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N6-Methyladenosine Role in Acute Myeloid Leukaemia

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N6-Methyladenosine Role in Acute Myeloid Leukaemia International Journal of Molecular Sciences Review N6-Methyladenosine Role in Acute Myeloid Leukaemia Zaira Ianniello and Alessandro Fatica * ID Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-06-4991-2341 Received: 30 July 2018; Accepted: 8 August 2018; Published: 9 August 2018 Abstract: We are currently assisting in the explosion of epitranscriptomics, which studies the functional role of chemical modifications into RNA molecules. Among more than 100 RNA modifications, the N6-methyladenosine (m6A), in particular, has attracted the interest of researchers all around the world. m6A is the most abundant internal chemical modification in mRNA, and it can control any aspect of mRNA post-transcriptional regulation. m6A is installed by “writers”, removed by “erasers”, and recognized by “readers”; thus, it can be compared to the reversible and dynamic epigenetic modifications in histones and DNA. Given its fundamental role in determining the way mRNAs are expressed, it comes as no surprise that alterations to m6A modifications have a deep impact in cell differentiation, normal development and human diseases. Here, we review the proteins involved in m6A modification in mammals, m6A role in gene expression and its contribution to cancer development. In particular, we will focus on acute myeloid leukaemia (AML), which provides an initial indication of how alteration in m6A modification can disrupt normal cellular differentiation and lead to cancer. Keywords: m6A; RNA; AML; leukaemia; epitranscriptomics 1. Introduction Leukaemogenesis is caused by gene mutations and chromosomal aberrations resulting in changes of gene expression and, eventually, alteration of cell growth/differentiation programs [1]. Over the past decades, epigenetic modifications (e.g., DNA methylation and histone modifications) have been shown to play a significant role in this process and are now recognized as targets of therapy for different types of leukaemia and other haematological malignancies [2]. More recently, researchers have identified a new layer of gene expression regulation at the RNA levels that consists of reversible chemical modification of messenger RNAs (mRNAs), which led to the birth of the emerging field of “epitranscriptomics” [3,4]. Among more than 100 chemical modifications that can occur within various type of RNA molecules, N6-methyladenosine (m6A) is the most abundant internal chemical modification of mRNA and is the one with the greatest impact on its dynamic regulation. The m6A modification is installed by “writers” and removed by “erasers”; in addition, it can recruit specific “reader” proteins. m6A modification and the associated regulatory proteins play a critical role in gene expression by affecting different steps of the mRNA life, including splicing, nuclear export, stability and translation [4,5]. The reversible and dynamic nature of m6A modification and its ability to fine-tune and coordinate gene expression programs has attracted the interest of many research groups in order to define its contribution to cell differentiation, normal development and human diseases [4]. In particular, it has been shown that deregulation of m6A modification alters embryonic stem cell maintenance and differentiation [4]. As acquisition of stem cell properties and defects in Int. J. Mol. Sci. 2018, 19, 2345; doi:10.3390/ijms19082345 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2018, 19, 2345 2 of 12 cell differentiation are common features of many cancers, this indicates that alterations of m6A levels might have an important role in cancer development. In this review, we describe the mammalian proteins involved in m6A modification and the effect of the latter on mRNA expression. In particular, we will focus on the role of m6A in acute myeloid leukaemia (AML), which provides an initial indication of how alteration in m6A levels can disrupt normal cellular differentiation and contribute to carcinogenesis. 