A Primer for Junior Trainees: Recognition of RNA Modifications by Binding Proteins

Murphy Angelo; Yash Bhargava; Scott Aoki

doi:10.20944/preprints202310.0213.v1

Submitted:

02 October 2023

Posted:

04 October 2023

Read the latest preprint version here

Abstract

The complexity of RNA cannot be fully expressed with the canonical A, C, G, and U alphabet. To date, over 140 distinct chemical modifications to RNA have been discovered. RNA modifications can profoundly impact the cellular outcomes of messenger RNAs (mRNAs), transfer and ribosomal RNAs, and noncoding RNAs. Additionally, aberrant RNA modifications are associated with human disease. RNA modifications are a rising topic within the fields of biochemistry and molecular biology. This review aims to provide budding scientists with an appreciation for the significance of RNA modifications, alongside the skills required to identify and fluently discuss fundamental RNA-protein interactions. The Pumilio RNA-binding protein and YT521-B homology (YTH) family of modified RNA-binding proteins serve as examples to highlight the fundamental biochemical interactions that underlie the specific recognition of both unmodified and modified ribonucleotides, respectively.

Keywords:

RNA

;

RNA binding proteins

;

RNA modifications

;

RNA-protein interactions

;

review

Subject:

Biology and Life Sciences - Biochemistry and Molecular Biology

Running Head: RNA binding protein interactions with modified RNA

The Central Dogma of molecular biology

The discovery of RNA modifications has introduced a new layer of complexity to the ever-changing landscape of biochemistry and molecular biology. Biochemistry and molecular biology involve the study of the structure, function, and interactions between macromolecules essential to life. Molecular biology is based on the interplay between deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein. These macromolecules are essential for life, with DNA serving as an information storage, RNA as an intermediary dealer of DNA’s information and a jack of all trades, and protein as a versatile, functional building block that makes a cell go. This process, where DNA is made into RNA which is made into protein, is the Central Dogma of Molecular Biology (find the original citation XXX). Despite a number of exceptions to the Central Dogma, concept continues to serve as a fundamental framework for comprehending molecular biology (Ille, Lamont and Mathews 2022). This review focuses on the chemical interactions of RNA with RNA binding proteins, the impacts of RNA modifications on these interactions, and the connection between RNA modifications and the Central Dogma. Understanding how RNAs interact with proteins gives insights into the processes and mechanisms responsible for gene regulation, life, and disease. A greater understanding of RNA biology will lead to new tools to investigate their roles in organisms and new therapies for human and animal diseases.

Overview of RNA and RNA modifications.

There are three key structural differences between RNA and DNA (Minchin and Lodge 2019). First, RNA has a hydroxyl group at the 2’ position of its ribose sugar (Fig 1A). DNA does not, thus defining its “Deoxyribose” name. Second, RNA uses adenine (A), cytosine (C), guanine (G), and uracil as bases (Fig 1B). DNA also uses A, C, G, but typically uses thymine (T) instead of U (Minchin and Lodge 2019), with some notable exceptions (XXX- e.g (Takahashi and Marmur 1963)). Both DNA and RNA can base pair and go from single stranded nucleic acid to antiparallel double stranded helix (Fig 1C). DNA and RNA can form other structural assemblies, and they can fold on each other for tertiary structures (Fig 1C), similar to protein. However, the third difference is that RNA is found in cells as single stranded, double stranded, and tertiary structures. DNA is primarily found as double-stranded helices, stabilizing the nucleic acid, protecting it from degradation to permit long-term transfer of biological information. Thus, DNA and RNA have structural similarities, but their inherent chemical attributes enable them to be used for different purposes in biology.

Figure 1. DNA, RNA, and RNA modifications. (A) Chemical structures of DNA thymidine and RNA uridine. Chemical differences highlighted in green. (B) Adenine and a selection of natural RNA base modifications. N6-methyladenosine, m6A; N6,N6-dimethyladenosine, m⁶2A; 2-methyladenosine, m2A; 8-methyladenosine, m8A; N6-acetyladenosine, ac6A; 1-methylinosine, m1I; 2-methylthio-N6-methyladenosine, ms2m6A. Chemical differences again highlighted in green.

