Introduction
The regulatory role of RNA modifications
m6A RNA modification
Introduction to m6A RNA modification
Regulatory role of m6A RNA modification in molecular functions
m1A RNA modification
Introduction of m1A RNA modification
Regulatory role of the m1A RNA modification in molecular functions
m5C RNA modification
Introduction of the m5C RNA modification
RNA modification | Writers | Readers | Erasers |
---|---|---|---|
m6A | METTL3; METTL14; WTAP; RBM15; ZC3H13 | YTH domain family of proteins (YTHDF1, YTHDF2, YTHDF3, YTHDC1 and YTHDC2); HNRNP (HNRNPA2B1 and HNRNPC); eIF3; IGF2BP (IGF2BP1, IGF2BP2, and IGF2BP3); FMR1; LRPPRC | FTO; ALKBH5 |
m1A | TRMT6/61A; TRMT61B; TRMT10C | YTHDF1; YTHDF2; YTHDF3; YTHDC1 | ALKBH1; ALKBH3 |
m5C | NSUN2; DNMT2 | ALYREF; YBX1 | N.A. |
Regulatory role of the m5C RNA modification in molecular functions
Modifications | Process | Enzymes involved | Description | Ref | |
---|---|---|---|---|---|
m6A RNA modification | mRNA splicing | HNRNPC | HNRNPC modulates the splicing of mRNAs by changing RNA structure and regulating the combination of RNA and reader | [10] | |
HNRNPG | HNRNPG cooperates with modified pre-mRNA and the phosphorylated C-terminal domain of RNA polymerase II to regulate splicing | [47] | |||
FTO | FTO prefers to bind to introns of nascent mRNA | [48] | |||
ALKBH5 | ALKBH5 relates to splicing factors tightly according to the analysis of immunofluorescence | [11] | |||
mRNA export | METTL3 | METTL3 regulates the export of mature mRNA by modulating clock genes Per2 and Arntl | [49] | ||
YTHDC1 | YTHDC1 mediates the export of decorated mRNA by interacting with SRSF3 and regulating the combination of SRSF3 an NXF1 on RNA | [50] | |||
ALKBH5 | Knockdown of ALKBH5 leads to acceleration in mRNA export | [11] | |||
mRNA stability | ALKBH5 | The stability of mRNA was decreased slightly in RNA lacking ALKBH5 | [11] | ||
N.A. | Neighbouring sites of m6A and HuR weaken the function of HuR and increase the instability of mRNA | [52] | |||
N.A. | ELAV1/HuR, which is one of m6A-binding proteins and stabilizes transcripts with the cooperation of the ARE domain | [53] | |||
mRNA translation | YTHDF2 | YTHDF2 regulates translation by transferring the bound RNA from the translatable pool to processing bodies to promote mRNA decay | [12] | ||
YTHDF2 induces the dysfunction of FTO in the 5'UTRs and contribute to promoting cap-independent translation | [28] | ||||
YTHDF1 | YTHDF1 increases the efficiency of translation by binding to m6A | [37] | |||
YTHDF3 | YTHDF3 interacts with ribosomal proteins along with YTHDF1 to regulate translation | [54] | |||
YTHDF3 decays of convinced translation related region in mRNA together with YTHDF2 | [55] | ||||
METTL3 | When knocking out METTL3 in mESCs and Ebs, the translation efficiency is increased | [57] | |||
METTL3 recruits eIF3 to the initiation complex directly and enhance translation level | [56] | ||||
m1A RNA modification | mRNA stability | N.A. | m1A in highly structured or GC-rich regions of 5'UTRs alters mRNA structural stability by modifying the predicted secondary structure | ||
mRNA translation | N.A. | m1A upregulated translation by depressing binding of releasing factor | [26] | ||
N.A. | m1A prevents effective translation of CDS in mt-mRNA | [65] | |||
N.A. | The protein level would be superior when the transcript was modified by m1A at/around the initiation codon | [69] | |||
m5C RNA modification | mRNA export | ALYREF | ALYREF adjusts the export of transcripts by recognizing the unique RNA-binding motif | [77] | |
mRNA translation | NSUN2 | Deleting NSUN2 in HDFs can induce the elevation of p27, and overexpressing NSUN2 induces the opposite outcome | [79] | ||
m5C catalysed by NSUN2 in 3'UTRs of p21 mRNA coordinates with m6A methylated by METTL3/METTL14 together to enhance p21 expression | [80] | ||||
N.A. | Translation diminishes significantly in both bacterial whole-cell extracts and HeLa cell extracts when m5C modifies the coding regions of mRNA | ||||
N.A. | m5C found on IL-17A mRNA can promote the translation of IL-17A | [82] | |||
Other | hm5C | mRNA translation | N.A. | hm5C associates with translation activation in Drosophila | [69] |
