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Classification and function of RNA–protein interactions

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Abstract Almost all RNAs need to interact with proteins to fully exert their functions, and proteins also bind to RNAs to act as regulators. It has now become clear that RNA–protein interactions play important roles in many biological processes among organisms. Despite the great progress that has been made in the field, there is still no precise classification system for RNA–protein interactions, which makes it challenging to further decipher the functions and mechanisms of these interactions. In this review, we propose four different categories of RNA–protein interactions according to their basic characteristics: RNA motif‐dependent RNA–protein interactions, RNA structure‐dependent RNA–protein interactions, RNA modification‐dependent RNA–protein interactions, and RNA guide‐based RNA–protein interactions. Moreover, the integration of different types of RNA–protein interactions and the regulatory factors implicated in these interactions are discussed. Furthermore, we emphasize the functional diversity of these four types of interactions in biological processes and disease development and assess emerging trends in this exciting research field. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications RNA Interactions with Proteins and Other Molecules > Protein‐RNA Recognition RNA Processing > RNA Editing and Modification
RNA–protein interactions depend on RNA‐binding motifs. (a,b) Schematic of selective let‐7 suppression by LIN28. LIN28 is a bipartite RNA‐binding protein with two C‐terminal zinc knuckle domains (ZKDs) and an N‐terminal cold shock domain (CSD). (a) In CSD+ let‐7 with the (U)GAU motif, LIN28 recruits TUTase to CSD+ let‐7, catalyzes uridylation, and results in direct degradation of CSD+ let‐7 by DIS3L2 exonuclease. (b) In CSD let‐7 without the (U)GAU motif, LIN28 recruits DICER, forms a RISC, and suppresses let‐7. (c) Schematic of RNA recognition by the IGF2BP protein family. IGF2BP protein family members feature four KH domains and two RRMs. The IGF2BP protein family interacts with CA‐rich motifs and motifs with a GGACU core
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RNA‐dependent RNA targeting by the CRISPR‐Cas system. (a) Schematic of the CRISPR/Cas13 system. CRISPR/Cas13 is a type VI adaptive immune system targeting RNAs. (b) Schematic of RNA editing for programmable A‐to‐I replacement (REPAIR) and RNA editing for specific C‐to‐U exchange (RESCUE), both of which are modified CRISPR/Cas13 systems for RNA editing
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Overview of ncRNAs that guide RNA–protein interactions in the cell. (a) miRNAs/siRNAs guide RISCs to regulate mRNA targets via canonical or noncanonical base pairing. (b) piRNAs are generated via the ping‐pong mechanism and guide PIWI proteins to silence transposon transcription and regulate the expression of target RNAs. (c) snoRNAs (including box C/D snoRNAs and box H/ACA snoRNAs) interact with proteins to form snoRNPs that play important roles in guiding the RNA modification (2′‐O‐methylation or ψ) of RNAs. (d) snRNAs combined with Sm proteins or Lsm proteins function in alternative splicing
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Schematic of m5C reader‐mediated regulation of m5C‐modified mRNAs. (a) The nuclear m5C reader ALYREF binds to m5C‐modified mRNAs and regulates mRNA export from the nucleus. (b) The m5C reader YBX1 binds to HDGF m5C‐modified mRNA, recruits ELAVL1 to maintain mRNA stability, and promotes the pathogenesis of UCB. YBX1 binds to both m5C‐modified RNA and unmodified RNA but exhibits a much higher affinity for m5C‐modified RNA
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Schematic of m6A reader‐mediated regulation of m6A‐modified mRNAs. (a) The nuclear m6A reader YTHDC1 recruits the pre‐mRNA splicing factor SRSF3 and blocks SRSF10 access to mRNA, which promotes exon inclusion in target mRNAs and regulates mRNA alternative splicing. (b) The cytoplasmic m6A reader YTHDF1 recruits eIFs and promotes mRNA translation depending on the 5′ cap structure. (c) The cytoplasmic m6A reader YTHDF2 recruits the deadenylase complex CCR4‐NOT by binding the SH domain of the CNOT1 subunit. The CCR4‐NOT deadenylase complex then accelerates the deadenylation and degradation of m6A mRNA. (d) In processing bodies (P‐bodies), IGF2BPs recruit mRNA stabilizers such as HuR and MATR3 and protect target mRNAs from degradation. (e) In the cytoplasm, IGF2BPs recruit ribosomes and facilitate target mRNA translation. (f) Under stress conditions such as heat shock, IGF2BPs promote target mRNA storage in stress granules
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RNA structure‐dependent RNA–protein interactions. (a) ADAR interacts with double‐stranded regions of RNA. The red star indicates the A‐to‐I editing site. (b) A model of SND1 bound to double‐stranded RNA containing I‐U mispairs. (c) DICER binds with TRBP to form a complex, mediating pre‐miRNA maturation. (d) The secondary structure of the K‐turn (left) and the K‐turn in box C/D snoRNA bound to 15.5K (right)
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RNA Processing > RNA Editing and Modification
RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications

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