RNA modifications can occur on all four bases and encompass a diverse array of chemical changes to the nitrogenous base or ribonucleoside sugar. The study of naturally occurring ribonucleoside modifications began in 1951 with the discovery of pseudouridine (Ψ) (Cohn and Volkin 1951), an isomer of uridine with a carbon-carbon bond attaching the base to the ribose sugar and an added nitrogen (Fig XXX). Since this discovery, over 140 additional modifications have been identified (Cantara et al. 2011; Lorenz, Lünse and Mörl 2017; Boccaletto et al. 2022). The pace of identifying new modifications is rapidly accelerating due to the enhanced precision and accuracy provided by modern molecular biology equipment and techniques, along with the growing appreciation of RNA modifications and their involvement in a myriad of cellular pathways (Hong et al. 2020). Other common modification examples include the addition of a hydroxymethyl group on cytidine to form 5-hydroxymethylcytidine (5hmC, Fig. 2A, XXX) and the methylation of adenosine to form N6-methyladenosine (m⁶A, Fig. 2B, XXX). These chemical changes occur via specialized enzymatic pathways unique to the modification and biological context (Fu et al. 2013; Alseth, Dalhus and Bjoras 2014). Therefore, RNA modifications are found at in differing amounts and RNA sites, dependent on the organism, cell type, environment, and other factors.

Figure 2. Writers, erasers, and readers of m6A. Writer enzymes (e.g. METTL3/14) add a methyl group to the nitrogen-6 position of adenosine to make N6-methyladenosine (m6A) RNA. Eraser enzymes (e.g. FTO, ALKBH5) can remove these methyl marks. Reader RNA-binding proteins (e.g. YTHDFs, IGF2BPs) specifically recognize and bind m6A RNA. Unmodified RNA may be recognized by other RNA-binding proteins (e.g. PUFs, PABPs).

The writers and erasers of m⁶A

RNA modifications are managed by molecular writers and erasers (Fig. 3A) (Patil, Pickering and Jaffrey 2018; Shi, Wei and He 2019). Writers are enzymes that add a specific RNA modification, while erasers are enzymes that remove the modification. Writers and erasers work together to create and manage the epitranscriptome—the dynamic balance of RNA modifications within the cell. This regulation has far-reaching implications on the molecular function and expression of the modified RNA targets (Lin et al. 2016; Oakes et al. 2017; McCown et al. 2019; Zhao et al. 2019).

The m⁶A writers and erasers are particularly well-characterized (Fig. 3) (Shi, Wei and He 2019; Jiang et al. 2021) and have a significant impact on gene expression, animal development, and human disease (Lin et al. 2016; Yoon et al. 2017; Choe et al. 2018; Paris et al. 2019). As such, this review will use m6A as a prototypical example of the chemistry, biochemistry, and biology of an RNA modification and how it interacts with proteins. Discovered in the 1970s (XXX), the modification is prevalent in vertebrate RNA (Dominissini et al. 2012) and found on thousands of their messenger RNAs (mRNAs), the RNAs used to code for proteins. The mRNAs have modifications concentrated on near stop codons and in their 3’ untranslated regions (Dominissini et al. 2012; Patil, Pickering and Jaffrey 2018). The methyltransferase complexes modify adenosine into m⁶A. Although consisting of several proteins, the cores of these complexes involved the methyltransferase-like (METTL) enzymes that catalyze the reaction. For example, METTL3 and METTL14 assemble and can modify adenosines in mRNAs, but rely on other proteins for enzymatic activity and site selection (Liu et al. 2014; Huang et al. 2021). METTL3 is the enzyme catalytic subunit but relies on METTL14 and other proteins to maintain the correct conformation for enzymatic activity. Complex proteins can also impart preferences for m⁶A modification sites (Bokar et al. 1994). All methyltransferase complexes prefer specific RNA sequences known as motifs (Fig. 3C). The targeted RNA sequence for METTL3/METTL14 is RRACH motif, where R = A or G, and H = A, C, or U (Wei and Moss 1977; Harper et al. 1990). The central A of this motif is enzymatically converted to m⁶A. There are two established m⁶A erasers: Alkylation B Homolog 5 (ALKBH5) and Fat Mass and Obesity-Associated protein (FTO) (Zheng et al. 2013; Zhao et al. 2014). These demethylases work by modifying the N⁶ methyl group further to chemistry that can restore the base into unmodified adenosine (Zhao et al. 2014). Both writers and erasers are associated with human disease. Overexpression of the METTL3/METTL14 m⁶A writers are associated with liver, gastric, and colon cancer (XXX- better to have original citations for particular cancers). The FTO m⁶A eraser is associated with obesity (Fawcett and Barroso 2010). In summary, writers and readers are the enzymatic Ying-Yang for RNA modifications like m⁶A. Perturbation of this dynamic balance can lead to disease.

