demonstrates the interaction between lncRNA, mRNAs and G-quadruplexes in the regulation of DEAD-box helicases in antiviral innate immunity signaling pathways (Table 2).
Discussion
Several lncRNAs and mRNA coding genes have been found to contain G-quadruplexes or regulate expression of genes through modulation of these structures. G-quadruplexes have prominent roles in the regulation of gene expression and interventions with these structures are emerging as novel therapeutic opportunities in genetic diseases such as cancer. Therefore, identification of lncRNAs/mRNAs that modulate G-quadruplexes is important.
G-quadruplexes are also being discovered in miRNA precursors suggesting a role for RNA G-quadruplexes in the regulation of miRNA biogenesis and control of interaction of non-coding RNAs with their partners [79].
Notably, numerous identified G-quadruplexes in non-coding RNAs has been shown to be unstable, being detected only in the presence of certain ligands or ions [79]. Moreover, G-quadruplexes in pri-miRNAs and pre-miRNAs are present in a well-regulated balance with the hairpin structure. This balance can permit appropriate regulation of gene expression [79].
Secondary structures formed within non-coding RNAs can determine their mode of action and their effect on targets of these transcripts. Notably, the G-quadruplex structures within precursor miRNAs can affect the structure of hairpin stem loops that have essential roles in recognition of these structures by Dicer recognition and additional maturation steps [22]. The importance of this finding is further highlighted by the observation that approximately 16% of identified human pre-miRNAs can embrace G-quadruplex structures instead of acknowledged stem-loops [80]. Consistently, a number of studies have suggested stimulation of G-quadruplex development and dimerization as a new approach for regulation of functions of certain miRNAs [47]. Meanwhile, G-quadruplex structures exist in the 3′ UTR of mRNAs, a region which is targeted by miRNAs. Therefore, G-quadruplexes can affect miRNA-mRNA interactions.
Among G-quadruplex-containing lncRNAs are those with significant roles in carcinogenesis, such as NEAT1, H19 and GSEC, providing additional evidence for association between these structures and malignant transformation of cells. In addition, G-quadruplexes within non-coding RNAs might affect the pathogenesis of neurologic disorders such as Alzheimer’s disease [45].
Conclusions
Taken together, we have summarized evidence for prevalent presence of G-quadruplexe structures in both miRNAs and lncRNAs and association between construction of these structures within pri- and pre-miRNAs and miRNA synthesis. Moreover, G-quadruplexes have been found to affect binding of miRNAs and lncRNAs with their target transcripts and interacting proteins, respectively.
G-quadruplexes represent novel targets for therapeutic interventions. As some transcripts can alter these structures, manipulation of expression of these transcripts is a possible therapeutic option in this regard. Meanwhile, G-quadruplex structures have been found in several disease-associated lncRNAs and miRNAs. Thus, alteration in the stability of G-quadruplexes within these transcripts is a possible mechanism for dysregulation of these transcripts in human disorders, such as cancer and other genetic diseases.
Since the presence of these structures in RNA molecules might participate in the mechanisms that pathogenic organisms or tumors exploit to evade the hosts’ immune responses, future research in this field would pave the way for identification of novel strategies to combat these two kinds of disorders.
Availability of data and materials
The analyzed data sets generated during the study are available from the corresponding author on reasonable request.
References
Largy E, Mergny JL, Gabelica V. Role of alkali metal ions in G-quadruplex nucleic acid structure and stability. Metal Ions Life Sci. 2016;16:203–58 (Epub 2016/02/11. eng).
Sundquist WI, Klug A. Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 1989;342(6251):825–9 (Epub 1989/12/14. eng).
Sen D, Gilbert W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature. 1988;334(6180):364–6 (Epub 1988/07/28. eng).
Verma A, Halder K, Halder R, Yadav VK, Rawal P, Thakur RK, et al. Genome-wide computational and expression analyses reveal G-quadruplex DNA motifs as conserved cis-regulatory elements in human and related species. J Med Chem. 2008;51(18):5641–9 (Epub 2008/09/05. eng).
Huppert JL. Structure, location and interactions of G-quadruplexes. FEBS J. 2010;277(17):3452–8.
Gros J, Rosu F, Amrane S, De Cian A, Gabelica V, Lacroix L, et al. Guanines are a quartet’s best friend: impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes. Nucleic Acids Res. 2007;35(9):3064–75 (Epub 2007/04/25. eng).
Eddy J, Maizels N. Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res. 2006;34(14):3887–96.
