Roquin recognizes a non-canonical hexaloop structure in the 3′-UTR of Ox40

Abstract

The RNA-binding protein Roquin is required to prevent autoimmunity. Roquin controls T-helper cell activation and differentiation by limiting the induced expression of costimulatory receptors such as tumor necrosis factor receptor superfamily 4 (Tnfrs4 or Ox40). A constitutive decay element (CDE) with a characteristic triloop hairpin was previously shown to be recognized by Roquin. Here we use SELEX assays to identify a novel U-rich hexaloop motif, representing an alternative decay element (ADE). Crystal structures and NMR data show that the Roquin-1 ROQ domain recognizes hexaloops in the SELEX-derived ADE and in an ADE-like variant present in the Ox40 3′-UTR with identical binding modes. In cells, ADE-like and CDE-like motifs cooperate in the repression of Ox40 by Roquin. Our data reveal an unexpected recognition of hexaloop cis elements for the posttranscriptional regulation of target messenger RNAs by Roquin.

RNA–protein interaction detection in living cells

“…7a) 30,31 . RC3H1 and its paralog RC3H2 are known RNA-binding proteins that promote RNA decay 32,33 . Similar to RC3H1 , upregulation of RC3H2 in breast cancer was also correlated with poorer survival (Fig.…”

Identification of RNA-binding Proteins in Macrophages by Interactome Capture

“…The NTA is followed by a helix-turn-helix motif. Interestingly, a helix-turnhelix motif contributes to RNA binding of ROQUIN (67)(68)(69), which implicates a candidate for the RNA-interaction in HCLS1. A coiled-coil region represents the main F-actin binding site and functions synergistically with the helix-turn-helix motif (70 -72).…”

Post‐transcriptional control of immune responses and its potential application

“…For instance, via genome‐wide identification of Roquin target mRNAs, Roquin has been demonstrated to bind to CDEs, which canonically form triloop stem‐loop structures . In addition to this structure, recent reports using systematic evolution of ligands by exponential enrichment (SELEX) and photoactivatable ribonucleoside‐enhanced cross‐linking and immunoprecipitation (PAR‐CLIP) methods have shown that Roquin‐1 also recognises noncanonical hexaloop structures and linear binding elements (LBEs), respectively . Thus, our understanding of cis‐elements remains incomplete and further studies are necessary to comprehensively identify and validate potential RBP binding sites.…”