Figure 3. Six types of intermolecular forces drive RNA-protein interactions. (A) Opposite charges attract. (B) Hydrogen bonds occur commonly among polar molecules such as water. The difference in electronegativity creates opposite partial charges that attract one another. Images adapted from Biorender (Biorender.com). (C) Salt bridges represent the combination of hydrogen bonding and electrostatic interactions. Example from PDB ID: 5W4A (AOKI et al. 2021). (D) Hydrophobic interactions form in polar solvents. Nonpolar regions aggregate to minimize disruption of favorable solvent-solvent interactions. (E) London dispersion forces, a subtype of Van der Waals interactions, occur due to temporary induced dipoles. (F) Parallel-displaced pi stacking is favorable due to attractions between the positive hydrogen substituents (_+) and the negatively-charged (_-), delocalized pi system.

The readers of m⁶A

Readers are binding proteins that recognize specific RNA modifications, an interaction that can lead to regulation of the RNA target. The best characterized readers for m⁶A are the YTH domain family of proteins (YTHDFs) and YTH domain containing proteins (YTHDCs). YTHDFs and YTHDCs recognize m⁶A in the nucleus and cytoplasm to resulting in different biochemical functions, contingent on the specific reader protein and the cellular context (Liao, Sun and Xu 2018). For example, YTHDF2 and other YTH proteins can attract mRNA decay machinery through the recruitment the CCR4-NOT deadenylation complex (Du et al. 2016) CCR4-NOT removes the poly-A tail of mRNAs, leading to mRNA turnover. Additional functions of the YTH proteins are still being studied, but a critical aspect is that these proteins must bind to their RNA target to elicit their biochemical function (XXX- He and the first YTH ID). Thus, the molecular recognition of YTH and other RNA binding proteins depend on their interactions with target RNA.

Common RNA-Protein Interactions

To understand how readers recognize specific RNA modifications, it is essential to have a foundation of the chemical interactions between RNA and protein. RNA-protein interactions commonly encompass: 1) electrostatic interactions, 2) hydrogen bonding, 3) salt bridges, 4) hydrophobic interactions, 5) Van der Waals interactions, and 6) pi stacking interactions (Fig. 4) (Corley, Burns and Yeo 2020).

Electrostatic interactions arise from the attraction or repulsion between charged particles (Fig. 4A). The fundamental idea is that opposite charges attract while like charges repel. Protein amino acids have neutral, positive, or negative charges. The propensity of a particular amino acid to carry or lack charge is governed by the chemical structure of its side chain as well as the pH of the surrounding environment (Zhao et al. 2014). While unmodified A, C, G, and U are almost universally neutrally charged within the cell, some RNA modifications carry charge at physiological conditions (Anderson, Droogmans and Grosjean 2005; Lorenz, Lünse and Mörl 2017). Notably, the phosphate group contained in the backbone of nucleic acids carries a negative charge. Consequently, many readers have positively charged residues that nonspecifically attract nucleic acid (Järvelin et al. 2016; Balcerak et al. 2019).