2. m6A Writers, Erasers and Readers In mammalian cells, about 0.4% of adenosines inside mRNAs are m6A-modified (1–5 m6A sites per transcript) [4,5]. The main complex responsible for m6A modifications of mRNAs is composed of the methyltransferase-like protein 3 (METTL3) and the methyltransferase-like protein 14 (METTL14). This core heterodimeric complex specifically methylates the adenosine within the DRACH motif (D = A/G/U, R = A/G; H = A/C/U) (Figure1). METTL3 is the catalytic component of the complex while METTL14 is required for structural stabilization and RNA binding [6–8]. In vivo, the activity of METTL3/METTL14 is regulated by an additional complex (referred to as MACOM, m6A-METTL-associated complex) composed of Wilms tumor 1-associated protein (WTAP), Vir-like m6A methyltransferase-associated (VIRMA, also known as KIAA1429), Cbl proto-oncogene-like 1 (CBLL1, also known as Hakai), RNA-binding motif 15 (RBM15), and zinc finger CCCH-type containing 13 (ZC3H13) proteins [5] (Table1). Notably, the percentage of m 6A sites is lower than the occurrence of the consensus motif, indicating that the core methylation complex is specifically recruited by the MACOM complex on specific sites within mRNAs. In particular, modified adenosines are specifically enriched in regions adjacent to the stop codon, 30-UTR (Untranslated region) and within long internal exons [9,10]. It is very likely that additional cell-specific regulators of m6A modification still need to be identified. Table 1. Mammalian m6A (N6-methyladenosine) regulators. Protein Classification Function METTL3 Writer Installs m6A in mRNA; promotes translation METTL14 Writer Cooperates with METTL3 in m6A installation METTL16 Writer Installs m6A in U6 snRNA and pre-mRNA 6 FTO Eraser Remove m A and m6Am from mRNA ALKBH5 Eraser Remove m6A from mRNA WTAP Component of the regulatory MACOM complex Regulates m6A installation VIRMA Component of the regulatory MACOM complex Regulates m6A installation CBLL1 Component of the regulatory MACOM complex Regulates m6A installation RBM15 Component of the regulatory MACOM complex Regulates m6A installation ZC3H13 Component of the regulatory MACOM complex Regulates m6A installation ABCF1 Direct reader Stimulates translation eIF3 Direct reader Stimulates translation HNRPA2B1 Direct reader Stimulates microRNA processing IGF2BPs Direct readers Increase mRNA stability YTHDC1 Direct reader Stimulates splicing and mRNA export YTHDC2 Direct reader Stimulates mRNA decay and translation YTHDF1 Direct reader Stimulates translation YTHDF2 Direct reader Stimulates mRNA decay YTHDF3 Direct reader Stimulates mRNA decay and translation FMR1 Indirect reader Inhibits translation HNRNPC Indirect reader Regulates splicing ELAVL1 m6A repelled protein Increases mRNA stability G3BPs m6A repelled protein Increase mRNA stability m6A modification is essential for embryonic development. Deletion of METTL3 in mice is embryonic lethal. Moreover, the importance of m6A is further shown by the fact that the complete ablation of METTL3 and METTL14 in mESCs (mouse embryonic stem cells) impairs the transition of naïve mESCs into the primed state and blocks the subsequent differentiation [11,12]. Similarly, Int. J. Mol. Sci. 2018, 19, x FOR PEER REVIEW 3 of 12 m6A modification is essential for embryonic development. Deletion of METTL3 in mice is embryonic lethal. Moreover, the importance of m6A is further shown by the fact that the complete ablation of METTL3 and METTL14 in mESCs (mouse embryonic stem cells) impairs the transition of Int. J. Mol. Sci. 2018, 19, 2345 3 of 12 naïve mESCs into the primed state and blocks the subsequent differentiation [11,12]. Similarly, deletion in mice of the regulatory MACOM complex components, WTAP and RBM15, produced embryonicdeletion in lethality mice of [13–15]. the regulatory MACOM complex components, WTAP and RBM15, produced embryonicMore recently, lethality the [13 U6–15 snRNA]. m6A methyltransferase-like protein 16 (METTL16) has been shown to targetMore intronic recently, regions the U6 of snRNA pre-mRNAs m6A methyltransferase-like and lncRNAs (Long proteinnon-coding 16 (METTL16) RNA) [16–18]. has been METTL16 shown bindingto target sites intronic do not regions overlap of with pre-mRNAs that one of and the lncRNAs METTL3/METTL14 (Long non-coding methylation RNA) complex, [16–18]. indicating METTL16 independentbinding sites dofunctions not overlap in m with6A thatmodification. one of the METTL3/METTL14However, METTL16 methylation plays an complex,important indicating role in regulatingindependent the functions cellular in homeostasis m6A modification. of the However,methyl donor METTL16 SAM plays (S-adenosylmethionine) an important role in regulating [16–18], therebythe cellular indirectly homeostasis contributing of the methylto global donor cellular SAM methylation. (S-adenosylmethionine) [16–18], thereby indirectly contributingm6A marks to globalwithin cellular transcripts methylation. can be removed by the alkB homologue 5 (ALKBH5) and fat mass and obesity-associatedm6A marks within (FTO) transcripts proteins can (Figure be removed 1). These by two the proteins alkB homologue mainly localized 5 (ALKBH5) to the nuclear and fat compartmentmass and obesity-associated where the removal (FTO) of proteins m6A modificati (Figure1).on These occurs. two proteinsFTO has mainlyan additional localized role to thein demethylatingnuclear compartment the N6-2 where′-O-dimethylade the removalnosine of m6A (m6Am) modification modification occurs. close FTO to
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