Tian T, Chen Y-Q, Wang S-R, Zhou X. G-Quadruplex: a regulator of gene expression and its chemical targeting. Chem. 2018;4(6):1314–44.
Riou J, Guittat L, Mailliet P, Laoui A, Renou E, Petitgenet O, et al. Cell senescence and telomere shortening induced by a new series of specific G-quadruplex DNA ligands. Proc Natl Acad Sci. 2002;99(5):2672–3677.
Reina C, Cavalieri V. Epigenetic modulation of chromatin states and gene expression by G-quadruplex structures. Int J Mol Sci. 2020;21(11):4172 (Epub 2020/06/18. eng).
Rhodes D, Lipps HJ. G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 2015;43(18):8627–37.
Patel DJ, Phan AT, Kuryavyi V. Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res. 2007;35(22):7429–55.
Lago S, Nadai M, Cernilogar FM, Kazerani M, Moreno HD, Schotta G, et al. Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome. Nat Commun. 2021;12(1):1–13.
Robinson J, Raguseo F, Nuccio SP, Liano D, Di Antonio M. DNA G-quadruplex structures: more than simple roadblocks to transcription? Nucleic Acids Res. 2021;49(15):8419–31.
Monsen RC, DeLeeuw L, Dean WL, Gray RD, Sabo TM, Chakravarthy S, et al. The hTERT core promoter forms three parallel G-quadruplexes. Nucleic Acids Res. 2020;48(10):5720–34.
Sharma S, Mukherjee AK, Roy SS, Bagri S, Lier S, Verma M, et al. Human telomerase is directly regulated by non-telomeric TRF2-G-quadruplex interaction. Cell Rep. 2021;35(7):109154.
Mei Y, Deng Z, Vladimirova O, Gulve N, Johnson FB, Drosopoulos WC, et al. TERRA G-quadruplex RNA interaction with TRF2 GAR domain is required for telomere integrity. Sci Rep. 2021;11(1):1–14.
Zheng K-W, Zhang J-Y, He Y-D, Gong J-Y, Wen CJ, Chen J-N, et al. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res. 2020;48(20):11706–20.
Li L, Williams P, Ren W, Wang MY, Gao Z, Miao W, et al. YY1 interacts with guanine quadruplexes to regulate DNA looping and gene expression. Nat Chem Biol. 2021;17(2):161–8.
Bochman ML, Paeschke K, Zakian VA. DNA secondary structures: stability and function of G-quadruplex structures. Nat Rev Genet. 2012;13(11):770–80.
Awadasseid A, Ma X, Wu Y, Zhang W. G-quadruplex stabilization via small-molecules as a potential anti-cancer strategy. Biomed Pharmacother. 2021;139:111550.
Ghosh A, Ekka MK, Tawani A, Kumar A, Chakraborty D, Maiti S. Restoration of miRNA-149 expression by TmPyP4 induced unfolding of quadruplex within its precursor. Biochemistry. 2018;58(6):514–25.
Ruggiero E, Richter SN. G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy. Nucleic Acids Res. 2018;46(7):3270–83.
Cimino-Reale G, Zaffaroni N, Folini M. Emerging role of G-quadruplex DNA as target in anticancer therapy. Curr Pharm Des. 2016;22(44):6612–24.
Zahler AM, Williamson JR, Cech TR, Prescott DM. Inhibition of telomerase by G-quartet DMA structures. Nature. 1991;350(6320):718–20.
Kosiol N, Juranek S, Brossart P, Heine A, Paeschke K. G-quadruplexes: a promising target for cancer therapy. Mol Cancer. 2021;20(1):1–18.
Paudel BP, Moye AL, Abou Assi H, El-Khoury R, Cohen SB, Holien JK, et al. A mechanism for the extension and unfolding of parallel telomeric G-quadruplexes by human telomerase at single-molecule resolution. Elife. 2020;9:e56428.
Balasubramanian S, Hurley LH, Neidle S. Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat Rev Drug Discov. 2011;10(4):261–75.
De S, Michor F. DNA secondary structures and epigenetic determinants of cancer genome evolution. Nat Struct Mol Biol. 2011;18(8):950–5.
Banerjee N, Panda S, Chatterjee S. Frontiers in G-quadruplex therapeutics in cancer: selection of small molecules, peptides and aptamers. Chem Biol Drug Des. 2021;99:1–31.
Lerner LK, Sale JE. Replication of G quadruplex DNA. Genes. 2019;10(2):95.