Hydrogen bonding occurs when the partial positive charge of a hydrogen atom, bound to an electronegative atom, attracts an electronegative partner (Fig 4B). Electronegativity denotes an atom's propensity to attract electrons. When highly electronegative atoms, like oxygen or nitrogen, are bound to hydrogen atoms, regions of partial negative charge and partial positive charge are formed, indicated as δ- or δ+, respectively. The partial positive charge occurs on the less electronegative hydrogen, in this case. Conversely, the partial negative charge occurs on the more electronegative group. When correctly oriented, these oppositely charged regions can establish attractions. Neutral hydrogen bonds at 2.4–3.0 Å distance contribute about 0.5–1.5 kcal/mol per interaction, and charged hydrogen bonds, or “salt bridges,'' within a 4.0 Å distance contribute 3.5–4.5 kcal/mol per interaction (Fig 4C) (Herschlag and Pinney 2018). Protein and RNA contains chemical moieties capable of hydrogen bonding, and RNA and protein modifications frequently introduce additional groups that change this capability (Järvelin et al. 2016; Balcerak et al. 2019; Hofweber and Dormann 2019). While generally weaker than covalent or ionic interactions, the lump sum contribution of hydrogen bonds can have considerable impact on the RNA binding protein selectivity for a given modification. Analyses have estimated the prevalence of hydrogen bonds to the base, the ribose 2’-OH, and the RNA phosphate backbone at 36%, 24%, and 41% of RNA-protein hydrogen bonds respectively (Treger and Westhof 2001; Gupta and Gribskov 2011).

Hydrophobic interactions (Fig 4D) occur as a result of molecules trying to minimize contact with the surrounding water. The interactions occur between non-polar regions at distances of 3.8–5.0 Å and contribute approximately 1–2 kcal/mol (Dill et al. 2008; Onofrio et al. 2014). RNA and protein have hydrophilic or hydrophobic moieties which group with like elements (Anderson, Droogmans and Grosjean 2005; Hofweber and Dormann 2019; McCown et al. 2020). Hydrogen bonding will drive hydrophilic interactions. Amino acids with many nonpolar carbon—carbon bonds, like leucine, isoleucine, phenylalanine, tryptophan, and others, are hydrophobic and will fold together to form a “hydrophobic core.” This core may also interact with a hydrophobic moiety on RNA (Allain 1997; Yang 2002; Yu et al. 2014; Zhu et al. 2014a). Up to 50% of RNA-protein interface interactions may be hydrophobic, depending on the RBP (Hu et al. 2018).

There are two types of Van der Waals forces: the weaker London Dispersion Forces and the stronger dipole-dipole forces (Petrucci et al. 1997). London Dispersion Forces arise due to temporary induced dipoles, or imbalances in the charge distribution surrounding molecules (Fig. 4E). Permanent dipoles are hydrogen bonds exceeding a threshold distance of typically 3.0 Å (Allers and Shamoo 2001; Jones et al. 2001). Both Van der Waals forces are weak electrostatic interactions of about 0.5–1 kcal/mol (Corley, Burns and Yeo 2020). They largely play stabilizing roles in the binding of proteins to RNA (Corley, Burns and Yeo 2020).

Aromatic rings aligning face-to-face or face-to-edge results in pi stacking (Fig. 4F). These interactions typically form at distances of 2.7–4.3 Å and are relatively strong, contributing about 2–6 kcal/mol per interaction (Wilson, Holland and Wetmore 2016). They are frequently observed in protein and RNA interactions due to the aromaticity present in RNA and many amino acids. In YTH and other RNA Binding Proteins, pi stacking interactions play a crucial role in shaping the active site, effectively sandwiching the targeted base in place (Oubridge et al. 1994; Zhu et al. 2014b).