Ψ | mRNA splicing | N.A. | Ψ, which is near the 3' splice site in the polypyrimidine tract, prevents pre-mRNA splicing by regulating U2AF | [83] | |
mRNA stability | N.A. | The higher expression of heat shock-induced Pus7-dependent pseudouridylated transcripts in wild-type yeast than in Pus7-knockdown yeast indicates that Ψ has the capability to maintain stability of RNA | [84] | ||
mRNA translation | N.A. | Compared to U modifications located at similar sequences, Ψ-containing mRNA indicates an increase in translation levels of approximately 25% | [84] | ||
N.A. | Ψ doubles the expression of an unmodified transcript | [85] | |||
N.A. | When a separate Ψ modifies the special position of codon "UUU", mRNA translation can be limited | [81] | |||
I | mRNA structure | N.A. | I fastens pairs of nucleotides to influence the native secondary structure of mRNA | [86] | |
mRNA translation | N.A. | Guanosine, adenosine and uracil are the products decoded from I by the translation machinery | [87] | ||
U | Protein expression | N.A. | Protein level alterations accompany C-to-U editing of RNA | [88] | |
2'-O-Me | Viral RNA infection | N.A. | 2'-O-Me-modified viral RNA disrupts native host antiviral responses by escaping suppression mediated by IFIT | [89] | |
mRNA translation | N.A. | 2'-O-Me modifies specific regions of mRNA that are translated to glutamate, lysine and glutamine, hinting that 2'-O-Me has the potential to affect translation efficiency | [90] |
Other RNA modifications
hm5C
Ψ
I and U
2’-O-Me
Regulatory roles of RNA modifications in pathogenesis
Aberrant m6A RNA modifications in diseases
Aberrant m1A RNA modification in diseases
Aberrant m5C RNA modification in diseases
Aberrant hm5C, Ψ, I, U and 2’-O-Me RNA modifications in diseases
Modification | Disease | Enzyme | Target | Description | Ref |
---|---|---|---|---|---|
m6A | AML | FTO | ASB2/ RARA | FTO decreases m6A abundance on ASB2 and RARA mRNA in certain subtypes of AML and diminishes the amount of protein | |
MYC | FTO decreases m6A frequency on MYC mRNA by limiting YTHDF2-mediated RNA decay | [109] | |||
METTL3 | BCL2/ PTEN | METTL3 promotes the translation of BCL2 and PTEN mRNA by upregulating m6A levels | [110] | ||
SP1 | METTL3 supports the expression of SP1 by binding to the unique region with the help of the transcription factor CEBPZ | [111] | |||
METTL 14 | MYB/ MYC | METTL14 enhances the expression of MYB and MYC mRNA in AML | [112] | ||
ALKBH5 | N.A. | Approximately 10.5% of AML patients carry CNVs of ALKBH5, which predicts poor prognosis and p53 mutations | [113] | ||
Gastric cancer | METTL3 | HDGF | METTL3 causes m6A to accumulate on HDGF mRNA, which indicates proliferation and poor prognosis of gastric cancer | [114] | |
ZMYM1 | METTL3 enhances the stability of ZMYM1 mRNA to accelerate EMT and metastasis | [115] | |||
SEC62 | METTL3 reduces m6A on SEC62 with the help with MiR-4429 | [116] | |||
Hepatic carcinoma | METTL3 | SOCS2 | METTL3 works with YTHDF2 together to enhance the degradation of SOCS2 m6A-containing mRNA, which leads to HCC | [117] | |
YTHDF2 | EGFR | YTHDF2 suppresses ERK/MAPK signalling cascades and cell proliferation via destabilizing the EGFR mRNA | [118] | ||
METTL14 | N.A. | The expression of METTL14 is decreased in HCC, especially in metastatic HCC | [119] | ||
Pancreatic cancer | METTL3 | N.A. | METTL3 protein, m6A abundance and mRNA levels are much higher in tumour specimens than in para-cancerous specimens | [120] | |
YTHDF2 | YAP | Increased YTHDF2 promotes proliferation and suppresses migration of pancreatic cancer by destabilizing YAP mRNA | [121] | ||
Lung cancer | METTL3 | EGFR/ TAZ | METTL3 enhances the translation of EGFR and TAZ mRNA in lung cancer | [56] | |
SUMOylated METTL3 | N.A. | SUMOylated METTL3 promotes NSCLC by diminishing the amount of m6A | [122] | ||
YTHDF2 | 6PGD | YTHDF2 enhances 6PGD mRNA translation by binding to m6A sites uniquely in lung cancer cells | [123] | ||
FTO | USP7 | FTO stabilizes and increases the expression of USP7 by reducing m6A content | [124] | ||
FTO | MZF1 | Overexpressed FTO accelerates oncogene MZF1 expression by diminishing m6A and stabilizing MZF1 in LUSC | |||