Di Antonio M, Rodriguez R, Balasubramanian S. Experimental approaches to identify cellular G-quadruplex structures and functions. Methods. 2012;57(1):84–92 (Epub 02/11. eng).
Biffi G, Di Antonio M, Tannahill D, Balasubramanian S. Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells. Nat Chem. 2014;6(1):75–80 (Epub 2013/12/19. eng).
Hänsel-Hertsch R, Beraldi D, Lensing SV, Marsico G, Zyner K, Parry A, et al. G-quadruplex structures mark human regulatory chromatin. Nat Genet. 2016;48(10):1267–72 (Epub 2016/09/13. eng).
Zhao Y, Zhang JY, Zhang ZY, Tong TJ, Hao YH, Tan Z. Real-time detection reveals responsive cotranscriptional formation of persistent intramolecular DNA and intermolecular DNA:RNA hybrid G-quadruplexes stabilized by R-loop. Anal Chem. 2017;89(11):6036–42 (Epub 2017/04/28. eng).
Stocks M. Intrabodies as drug discovery tools and therapeutics. Curr Opin Chem Biol. 2005;9(4):359–65 (Epub 2005/06/28. eng).
Zheng KW, Zhang JY, He YD, Gong JY, Wen CJ, Chen JN, et al. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res. 2020;48(20):11706–20 (Epub 2020/10/13. eng).
Simko EA, Liu H, Zhang T, Velasquez A, Teli S, Haeusler AR, et al. G-quadruplexes offer a conserved structural motif for NONO recruitment to NEAT1 architectural lncRNA. Nucleic Acids Res. 2020;48(13):7421–38.
Fukuhara M, Ma Y, Nagasawa K, Toyoshima F. A G-quadruplex structure at the 5′ end of the H19 coding region regulates H19 transcription. Sci Rep. 2017;7(1):1–13.
Roach RJ, Garavís M, González C, Jameson GB, Filichev VV, Hale TK. Heterochromatin protein 1α interacts with parallel RNA and DNA G-quadruplexes. Nucleic Acids Res. 2020;48(2):682–93.
Matsumura K, Kawasaki Y, Miyamoto M, Kamoshida Y, Nakamura J, Negishi L, et al. The novel G-quadruplex-containing long non-coding RNA GSEC antagonizes DHX36 and modulates colon cancer cell migration. Oncogene. 2017;36(9):1191–9.
Sahakyan AB, Murat P, Mayer C, Balasubramanian S. G-quadruplex structures within the 3′ UTR of LINE-1 elements stimulate retrotransposition. Nat Struct Mol Biol. 2017;24(3):243–7.
Chang YC, Chiu C-C, Yuo C-Y, Chan W-L, Chang Y-S, Chang W-H, et al. An XIST-related small RNA regulates KRAS G-quadruplex formation beyond X-inactivation. Oncotarget. 2016;7(52):86713.
Booy EP, McRae EK, Howard R, Deo SR, Ariyo EO, Dzananovic E, et al. RNA helicase associated with AU-rich element (RHAU/DHX36) interacts with the 3′-tail of the long non-coding RNA BC200 (BCYRN1). J Biol Chem. 2016;291(10):5355–72.
Imperatore JA, Then ML, McDougal KB, Mihailescu MR. Characterization of a G-quadruplex structure in pre-miRNA-1229 and in its Alzheimer’s disease-associated variant rs2291418: implications for miRNA-1229 maturation. Int J Mol Sci. 2020;21(3):767.
Podleśny-Drabiniok A, Marcora E, Goate AM. Microglial phagocytosis: a disease-associated process emerging from Alzheimer’s disease genetics. Trends Neurosci. 2020;43(12):965–79.
Tan W, Yi L, Zhu Z, Zhang L, Zhou J, Yuan G. Hsa-miR-1587 G-quadruplex formation and dimerization induced by NH(4)(+), molecular crowding environment and jatrorrhizine derivatives. Talanta. 2018;1(179):337–43 (Epub 2018/01/10. eng).
Mirihana Arachchilage G, Kharel P, Reid J, Basu S. Targeting of G-quadruplex harboring pre-miRNA 92b by LNA rescues PTEN expression in NSCL cancer cells. ACS Chem Biol. 2018;13(4):909–14.
Tan W, Zhou J, Gu J, Xu M, Xu X, Yuan G. Probing the G-quadruplex from hsa-miR-3620-5p and inhibition of its interaction with the target sequence. Talanta. 2016;154:560–6.