Figure 4. Structural features of Pumilio, an RNA-binding protein. (A) Crystal structure of human Pumilio 2 homology domain (hPUM2-HD) in complex with RNA (PDB ID: 3Q0Q (LU AND HALL 2011)). The RNA binding domain is composed of 8 α-helical PUF repeats (green and blue), each binding a single RNA base (color coded). Dashed boxes are enlarged in B and C. (B) Coordination of adenosine RNA. Recognition of adenosine at site 4 (“A4”) is mediated by pi stacking with Arginine888 (Arg888) and Tyrosine924 (Tyr924) and hydrogen bonds (dashed lines) with Glutamine891 (Gln891), Arginine888 (Arg888), and Tyrosine921 (Tyr921). (C) Recognition of uridine at site 3 (“U3”) is mediated by pi stacking with Tyrosine924 (Tyr924) and Asparagine960 (Asn960),hydrogen bonds with Glutamine927 (Gln927) and Asparagine923 (Asn923), and electrostatic attractions (dashed lines) between Lysine956 (Lys956) and the RNA phosphate backbone. Images by Pymol (SCHRÖDINGER).

Recognition of RNA by RNA binding proteins

All RNA binding proteins follow similar principles when interacting with their targets. First, they have specificity interactions that designate their sequence or secondary structure preferences. Second, they use positively charged amino acid side chains to account for the negatively charged phosphate backbone. Third, they often specify for the 2’ hydroxyl in RNA to differentiate between DNA.

The Pumilio and FBF protein family (PUFs) of RNA binding proteins serve as a good example of sequence specific RNA interactors that use these three concepts. PUFs contain a conserved RNA-binding domain known as the Pumilio homology domain (PUM-HD) (Quenault, Lithgow and Traven 2011), of which there are many atomic-resolution crystal structures determined without and with RNA (XXX). The human Pumilio 2 homology domain (hPUM2-HD) structure bound to RNA shows how the canonical PUM-HD has eight ɑ-helical repeats that binds to a conserved RNA sequence, UGUANAUA, with N being A, C, G, or U (Gerber et al. 2006; Morris, Mukherjee and Keene 2008; Hafner et al. 2010). Each α-helical repeat recognizes one unpaired base via three amino acid side chains (Campbell, Valley and Wickens 2014). Two side chains interact with an edge of the base, while the third residue forms pi stacking interactions in the plane between two bases (Goldstrohm, Hall and McKenney 2018). Thus, in following with the first principle, amino acid side chains form a tripartite code for sequence binding specificity. PUM-HD also has arginine, lysine, and histidine side chains surrounding the RNA binding surface, following the second principle of positively charged groups attracting negatively charged RNA (new Fig panel?). hPUM2-HD does not have amino acids specifying the 2’ hydroxyl of RNA. Notably, this PUM-HD can bind to both RNA and DNA (XXX). To summarize, the RNA-bound hPUM2-HD structure shows many of the basic characteristics observed in other RNA binding proteins. Deviations to the basic principles, such as the lack of specificity for the 2’ hydroxyl, allows the protein to bind to a broader range of substrates.

Recognition of adenosine at the fourth RNA position is specific and occurs almost entirely through interactions with the nucleobase (Fig. 6B). The ringed tyrosine and positively charged, flat arginine contributes favorable pi stacking interactions, while glutamine forms a hydrogen bond with the adenosine nitrogen (Fig 6B). Uridine at the 3rd RNA position has its base similarly sandwiched between amino acid side chains, but specificity is dictated by a different set of protein residues (Fig. 6C). Uridine and adenosine are very different bases. Uridine is a pyrimidine with a single ring, while adenosine is a purine with two rings. The uracil base of uridine has oxygen moieties attached to its ring. The adenine base of adenosine has nitrogen attached to its ring. PUM-HD uses the oxygen and nitrogen as chemical signatures to differentiate uridine from adenosine. The oxygens on the uracil base form hydrogen bonds with the nitrogens of glutamine and asparagine in PUM-HD. This binding interaction is incompatable with an adenine base. At the remaining six recognition sites, PUM-HD uses specific combinations of amino acids in each α-helical repeat to target specific nucleobases (Lu and Hall 2011). Thus, RNA binding proteins like PUF target specific RNAs by selecting amino acids that account for the particular chemical signature of their desired targets.

