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Ilf3 and NF90 functions in RNA biology

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Double‐stranded RNA‐binding proteins (DRBPs) are known to regulate many processes of RNA metabolism due, among others, to the presence of double‐stranded RNA (dsRNA)‐binding motifs (dsRBMs). Among these DRBPs, Interleukin enhancer‐binding factor 3 (Ilf3) and Nuclear Factor 90 (NF90) are two ubiquitous proteins generated by mutually exclusive and alternative splicings of the Ilf3 gene. They share common N‐terminal and central sequences but display specific C‐terminal regions. They present a large heterogeneity generated by several post‐transcriptional and post‐translational modifications involved in their subcellular localization and biological functions. While Ilf3 and NF90 were first identified as activators of gene expression, they are also implicated in cellular processes unrelated to RNA metabolism such as regulation of the cell cycle or of enzymatic activites. The implication of Ilf3 and NF90 in RNA biology will be discussed with a focus on eukaryote transcription and translation regulation, on viral replication and translation as well as on noncoding RNA field. WIREs RNA 2015, 6:243–256. doi: 10.1002/wrna.1270 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
Complete map of the mouse Ilf3 gene. Top: schematic gene organization in kilo base pairs (kbp). Bottom: intron–exon organization with numbered boxes corresponding to exons. Open boxes: exons common to Ilf3 and NF90. Green box: exon 2 containing the translation start at the end of the sequence. Blue box: alternatively spliced exon 3 only retained in long isoforms. Red boxes: exons 13–16 containing the double‐stranded RNA‐binding motif sequences. Pink box: exon 19 specific for NF90 transcripts containing the stop codon (TAG) and the polyadenylation signal (AATACA). Orange boxes: exons 20–22 only found in Ilf3 mRNA with the stop codon (TAA) and the polyadenylation signal (AATACA) present in the exon 22.
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Subcellular localization of Ilf3 and NF90 proteins depending on their post‐translational modifications. SAM, S‐adenosyl‐methionine, a methyl donor; Pn, phosphorylation; R‐CH3, arginine methylation; L‐Ilf3 and L‐NF90, long Ilf3 and NF90 isoforms; S‐Ilf3 and S‐NF90, short Ilf3 and NF90 isoforms. Solid lines: proven events; dotted lines: hypothetical events. Note that S‐NF90 is only present in the cytoplasm whereas L‐NF90 and L/S‐Ilf3 are found in both the cytoplasm and the nucleus.
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Ilf3 and NF90–protein interactome. Inside the petals: cellular and viral protein partners of Ilf3 and NF90. On top of the petals: cellular functions ascribed to Ilf3 and NF90 interacting with the indicated proteins.
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Ilf3 and NF90–RNA interactome. Inside the petals: cellular (blue), viral (pink) mRNAs, and noncoding RNAs (purple) shown to interact with Ilf3 and NF90. On top of the petals: biological significance of Ilf3 and NF90‐RNA interaction.
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Domain organization of mouse Ilf3 (top) and NF90 (bottom) long isoforms. Residues 1–701 are common to both proteins. Orange box: nucleolar localization signal. Green box: putative nuclear localization signal. Blue boxes: double‐stranded RNA‐binding motifs. Brown box: single‐stranded RNA‐ and DNA‐binding site motif. Purple boxes: glycine rich motifs. Red box: specific C‐terminal sequence encompassing residues 702–911 for Ilf3 and residues 702–716 for NF90.
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RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition

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