Glioblastoma | METTL3/ METTL14 | ADAM19 | Decreased METTL3 or METTL14 determines the diminution of m6A on ADAM19 mRNA, which promotes the expression of protein and contributes to glioblastoma | ||
ALKBH5 | FOXM1 | Increased levels of ALKBH5 lead to decreased levels of m6A on FOXM1 mRNA and enhance protein translation, which predicts poor prognosis | |||
METTL3 | SOX2 | Elevated METTL3 stabilizes SOX2 mRNA and enhances radio-resistance of glioblastoma | [131] | ||
Prostate cancer | YTHDF2 | N.A. | Downregulated YTHDF2 suppresses the proliferation and migration of prostate cancer by elevating m6A contents | [132] | |
Bladder cancer | METTL3 | PTEN | With the help of pri-miR221/222, upregulated METTL3 leads to downregulated PTEN and tumorigenesis of cancer | [133] | |
Breast cancer | ALKBH5 | KLF4/ NANOG | m6A on KLF4 and NANOG can be suppressed by the cooperation of ZNF17 and ALKBH5 to promote protein expression and contribute to breast cancer | ||
METTL3 | HBXIP | Enhanced levels of m6A on HBXIP are attributed to increased METTL3 and promote the proliferation of breast cancer stem cells | [136] | ||
FTO | BNIP3 | Elevated FTO leads to decreased expression of BNIP3 and metastasis of breast cancer | [137] | ||
Cervical cancer | FTO | β-catenin | High expression of FTO and low levels of β-catenin lead to chemoradiotherapy resistance in cervical squamous cell carcinoma | [138] | |
Endometrial cancer | METTL14/METTL3 | N.A. | Either mutated METTL14 or reduced METTL3 activates the AKT signalling pathway and stimulates proliferation and tumorigenicity by limiting the expression of m6A | [139] | |
Ocular melanoma | YTHDF1 | HINT2 | YTHDF1 promotes the translation of methylated HINT2 mRNA and inhibits the progression of ocular melanoma | [140] | |
m1A | Ovarian/Breast cancer | ALKBH3 | CSF-1 | Accumulated ALKBH3 indicates improved CSF-1 mRNA expression and invasion of cancer cells | [141] |
Gastrointestinal cancer | ALKBH3 | ErbB2/ AKT1S1 | Aberrant m1A modifications regulate gastrointestinal cancer by modulating the mTOR pathway associated with cell proliferation | [142] | |
Urothelial carcinoma | ALKBH3 | N.A. | ALKBH3 promotes the progression, angiogenesis and invasion of urothelial carcinomas via NOX-2-ROS and TWEAK/Fn14-VEGF signals | [143] | |
m5C | Skin cancer | NSUN2 | N.A. | Inactivating NSUN2 prevents protein translation and stimulates the tumour-initiating population of skin cancer | [144] |
Breast cancer | NSUN2 | N.A. | NSUN2 is reported to be upregulated at the mRNA and protein levels | [145] | |
Urothelial carcinoma | YBX1 | HDGF | m5C modified 3'UTR in HDGF mRNA can be recognized by YBX1 and activate the advancement of UCB | [78] | |
Lung cancer | N.A. | N.A. | M5C RNA modification is upregulated in circulating tumour cells from patients with lung cancer | [146] | |
Ψ | Prostate cancer | DKC1 | N.A. | Certain nucleolar RNAs (H/ACA snoRNAs) and DKC1 that transfer U to Ψ contribute to the progression of cancer | [147] |
Haematological malignancies | N.A. | N.A. | H/ACA snoRNAs are limited in acute leukaemia, lymphoma and multiple myeloma | ||
I | Hepatocellular carcinoma | ADAR1 | AZIN1 | Edited AZIN1 stimulates S/G conversion and induces proliferation and poor prognosis in hepatocellular carcinoma | |
ADAR1 | BLCAP | Increased editing of BLCAP accelerates cell proliferation by activating the Akt/mTOR signalling pathway or STAT3 | [158] | ||
Cervical cancer | ADAR1 | BLCAP | Increased editing of BLCAP accelerates cell proliferation by activating the Akt/mTOR signalling pathway or STAT3 | [157] | |
Breast cancer | ADAR1 | DHFR | Editing of DHFR by ADAR1 stabilizes mRNA and accelerates cell growth | [159] | |
Gastric cancer | ADAR2 | PODXL | Downregulated ADAR2 reduces the decoration on PODXL and increases the malignancy of gastric cancer | [160] | |
Lung adenocarcinoma | ADARB1 | N.A. | ADARB1 has low expression in H358 and A549 lung adenocarcinoma cells | [161] | |
U | Thyroid carcinoma | UPP1 | N.A. | It is reported that the expression of UPP1 significantly depends on lymph node metastasis, tumour stage and size | [164] |