Figure 5. Structural features of YTH, a modified RNA binding protein. (A) Crystal structure of human YTHDF1 in complex with N6-methyladenosine (m⁶A) RNA (PDB ID: 4RCJ (Xu et al. 2015)). The modified RNA binding domain has a globular fold that forms a specificity pocket for the m⁶A modified RNA base. RNA color coded. Dashed box enlarged. (B) The m⁶A binding pocket. Tryptophan⁴¹¹ (Trp411), Tryptophan⁴⁶⁵ (Trp465), and Tryptophan⁴⁷⁰ (Trp470) form a hydrophobic cage that envelopes m⁶A. Pi stacking with Tryptophan⁴⁷⁰ and hydrogen bonds (dashed lines) with Cysteine⁴¹² (Cys412) and Tyrosine³⁹⁷ (Tyr397) help stabilize the m⁶A nucleotide within the binding pocket. Salt bridges form between Lysine⁴⁶⁹ (Lys469) and the RNA phosphate backbone. Images by Pymol (Schrödinger).

Recognition of m⁶A RNA by RNA binding proteins

RNA binding proteins that can bind modified RNAs like m⁶A use the same binding strategies as RNA binding proteins that target unmodified RNA. m⁶A has a methyl group added to its N⁶ adenosine nitrogen (Fig. 2B). As a result, a nonpolar, bulky methyl group is in place of a hydrogen that can form hydrogen bonds. Similar to PUM-HD forming a specificity pocket that matches the chemistry of a particular RNA base, RNA binding proteins that target modified RNAs chemically accommodate the modification to differentiate between modified and unmodified RNAs. For example, the specificity of the YTH domain for m⁶A is explained in the atomic resolution crystal structure of YTHDF1 bound with m⁶A -containing RNA (Fig. 5) (Xu et al. 2015). Like PUM-HD, the YTH domain has ringed amino acids that pi stack with the adenine base of m⁶A. Positively charged amino acids also form salt bridges with the RNA backbone serve to nonspecifically attract RNA substrates (Fig. 5F). Differences are observed at the YTH specificity pocket for m⁶A versus the PUM-HD pocket for unmodified adenosine. YTH forms a hydrophobic cage of amino acids surrounding the modification (Fig. 5B). The ring plane of a YTH tryptophan amino acid is perpendicular to the pi stacking amino acids to add a carbon-pi interaction with the methyl moiety of m⁶A. This interaction also allows the protein to differentiate m⁶A over an unmodified adenosine with a hydrophilic nitrogen. The YTH binding pocket is absent of any water molecules (Fig. 5C). This is predicted to improve the stability of the hydrophobic interactions and prevent solvent-solvent interactions (XXX cite?). Additionally, YTH hydrogen bonds with the nitrogens of m⁶A to hold the modified base in place (Fig. 5D). Thus, the specificity pocket of YTH is designed to accommodate a hydrophobic chemical modification to specify the modified adenosine and differentiate from unmodified RNA.

To summarize, the YTHDF1 and hPUM2-HD have similar strategies to target specific RNA substrates. First, both YTHDF1 and hPUM2-HD use amino acid side chains and a medley of chemical interactions to form a specificity pocket designed to accommodate the chemistry of the RNA targeted (Lu and Hall 2011; Xu et al. 2015). YTH hydrophobic interactions predominately assemble the pocket to accommodate the hydrophobic character of the m⁶A methyl group, while PUM-HD hydrophilic interactions drive its pocket specifity for the unmodified adenosine nitrogen. Second, ringed amino acids pi stack to present the base in a proper position for the binding pocket. And third, positively charged residues on the protein's surface attract the RNA phosphate backbone to nonspecifically enhance its affinity for all RNA substrates. Other RNA binding proteins follow the same principles but can only be appreciated when observing the structural interactions between RNA and protein.

