The RNA‐binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs

Abstract

Transposable elements (TEs) compose about half of the mammalian genome and, as embedded sequences, up to 40% of long noncoding RNA (lncRNA) transcripts. Embedded TEs may represent functional domains within lncRNAs, providing a structured RNA platform for protein interaction. Here we show the interactome profile of the mouse inverted short interspersed nuclear element (SINE) of subfamily B2 (invSINEB2) alone and embedded in antisense (AS) ubiquitin C-terminal hydrolase L1 (Uchl1), an lncRNA that is AS to Uchl1 gene. AS Uchl1 is the representative member of a functional class of AS lncRNAs, named SINEUPs, in which the invSINEB2 acts as effector domain (ED)–enhancing translation of sense protein-coding mRNAs. By using RNA-interacting domainome technology, we identify the IL enhancer-binding factor 3 (ILF3) as a protein partner of AS Uchl1 RNA. We determine that this interaction is mediated by the RNA-binding motif 2 of ILF3 and the invSINEB2. Furthermore, we show that ILF3 is able to bind a free right Arthrobacter luteus (Alu) monomer sequence, the embedded TE acting as ED in human SINEUPs. Bioinformatic analysis of Encyclopedia of DNA Elements–enhanced cross-linking immunoprecipitation data reveals that ILF3 binds transcribed human SINE sequences at transcriptome-wide levels. We then demonstrate that the embedded TEs modulate AS Uchl1 RNA nuclear localization to an extent moderately influenced by ILF3. This work unveils the existence of a specific interaction between embedded TEs and an RNA-binding protein, strengthening the model of TEs as functional modules in lncRNAs.—Fasolo, F., Patrucco, L., Volpe, M., Bon, C., Peano, C., Mignone, F., Carninci, P., Persichetti, F., Santoro, C., Zucchelli, S., Sblattero, D., Sanges, R., Cotella, D., Gustincich, S. The RNA-binding protein ILF3 binds to transposable element sequences in SINEUP lncRNAs.

SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies

“…NONO is known as a core component of paraspeckles in nuclei along with the lncRNA NEAT1 , and these paraspeckles may relate to transcriptome functional regulation and retention in the nucleus ( 50–53 ). ILF3 (Interleukin enhancer-binding factor 3) is known as RNA binding protein to participate in regulation of RNA splicing, stabilization ( 54 , 55 ) and nuclear retention to bind with transposable element in SINEUPs ( 56 ). Here, although we observed that some SINEUP-GFP RNAs were retained in the nucleus and co-localized with RBPs ( Supplementary Figure S2A ), we could not characterize these nuclear granules containing SINEUP RNAs.…”

An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs

“…In fact, our analysis by icSHAPE showed high-enrichment-score protected regions in the T domain, further validating the presence of a single-strand region in this domain in living cells, whereas low-enrichment-score regions in the T domain were preferentially double-stranded as a result of the constraints of the RNAfold software ( Supplementary Figure S5 , see ‘Materials and Methods’ section) ( 38 , 53 ). Thus, our NMR results provide new insights into the RNA regions of inverted SINE B2, and the T domain dynamics may be applicable to binding proteins for SINEUP activity in living cells ( 54 , 55 ). They therefore emphasize the importance of experiment-based structural examination.…”

Transposable element-derived sequences in vertebrate development

“…A recently described class of lncRNAs, called SINEUPs, up-regulates translation through an embedded inverted SINE element that forms a short hairpin [ 201 , 202 ]. This hairpin has been shown to be essential for the up-regulation function of SINEUP lncRNAs and serves as a recognition motif for the RNA-binding protein ILF3 (IL enhancer-binding Factor 3) [ 203 ]. The first representative member of this family, which was described in mouse, is responsible for the translational regulation of the ubiquitin carboxy-terminal hydrolase L1 ( uchl1/PARK5 ), which is essential for brain function and particularly for neuron maintenance [ 201 , 204 , 205 ].…”