O’Day E, Le MT, Imai S, Tan SM, Kirchner R, Arthanari H, et al. An RNA-binding protein, Lin28, recognizes and remodels G-quartets in the microRNAs (miRNAs) and mRNAs it regulates. J Biol Chem. 2015;290(29):17909–22.
Zhang J, Wang J, Li F, Zhu M, Wang S, Cui Q, et al. Normal expression of KCNJ11 is maintained by the G-quadruplex. Int J Biol Macromol. 2019;138:504–10 (Epub 2019/07/22. eng).
DeMarco B, Stefanovic S, Williams A, Moss KR, Anderson BR, Bassell GJ, et al. FMRP-G-quadruplex mRNA-miR-125a interactions: implications for miR-125a mediated translation regulation of PSD-95 mRNA. PLoS ONE. 2019;14(5):e0217275.
Maltby CJ, Schofield JP, Houghton SD, O’Kelly I, Vargas-Caballero M, Deinhardt K, et al. A 5′ UTR GGN repeat controls localisation and translation of a potassium leak channel mRNA through G-quadruplex formation. Nucleic Acids Res. 2020;48(17):9822–39.
Bolduc F, Turcotte M-A, Perreault J-P. The small nuclear ribonucleoprotein polypeptide A (SNRPA) binds to the G-quadruplex of the BAG-1 5′ UTR. Biochimie. 2020;176:122–7.
Ding X, Meng S, Zhou J, Yang J, Li H, Zhou W. Translational inhibition of α-Neurexin 2. Sci Rep. 2020;10(1):1–12.
Agarwala P, Pandey S, Ekka MK, Chakraborty D, Maiti S. Combinatorial role of two G-quadruplexes in 5′ UTR of transforming growth factor β2 (TGFβ2). Biochim Biophys Acta Gen Subj. 2019;1863(11):129416.
Al-Zeer MA, Dutkiewicz M, von Hacht A, Kreuzmann D, Röhrs V, Kurreck J. Alternatively spliced variants of the 5′-UTR of the ARPC2 mRNA regulate translation by an internal ribosome entry site (IRES) harboring a guanine-quadruplex motif. RNA Biol. 2019;16(11):1622–32.
Kawauchi K, Sugimoto W, Yasui T, Murata K, Itoh K, Takagi K, et al. An anionic phthalocyanine decreases NRAS expression by breaking down its RNA G-quadruplex. Nat Commun. 2018;9(1):1–12.
Herdy B, Mayer C, Varshney D, Marsico G, Murat P, Taylor C, et al. Analysis of NRAS RNA G-quadruplex binding proteins reveals DDX3X as a novel interactor of cellular G-quadruplex containing transcripts. Nucleic Acids Res. 2018;46(21):11592–604.
Guo S, Lu H. Conjunction of G-quadruplex and stem-loop in the 5′ untranslated region of mouse hepatocyte nuclear factor 4-alpha1 mediates strong inhibition of protein expression. Mol Cell Biochem. 2018;446(1):73–81.
Serikawa T, Eberle J, Kurreck J. Effects of genomic disruption of a guanine quadruplex in the 5′ UTR of the Bcl-2 mRNA in melanoma cells. FEBS Lett. 2017;591(21):3649–59.
McAninch DS, Heinaman AM, Lang CN, Moss KR, Bassell GJ, Mihailescu MR, et al. Fragile X mental retardation protein recognizes a G quadruplex structure within the survival motor neuron domain containing 1 mRNA 5′-UTR. Mol BioSyst. 2017;13(8):1448–57.
Rouleau S, Glouzon J-PS, Brumwell A, Bisaillon M, Perreault J-P. 3′ UTR G-quadruplexes regulate miRNA binding. RNA. 2017;23(8):1172–9.
Ariyo EO, Booy EP, Dzananovic E, McRae EK, Meier M, McEleney K, et al. Impact of G-quadruplex loop conformation in the PITX1 mRNA on protein and small molecule interaction. Biochem Biophys Res Commun. 2017;487(2):274–80.
Newman M, Sfaxi R, Saha A, Monchaud D, Teulade-Fichou M-P, Vagner S. The G-quadruplex-specific RNA helicase DHX36 regulates p53 pre-mRNA 3′-end processing following UV-induced DNA damage. J Mol Biol. 2017;429(21):3121–31.
Koukouraki P, Doxakis E. Constitutive translation of human α-synuclein is mediated by the 5′-untranslated region. Open Biol. 2016;6(4):160022.