New frontiers in RNA binding proteins

The Central Dogma of Molecular Biology outlines the flow of genetic information from DNA to RNA to protein. The pivotal position of RNA, in between the DNA responsible for heredity and the proteins which represent functional products, renders it as a key point of further research in the field of molecular biology. RNA modifications expand the RNA alphabet beyond the four standard ribonucleotides by introducing various alterations to their chemical structure. These RNA modifications are created or removed by enzymes which are characterized either as writers or erasers. These enzymes play a necessary role biology for gene regulation, development, obesity, and cancer (Fawcett and Barroso 2010; Zheng et al. 2013; Lin et al. 2016; Oakes et al. 2017; Yoon et al. 2017; Choe et al. 2018; Zhou and Pang 2018; McCown et al. 2019; Paris et al. 2019; Chen and Wong 2020; Huang et al. 2022). RNA binding protein readers have evolved to selectively bind distinct unmodified and modified RNA. While differing the structure and sequence, these binding proteins use a conserved set of principles to recognize target RNA. The differences and similarities of RNA binding proteins is on full display in atomic resolution RNA-protein structural models.

The study of RNA modifications is in a renaissance and undergoing exponential growth. Only a handful of modifications have been characterized, in part because of the lack of methods to identify their RNA targets and sites. Some methods use chemistry (e.g. XXX) or RNA binding proteins (e.g. XXX) to identify the sites, but these methods must be specifically tailored to each RNA modification. Universal methods to identify multiple types of RNA modifications are challenging but also in the infant stages of development (e.g. XXX). Determining the modification sites provides a starting point toward understanding how they affect RNA stability, folding, and function. Thus, the development of new, accurate methods for uncharacterized RNA modifications will be key to investigate the link between modifications, biology, and disease (Carlile et al. 2014; Delatte et al. 2016; Garalde et al. 2018; Khoddami et al. 2019; Acera Mateos et al. 2023). As discussed in this review, one key mechanism of m⁶A is the recruitment of RNA binding proteins through novel chemical interactions for RNA regulation. A safe prediction is that other RNA modifications will also recruit or prevent interactions with RNA binding proteins as their biological mechanism. Similar to YTH, PUM-HD, and others, these RNA binding proteins will undoubtedly follow similar strategies to recognize subtle chemical differences of modified RNA to deliver a profound impact on RNA form and function.

Funding

S.T.A. is funded by the NIH/NIGMS (R35 GM142691) and received start-up funds from the Indiana University School of Medicine and its Precision Health Initiative (PHI).

Conflicts of Interest

All authors declare that they have no conflicts of interest.

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A Primer for Junior Trainees: Recognition of RNA Modifications by Binding Proteins

Abstract

Keywords:

Subject:

The Central Dogma of molecular biology

Overview of RNA and RNA modifications.

The writers and erasers of m⁶A

The readers of m⁶A

Common RNA-Protein Interactions

Recognition of RNA by RNA binding proteins

Recognition of m⁶A RNA by RNA binding proteins

New frontiers in RNA binding proteins

Funding

Conflicts of Interest

References

MDPI Initiatives

Important Links

Subscribe

A Primer for Junior Trainees: Recognition of RNA Modifications by Binding Proteins

Abstract

Keywords:

Subject:

The Central Dogma of molecular biology

Overview of RNA and RNA modifications.

The writers and erasers of m6A

The readers of m6A

Common RNA-Protein Interactions

Recognition of RNA by RNA binding proteins

Recognition of m6A RNA by RNA binding proteins

New frontiers in RNA binding proteins

Funding

Conflicts of Interest

References

MDPI Initiatives

Important Links

Subscribe

The writers and erasers of m⁶A

The readers of m⁶A

Recognition of m⁶A RNA by RNA binding proteins