Lee SC, Zhang J, Strom J, Yang D, Dinh TN, Kappeler K, et al. G-Quadruplex in the NRF2 mRNA 5′ untranslated region regulates de novo NRF2 protein translation under oxidative stress. Mol Cell Biol. 2017;37(1):e00122-16.
Dai J, Liu Z-Q, Wang X-Q, Lin J, Yao P-F, Huang S-L, et al. Discovery of small molecules for up-regulating the translation of antiamyloidogenic secretase, a disintegrin and metalloproteinase 10 (ADAM10), by binding to the G-quadruplex-forming sequence in the 5′ untranslated region (UTR) of its mRNA. J Med Chem. 2015;58(9):3875–91.
Cammas A, Dubrac A, Morel B, Lamaa A, Touriol C, Teulade-Fichou M-P, et al. Stabilization of the G-quadruplex at the VEGF IRES represses cap-independent translation. RNA Biol. 2015;12(3):320–9.
Stefanovic S, DeMarco BA, Underwood A, Williams KR, Bassell GJ, Mihailescu MR. Fragile X mental retardation protein interactions with a G quadruplex structure in the 3′-untranslated region of NR2B mRNA. Mol BioSyst. 2015;11(12):3222–30.
Nie J, Jiang M, Zhang X, Tang H, Jin H, Huang X, et al. Post-transcriptional regulation of Nkx2-5 by RHAU in heart development. Cell Rep. 2015;13(4):723–32.
Crenshaw E, Leung BP, Kwok CK, Sharoni M, Olson K, Sebastian NP, et al. Amyloid precursor protein translation is regulated by a 3’UTR guanine quadruplex. PLoS ONE. 2015;10(11):e0143160.
Williams KR, McAninch DS, Stefanovic S, Xing L, Allen M, Li W, et al. hnRNP-Q1 represses nascent axon growth in cortical neurons by inhibiting Gap-43 mRNA translation. Mol Biol Cell. 2016;27(3):518–34.
Lago S, Nadai M, Ruggiero E, Tassinari M, Marušič M, Tosoni B, et al. The MDM2 inducible promoter folds into four-tetrad antiparallel G-quadruplexes targetable to fight malignant liposarcoma. Nucleic Acids Res. 2021;49(2):847–63.
Tan DJ, Winnerdy FR, Lim KW, Phan AT. Coexistence of two quadruplex–duplex hybrids in the PIM1 gene. Nucleic Acids Res. 2020;48(19):11162–71.
Hu M-H, Wu T-Y, Huang Q, Jin G. New substituted quinoxalines inhibit triple-negative breast cancer by specifically downregulating the c-MYC transcription. Nucleic Acids Res. 2019;47(20):10529–42.
Zhang X, Zhao B, Yan T, Hao A, Gao Y, Li D, et al. G-quadruplex structures at the promoter of HOXC10 regulate its expression. Biochim Biophys Acta Gene Regul Mech. 2018;1861(11):1018–28.
Huang H, Zhang J, Harvey SE, Hu X, Cheng C. RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF. Genes Dev. 2017;31(22):2296–309.
Tassinari M, Richter SN, Gandellini P. Biological relevance and therapeutic potential of G-quadruplex structures in the human noncoding transcriptome. Nucleic Acids Res. 2021;49(7):3617–33.
Mirihana Arachchilage G, Dassanayake AC, Basu S. A potassium ion-dependent RNA structural switch regulates human pre-miRNA 92b maturation. Chem Biol. 2015;22(2):262–72 (Epub 2015/02/03. eng).
Acknowledgements
Not applicable.
Funding
Open Access funding enabled and organized by Projekt DEAL.
Author information
Authors and Affiliations
Contributions
SGF and MED wrote the draft and revised it. MT and EJ designed and supervised the study. AB, AA and BMH collected the data and designed the tables and figures. All the authors read and approved the final manuscript.
Corresponding authors
Ethics declarations
Ethics approval and consent to participate
Not applicable.
Consent of publication
Not applicable.
Competing interests
The authors declare they have no competing interests.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
About this article
Cite this article
Ghafouri-Fard, S., Abak, A., Baniahmad, A. et al. Interaction between non-coding RNAs, mRNAs and G-quadruplexes. Cancer Cell Int 22, 171 (2022). https://doi.org/10.1186/s12935-022-02601-2
Received:
Accepted:
Published:
DOI: https://doi.org/10.1186/s12935-022-02601-2